Multiple sequence alignment - TraesCS4A01G051000

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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 TraesCS4A01G051000 chr4A 100.000 9332 0 0 1 9332 41960682 41951351 0.000000e+00 17234.0
1 TraesCS4A01G051000 chr4A 100.000 33 0 0 4630 4662 119794956 119794924 2.810000e-05 62.1
2 TraesCS4A01G051000 chr4D 96.271 3164 92 10 1471 4627 422246184 422249328 0.000000e+00 5166.0
3 TraesCS4A01G051000 chr4D 94.975 2746 91 15 4679 7406 422249315 422252031 0.000000e+00 4263.0
4 TraesCS4A01G051000 chr4D 92.875 2779 147 27 5095 7847 422513119 422515872 0.000000e+00 3988.0
5 TraesCS4A01G051000 chr4D 95.062 2167 77 11 1471 3615 422504450 422506608 0.000000e+00 3382.0
6 TraesCS4A01G051000 chr4D 94.061 1448 69 10 7897 9332 422515874 422517316 0.000000e+00 2182.0
7 TraesCS4A01G051000 chr4D 91.746 1478 83 16 1 1446 422244265 422245735 0.000000e+00 2017.0
8 TraesCS4A01G051000 chr4D 93.714 1034 40 8 3601 4630 422506624 422507636 0.000000e+00 1526.0
9 TraesCS4A01G051000 chr4D 92.344 1045 63 11 7448 8480 422252031 422253070 0.000000e+00 1471.0
10 TraesCS4A01G051000 chr4D 83.939 1432 158 32 68 1446 422502381 422503793 0.000000e+00 1304.0
11 TraesCS4A01G051000 chr4D 95.050 202 10 0 4871 5072 422512927 422513128 1.510000e-82 318.0
12 TraesCS4A01G051000 chr4D 83.382 343 44 9 8426 8762 422252950 422253285 1.180000e-78 305.0
13 TraesCS4A01G051000 chr4D 91.707 205 8 4 4679 4875 422507620 422507823 9.230000e-70 276.0
14 TraesCS4A01G051000 chr4D 91.304 46 2 2 4617 4662 346123361 346123404 2.810000e-05 62.1
15 TraesCS4A01G051000 chr4B 96.106 2645 83 11 1471 4105 519251044 519253678 0.000000e+00 4296.0
16 TraesCS4A01G051000 chr4B 94.835 2401 99 8 4679 7071 519254224 519256607 0.000000e+00 3723.0
17 TraesCS4A01G051000 chr4B 93.341 2508 127 19 5092 7582 519344129 519346613 0.000000e+00 3670.0
18 TraesCS4A01G051000 chr4B 94.890 1957 72 6 1471 3399 519340424 519342380 0.000000e+00 3035.0
19 TraesCS4A01G051000 chr4B 93.955 1373 65 10 7117 8480 519256598 519257961 0.000000e+00 2060.0
20 TraesCS4A01G051000 chr4B 91.393 1034 40 17 3601 4630 519342769 519343757 0.000000e+00 1371.0
21 TraesCS4A01G051000 chr4B 92.805 820 42 9 7896 8709 519347263 519348071 0.000000e+00 1171.0
22 TraesCS4A01G051000 chr4B 81.518 1423 155 48 71 1446 519338487 519339848 0.000000e+00 1072.0
23 TraesCS4A01G051000 chr4B 92.717 714 22 8 757 1446 519248667 519249374 0.000000e+00 1003.0
24 TraesCS4A01G051000 chr4B 94.118 527 16 3 4104 4630 519253729 519254240 0.000000e+00 787.0
25 TraesCS4A01G051000 chr4B 87.276 613 70 6 141 748 519248100 519248709 0.000000e+00 693.0
26 TraesCS4A01G051000 chr4B 90.962 520 40 5 8818 9331 519354037 519354555 0.000000e+00 693.0
27 TraesCS4A01G051000 chr4B 92.040 402 23 5 4679 5072 519343741 519344141 2.940000e-154 556.0
28 TraesCS4A01G051000 chr4B 92.694 219 8 4 3397 3615 519342541 519342751 9.100000e-80 309.0
29 TraesCS4A01G051000 chr4B 86.861 274 29 6 7580 7848 519346992 519347263 5.480000e-77 300.0
30 TraesCS4A01G051000 chr4B 96.460 113 4 0 8706 8818 519350771 519350883 4.450000e-43 187.0
31 TraesCS4A01G051000 chr4B 79.452 219 28 10 8546 8762 519258061 519258264 1.260000e-28 139.0
32 TraesCS4A01G051000 chr4B 87.611 113 14 0 1 113 519247993 519248105 2.110000e-26 132.0
33 TraesCS4A01G051000 chr5A 78.049 369 66 12 8974 9332 668229305 668229668 1.580000e-52 219.0
34 TraesCS4A01G051000 chr5A 93.023 43 3 0 4631 4673 271053391 271053433 7.820000e-06 63.9
35 TraesCS4A01G051000 chr5A 100.000 32 0 0 4631 4662 346127521 346127490 1.010000e-04 60.2
36 TraesCS4A01G051000 chr5D 77.966 354 48 10 4690 5015 409336211 409335860 2.660000e-45 195.0
37 TraesCS4A01G051000 chr6A 72.941 340 76 13 8980 9309 48197183 48196850 4.610000e-18 104.0
38 TraesCS4A01G051000 chr6A 95.000 40 0 2 4631 4668 504483112 504483073 2.810000e-05 62.1
39 TraesCS4A01G051000 chr7B 90.196 51 3 1 4631 4679 571397908 571397858 2.180000e-06 65.8
40 TraesCS4A01G051000 chr7B 97.222 36 1 0 4632 4667 418738841 418738806 2.810000e-05 62.1
41 TraesCS4A01G051000 chr1A 93.023 43 3 0 4620 4662 114347924 114347966 7.820000e-06 63.9
42 TraesCS4A01G051000 chr3B 93.182 44 0 3 4620 4662 381481201 381481242 2.810000e-05 62.1
43 TraesCS4A01G051000 chr5B 100.000 32 0 0 4631 4662 294094677 294094646 1.010000e-04 60.2
44 TraesCS4A01G051000 chr3A 88.235 51 4 2 4613 4662 528595028 528595077 1.010000e-04 60.2
45 TraesCS4A01G051000 chr7A 94.595 37 0 2 4631 4667 647301458 647301424 1.000000e-03 56.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G051000 chr4A 41951351 41960682 9331 True 17234.000000 17234 100.000000 1 9332 1 chr4A.!!$R1 9331
1 TraesCS4A01G051000 chr4D 422244265 422253285 9020 False 2644.400000 5166 91.743600 1 8762 5 chr4D.!!$F2 8761
2 TraesCS4A01G051000 chr4D 422512927 422517316 4389 False 2162.666667 3988 93.995333 4871 9332 3 chr4D.!!$F4 4461
3 TraesCS4A01G051000 chr4D 422502381 422507823 5442 False 1622.000000 3382 91.105500 68 4875 4 chr4D.!!$F3 4807
4 TraesCS4A01G051000 chr4B 519247993 519258264 10271 False 1604.125000 4296 90.758750 1 8762 8 chr4B.!!$F1 8761
5 TraesCS4A01G051000 chr4B 519338487 519354555 16068 False 1236.400000 3670 91.296400 71 9331 10 chr4B.!!$F2 9260

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
751 781 0.037326 TGGATGTTCGGCTCTCACAC 60.037 55.000 0.00 0.00 0.00 3.82 F
1125 1249 0.178990 GGCCTCTGAAGGTGGTGTTT 60.179 55.000 0.00 0.00 45.34 2.83 F
2000 4024 1.133976 GCTTATGGCCTGTCTGGTGAT 60.134 52.381 3.32 0.00 38.35 3.06 F
2700 4725 0.759346 ACCAGAGTCTTTTCCAGCGT 59.241 50.000 0.00 0.00 0.00 5.07 F
2821 4846 1.596603 CACTGTGCAGATGGTTGACA 58.403 50.000 6.17 0.00 0.00 3.58 F
3598 5789 2.627699 ACACATTTGGCCTTTTCGATGT 59.372 40.909 3.32 2.49 0.00 3.06 F
5430 7760 1.003545 GCCATGCAGTACTTGTATGCG 60.004 52.381 13.81 10.16 45.35 4.73 F
5514 7844 0.174845 ACTGTCGCCGCTTGCTTATA 59.825 50.000 0.00 0.00 38.05 0.98 F
6796 9139 1.195115 TGACCTCCCGAGATTCCTTG 58.805 55.000 0.00 0.00 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2391 4416 0.107066 ATGCATTGTCATCTCCCGCA 60.107 50.000 0.00 0.00 0.00 5.69 R
2700 4725 1.400142 CGTGAAAGTTGCAAGGACACA 59.600 47.619 18.79 7.58 0.00 3.72 R
3218 5245 1.814394 GACTGCATGCAAGGACAATCA 59.186 47.619 22.88 0.00 0.00 2.57 R
4349 6663 3.452627 AGAACACACTGTTTCCAGAGACT 59.547 43.478 0.00 0.00 41.28 3.24 R
4640 6954 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16 R
5489 7819 0.025001 CAAGCGGCGACAGTAATTCG 59.975 55.000 12.98 0.00 39.56 3.34 R
7114 9461 0.471022 AGCACCCCCGTTCCAAAAAT 60.471 50.000 0.00 0.00 0.00 1.82 R
7121 9468 0.893727 ATTGTTGAGCACCCCCGTTC 60.894 55.000 0.00 0.00 0.00 3.95 R
8587 11553 2.095415 AGTTTAATCGGCGCAAAGGTTC 60.095 45.455 10.83 0.00 0.00 3.62 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
21 22 2.739704 CGATCGCCAACGTGCACAT 61.740 57.895 18.64 0.00 41.18 3.21
51 52 1.754803 CTACTACCTTGGATGTGGCGA 59.245 52.381 0.00 0.00 0.00 5.54
69 70 0.884704 GACAACGCTTCCTCCTTGCA 60.885 55.000 0.00 0.00 0.00 4.08
276 277 2.716424 TCAAAGTGGGGATGAAGGAGTT 59.284 45.455 0.00 0.00 0.00 3.01
281 282 2.040412 GTGGGGATGAAGGAGTTCAAGT 59.960 50.000 0.00 0.00 45.88 3.16
349 350 1.069090 GTCAACTGTCACCGCCAGA 59.931 57.895 0.00 0.00 34.04 3.86
381 385 4.113815 CGGGGCAGATGGAGGCAA 62.114 66.667 0.00 0.00 0.00 4.52
393 397 1.349688 TGGAGGCAACCGAACAACTAT 59.650 47.619 0.00 0.00 37.17 2.12
404 408 4.643784 ACCGAACAACTATATCCGAAGACT 59.356 41.667 0.00 0.00 0.00 3.24
492 496 1.094785 CCATGCCTAAAAGGTCACCG 58.905 55.000 0.00 0.00 37.80 4.94
493 497 1.094785 CATGCCTAAAAGGTCACCGG 58.905 55.000 0.00 0.00 37.80 5.28
636 643 6.737254 ACATGAATTTCGTCCGTCTTAAAT 57.263 33.333 0.00 0.00 0.00 1.40
638 645 8.259049 ACATGAATTTCGTCCGTCTTAAATTA 57.741 30.769 0.00 0.00 33.03 1.40
639 646 8.173130 ACATGAATTTCGTCCGTCTTAAATTAC 58.827 33.333 0.00 0.00 33.03 1.89
687 695 0.692476 TCTGTGGTTGGATGGTCAGG 59.308 55.000 0.00 0.00 0.00 3.86
692 700 0.984230 GGTTGGATGGTCAGGTCTCA 59.016 55.000 0.00 0.00 0.00 3.27
709 717 2.590575 ACTGTCAACCGCGTTGGG 60.591 61.111 17.28 11.89 42.99 4.12
724 732 3.063045 GCGTTGGGGTTATCTTTACTTCG 59.937 47.826 0.00 0.00 0.00 3.79
730 760 5.188163 TGGGGTTATCTTTACTTCGTCATGA 59.812 40.000 0.00 0.00 0.00 3.07
738 768 6.406370 TCTTTACTTCGTCATGATTGGATGT 58.594 36.000 0.00 8.15 0.00 3.06
749 779 1.936547 GATTGGATGTTCGGCTCTCAC 59.063 52.381 0.00 0.00 0.00 3.51
750 780 0.684535 TTGGATGTTCGGCTCTCACA 59.315 50.000 0.00 0.00 0.00 3.58
751 781 0.037326 TGGATGTTCGGCTCTCACAC 60.037 55.000 0.00 0.00 0.00 3.82
766 801 7.519970 CGGCTCTCACACTGTTTTAAAGTTATT 60.520 37.037 0.00 0.00 0.00 1.40
794 829 0.918983 ATCATGGTTGGATGGTCGGT 59.081 50.000 0.00 0.00 0.00 4.69
827 863 2.036733 CGGATTAGAATTGTCGCCCCTA 59.963 50.000 0.00 0.00 0.00 3.53
893 986 1.159713 TCCACGATGATTGATGGCGC 61.160 55.000 0.00 0.00 31.87 6.53
894 987 1.438562 CCACGATGATTGATGGCGCA 61.439 55.000 10.83 0.00 0.00 6.09
895 988 0.316442 CACGATGATTGATGGCGCAC 60.316 55.000 10.83 0.00 0.00 5.34
896 989 0.462581 ACGATGATTGATGGCGCACT 60.463 50.000 10.83 0.00 0.00 4.40
897 990 1.202521 ACGATGATTGATGGCGCACTA 60.203 47.619 10.83 0.00 0.00 2.74
1125 1249 0.178990 GGCCTCTGAAGGTGGTGTTT 60.179 55.000 0.00 0.00 45.34 2.83
1309 1440 7.610580 TCCCCAAATTTAGTGAAAATCTTGT 57.389 32.000 0.00 0.00 36.76 3.16
1310 1441 7.666623 TCCCCAAATTTAGTGAAAATCTTGTC 58.333 34.615 0.00 0.00 36.76 3.18
1311 1442 7.508977 TCCCCAAATTTAGTGAAAATCTTGTCT 59.491 33.333 0.00 0.00 36.76 3.41
1312 1443 8.150296 CCCCAAATTTAGTGAAAATCTTGTCTT 58.850 33.333 0.00 0.00 36.76 3.01
1313 1444 8.981647 CCCAAATTTAGTGAAAATCTTGTCTTG 58.018 33.333 0.00 0.00 36.76 3.02
1314 1445 8.981647 CCAAATTTAGTGAAAATCTTGTCTTGG 58.018 33.333 0.00 0.00 36.76 3.61
1410 1547 7.493743 ACAATGCTCTTAACAGATGATGATC 57.506 36.000 0.00 0.00 0.00 2.92
1452 1589 8.565896 AAACTATGACATCTTGAATAGCAACA 57.434 30.769 0.00 0.00 31.96 3.33
1453 1590 8.565896 AACTATGACATCTTGAATAGCAACAA 57.434 30.769 0.00 0.00 31.96 2.83
1454 1591 8.565896 ACTATGACATCTTGAATAGCAACAAA 57.434 30.769 0.00 0.00 31.96 2.83
1455 1592 9.013229 ACTATGACATCTTGAATAGCAACAAAA 57.987 29.630 0.00 0.00 31.96 2.44
1456 1593 9.282247 CTATGACATCTTGAATAGCAACAAAAC 57.718 33.333 0.00 0.00 31.96 2.43
1459 1596 7.648908 TGACATCTTGAATAGCAACAAAACAAG 59.351 33.333 0.00 0.00 35.90 3.16
1460 1597 7.715657 ACATCTTGAATAGCAACAAAACAAGA 58.284 30.769 0.00 0.00 43.50 3.02
1461 1598 7.649306 ACATCTTGAATAGCAACAAAACAAGAC 59.351 33.333 0.00 0.00 42.65 3.01
1464 1601 7.701924 TCTTGAATAGCAACAAAACAAGACAAG 59.298 33.333 0.00 0.00 37.77 3.16
1467 1604 8.845227 TGAATAGCAACAAAACAAGACAAGATA 58.155 29.630 0.00 0.00 0.00 1.98
1624 3614 2.349590 TGATCTTGCATGTGTTCTCCG 58.650 47.619 0.00 0.00 0.00 4.63
1679 3679 4.151689 TGACGTGAAAATTAGGAAGCTTCG 59.848 41.667 19.91 7.25 0.00 3.79
1699 3702 8.784043 AGCTTCGTTTTCATTATTCTGTTACTT 58.216 29.630 0.00 0.00 0.00 2.24
1755 3759 3.456277 GTCTCCTTTCCCCACTCATGTAT 59.544 47.826 0.00 0.00 0.00 2.29
2000 4024 1.133976 GCTTATGGCCTGTCTGGTGAT 60.134 52.381 3.32 0.00 38.35 3.06
2021 4045 2.805671 TGAGACGCAGGTACACATTTTG 59.194 45.455 0.00 0.00 0.00 2.44
2022 4046 1.535462 AGACGCAGGTACACATTTTGC 59.465 47.619 0.00 0.00 0.00 3.68
2062 4086 3.159353 TGTGCTGCTATATCGACGTTT 57.841 42.857 0.00 0.00 0.00 3.60
2184 4209 4.771590 TGATTTGGAATCTGCAACAGTC 57.228 40.909 0.00 0.00 32.61 3.51
2245 4270 4.398319 GGAACACTTCTCCTCAAATCCAA 58.602 43.478 0.00 0.00 0.00 3.53
2391 4416 2.532715 TGCCCAGGAGAAAGGCCT 60.533 61.111 0.00 0.00 46.55 5.19
2529 4554 2.887568 GATGGTGCCGACTCAGCG 60.888 66.667 0.00 0.00 37.28 5.18
2634 4659 6.201425 CAGCATTCACAACATTAAATATGGCC 59.799 38.462 0.00 0.00 0.00 5.36
2700 4725 0.759346 ACCAGAGTCTTTTCCAGCGT 59.241 50.000 0.00 0.00 0.00 5.07
2808 4833 3.004862 TGCAGTATCTGATTGCACTGTG 58.995 45.455 16.37 2.76 45.07 3.66
2821 4846 1.596603 CACTGTGCAGATGGTTGACA 58.403 50.000 6.17 0.00 0.00 3.58
2862 4887 7.220740 AGCTTAATAATTCAGAGAAGCCTACC 58.779 38.462 0.00 0.00 40.07 3.18
3083 5108 5.745312 TGTCAGCTATATATCTTGGGGTG 57.255 43.478 0.00 0.00 0.00 4.61
3164 5189 8.421784 ACTTTGTAGAACTTGTGTATTCAGAGA 58.578 33.333 0.00 0.00 0.00 3.10
3166 5191 8.589335 TTGTAGAACTTGTGTATTCAGAGAAC 57.411 34.615 0.00 0.00 0.00 3.01
3200 5227 4.235079 TCATCCTAATGGGGTCACAAAG 57.765 45.455 0.00 0.00 33.42 2.77
3218 5245 4.956075 ACAAAGGACCAACTCTGTGAAATT 59.044 37.500 0.00 0.00 0.00 1.82
3435 5626 7.935338 ATTTGCACATTTCACAAGTTAAGAG 57.065 32.000 0.00 0.00 0.00 2.85
3437 5628 6.449635 TGCACATTTCACAAGTTAAGAGTT 57.550 33.333 0.00 0.00 0.00 3.01
3438 5629 7.561021 TGCACATTTCACAAGTTAAGAGTTA 57.439 32.000 0.00 0.00 0.00 2.24
3598 5789 2.627699 ACACATTTGGCCTTTTCGATGT 59.372 40.909 3.32 2.49 0.00 3.06
3599 5790 3.069443 ACACATTTGGCCTTTTCGATGTT 59.931 39.130 3.32 0.00 0.00 2.71
3669 5922 5.527214 TGTTAATACATACAGGCATGCTCAC 59.473 40.000 18.92 0.18 0.00 3.51
3837 6091 5.738619 AAAATTCCCCGCATTAGTTTCTT 57.261 34.783 0.00 0.00 0.00 2.52
4362 6676 7.303182 TCATAAAAGAGAGTCTCTGGAAACA 57.697 36.000 23.33 6.53 40.28 2.83
4384 6698 5.652891 ACAGTGTGTTCTCTACCCTGTATAG 59.347 44.000 0.00 0.00 0.00 1.31
4387 6701 5.651139 GTGTGTTCTCTACCCTGTATAGTCA 59.349 44.000 0.00 0.00 0.00 3.41
4404 6718 8.197439 TGTATAGTCATGAGTGTTCCAACATAG 58.803 37.037 13.54 0.00 41.59 2.23
4405 6719 5.489792 AGTCATGAGTGTTCCAACATAGT 57.510 39.130 1.14 0.00 41.59 2.12
4416 6730 8.621286 AGTGTTCCAACATAGTTTTCTACTTTG 58.379 33.333 0.00 0.00 41.59 2.77
4515 6829 4.635765 CACTGAGGTCTGACAACAAAGAAA 59.364 41.667 10.38 0.00 0.00 2.52
4631 6945 9.926751 GATTGCATATGTACATGTCTATAATGC 57.073 33.333 22.18 22.18 0.00 3.56
4632 6946 7.848223 TGCATATGTACATGTCTATAATGCC 57.152 36.000 24.37 13.33 0.00 4.40
4633 6947 7.623630 TGCATATGTACATGTCTATAATGCCT 58.376 34.615 24.37 0.00 0.00 4.75
4634 6948 8.757877 TGCATATGTACATGTCTATAATGCCTA 58.242 33.333 24.37 11.71 0.00 3.93
4635 6949 9.035607 GCATATGTACATGTCTATAATGCCTAC 57.964 37.037 18.81 0.00 0.00 3.18
4636 6950 9.534565 CATATGTACATGTCTATAATGCCTACC 57.465 37.037 18.81 0.00 0.00 3.18
4637 6951 6.354794 TGTACATGTCTATAATGCCTACCC 57.645 41.667 0.00 0.00 0.00 3.69
4638 6952 4.910458 ACATGTCTATAATGCCTACCCC 57.090 45.455 0.00 0.00 0.00 4.95
4639 6953 4.239495 ACATGTCTATAATGCCTACCCCA 58.761 43.478 0.00 0.00 0.00 4.96
4640 6954 4.663120 ACATGTCTATAATGCCTACCCCAA 59.337 41.667 0.00 0.00 0.00 4.12
4641 6955 4.699925 TGTCTATAATGCCTACCCCAAC 57.300 45.455 0.00 0.00 0.00 3.77
4642 6956 4.303794 TGTCTATAATGCCTACCCCAACT 58.696 43.478 0.00 0.00 0.00 3.16
4643 6957 4.724798 TGTCTATAATGCCTACCCCAACTT 59.275 41.667 0.00 0.00 0.00 2.66
4644 6958 5.063880 GTCTATAATGCCTACCCCAACTTG 58.936 45.833 0.00 0.00 0.00 3.16
4645 6959 4.724798 TCTATAATGCCTACCCCAACTTGT 59.275 41.667 0.00 0.00 0.00 3.16
4646 6960 2.694616 AATGCCTACCCCAACTTGTT 57.305 45.000 0.00 0.00 0.00 2.83
4647 6961 2.694616 ATGCCTACCCCAACTTGTTT 57.305 45.000 0.00 0.00 0.00 2.83
4648 6962 1.698506 TGCCTACCCCAACTTGTTTG 58.301 50.000 0.00 0.00 34.63 2.93
4659 6973 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
4660 6974 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
4661 6975 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
4662 6976 5.056553 ACTTGTTTGGGACTAAAGGCTTA 57.943 39.130 0.00 0.00 0.00 3.09
4663 6977 5.070685 ACTTGTTTGGGACTAAAGGCTTAG 58.929 41.667 0.00 1.18 40.46 2.18
4664 6978 4.986054 TGTTTGGGACTAAAGGCTTAGA 57.014 40.909 0.00 0.00 38.35 2.10
4665 6979 5.313280 TGTTTGGGACTAAAGGCTTAGAA 57.687 39.130 0.00 0.00 38.35 2.10
4666 6980 5.697067 TGTTTGGGACTAAAGGCTTAGAAA 58.303 37.500 0.00 0.00 38.35 2.52
4667 6981 6.130569 TGTTTGGGACTAAAGGCTTAGAAAA 58.869 36.000 0.00 0.00 38.35 2.29
4668 6982 6.264518 TGTTTGGGACTAAAGGCTTAGAAAAG 59.735 38.462 0.00 0.00 38.35 2.27
4669 6983 5.836024 TGGGACTAAAGGCTTAGAAAAGA 57.164 39.130 0.00 0.00 38.35 2.52
4670 6984 6.195600 TGGGACTAAAGGCTTAGAAAAGAA 57.804 37.500 0.00 0.00 38.35 2.52
4671 6985 6.607019 TGGGACTAAAGGCTTAGAAAAGAAA 58.393 36.000 0.00 0.00 38.35 2.52
4672 6986 7.064229 TGGGACTAAAGGCTTAGAAAAGAAAA 58.936 34.615 0.00 0.00 38.35 2.29
4673 6987 7.230712 TGGGACTAAAGGCTTAGAAAAGAAAAG 59.769 37.037 0.00 0.00 38.35 2.27
4674 6988 7.447545 GGGACTAAAGGCTTAGAAAAGAAAAGA 59.552 37.037 0.00 0.00 38.35 2.52
4675 6989 8.508062 GGACTAAAGGCTTAGAAAAGAAAAGAG 58.492 37.037 0.00 0.00 38.35 2.85
4676 6990 9.274206 GACTAAAGGCTTAGAAAAGAAAAGAGA 57.726 33.333 0.00 0.00 38.35 3.10
4677 6991 9.278978 ACTAAAGGCTTAGAAAAGAAAAGAGAG 57.721 33.333 0.00 0.00 38.35 3.20
4678 6992 9.495572 CTAAAGGCTTAGAAAAGAAAAGAGAGA 57.504 33.333 0.00 0.00 37.32 3.10
4679 6993 8.932434 AAAGGCTTAGAAAAGAAAAGAGAGAT 57.068 30.769 0.00 0.00 34.37 2.75
4680 6994 7.920160 AGGCTTAGAAAAGAAAAGAGAGATG 57.080 36.000 0.00 0.00 34.37 2.90
4681 6995 7.457561 AGGCTTAGAAAAGAAAAGAGAGATGT 58.542 34.615 0.00 0.00 34.37 3.06
4682 6996 8.598041 AGGCTTAGAAAAGAAAAGAGAGATGTA 58.402 33.333 0.00 0.00 34.37 2.29
4683 6997 8.661257 GGCTTAGAAAAGAAAAGAGAGATGTAC 58.339 37.037 0.00 0.00 34.37 2.90
4684 6998 9.209175 GCTTAGAAAAGAAAAGAGAGATGTACA 57.791 33.333 0.00 0.00 34.37 2.90
4688 7002 9.213799 AGAAAAGAAAAGAGAGATGTACATGTC 57.786 33.333 22.15 22.15 0.00 3.06
4689 7003 9.213799 GAAAAGAAAAGAGAGATGTACATGTCT 57.786 33.333 29.86 29.86 43.17 3.41
4706 7020 7.437713 ACATGTCTATAATCTGTCCCTTTGA 57.562 36.000 0.00 0.00 0.00 2.69
4752 7066 5.434352 TCTGTTGACAGTCACTACTACAC 57.566 43.478 1.52 0.00 44.12 2.90
4759 7073 4.333690 ACAGTCACTACTACACGAGGATT 58.666 43.478 0.00 0.00 33.48 3.01
4764 7078 6.015688 AGTCACTACTACACGAGGATTGAAAA 60.016 38.462 0.00 0.00 32.84 2.29
4886 7214 2.239907 AGGTGATAGGGCTTTTCCTCAC 59.760 50.000 0.00 0.00 37.02 3.51
4923 7251 6.374613 TGTCACTGAGTATCGACTATTGAGTT 59.625 38.462 3.68 0.00 38.61 3.01
5401 7731 1.560611 TGAGTGATGACATGGGCATGA 59.439 47.619 7.90 0.00 41.20 3.07
5430 7760 1.003545 GCCATGCAGTACTTGTATGCG 60.004 52.381 13.81 10.16 45.35 4.73
5489 7819 4.998788 TCATACGTCATAGGCAGATATGC 58.001 43.478 3.01 3.01 33.88 3.14
5514 7844 0.174845 ACTGTCGCCGCTTGCTTATA 59.825 50.000 0.00 0.00 38.05 0.98
5588 7918 2.590282 TTGGTGGTAAAAGGTAGGCC 57.410 50.000 0.00 0.00 0.00 5.19
5622 7952 3.459598 TGAGGGATAAGGCAAGCACTAAT 59.540 43.478 0.00 0.00 0.00 1.73
5770 8109 8.127327 GTGTTCTGATTGATGGATAATGTCTTG 58.873 37.037 0.00 0.00 0.00 3.02
5865 8206 8.370940 GGAGATTGGAGAGACATAAATGTGATA 58.629 37.037 0.00 0.00 41.95 2.15
5884 8225 9.988815 ATGTGATATAGACAAGATCAAGTTACC 57.011 33.333 0.00 0.00 31.62 2.85
6048 8389 5.302568 TCCCCAGAGCATTATTTTATTGCTG 59.697 40.000 0.76 0.00 43.20 4.41
6050 8391 4.986659 CCAGAGCATTATTTTATTGCTGCC 59.013 41.667 0.76 0.00 43.20 4.85
6086 8427 4.437930 GCATCTGTGAGCTATTCAACAACC 60.438 45.833 0.00 0.00 37.61 3.77
6155 8496 6.712095 TGTCTGCTGATGTAAGTCTTCATTTT 59.288 34.615 0.00 0.00 31.42 1.82
6182 8523 2.945668 ACTGTTGTTGAAAGAGACAGGC 59.054 45.455 6.73 0.00 41.42 4.85
6381 8723 2.027192 TCAGAGGATAAAAGCGGCACTT 60.027 45.455 1.45 0.00 41.70 3.16
6396 8738 2.045926 CTTCCAAGGCTCCCACCG 60.046 66.667 0.00 0.00 33.69 4.94
6442 8784 6.910191 ACAATCATGGAATGGGTCTGTATAA 58.090 36.000 0.00 0.00 46.73 0.98
6796 9139 1.195115 TGACCTCCCGAGATTCCTTG 58.805 55.000 0.00 0.00 0.00 3.61
6803 9147 1.202855 CCCGAGATTCCTTGCCATGAT 60.203 52.381 0.00 0.00 0.00 2.45
6837 9181 1.271379 TGCATGAGCTCCTTTTTGCTG 59.729 47.619 12.15 0.00 42.74 4.41
7144 9492 1.632589 GGGGGTGCTCAACAATTTCT 58.367 50.000 0.00 0.00 0.00 2.52
7189 9537 1.153549 GGACTGGATCGACCACTGC 60.154 63.158 3.02 0.00 44.64 4.40
7256 9605 4.697352 AGGATAATTCAGTGTTGTCTGTGC 59.303 41.667 0.00 0.00 36.85 4.57
7299 9648 8.730680 TCTTACAAAGGTTGCTGATCTTATTTC 58.269 33.333 0.00 0.00 0.00 2.17
7307 9656 2.560105 GCTGATCTTATTTCCCCATGGC 59.440 50.000 6.09 0.00 0.00 4.40
7535 9903 4.512944 CACTTTCTCTGTCTTTGCTGCTTA 59.487 41.667 0.00 0.00 0.00 3.09
7577 9947 2.124411 GTAGGTGATAAAGGCCCTGGA 58.876 52.381 0.00 0.00 0.00 3.86
7719 10470 5.006746 GGAGGTCTATACAGCAATTTGTTCG 59.993 44.000 0.00 0.00 32.56 3.95
7786 10537 5.355350 CCAGATCACCTTCAACCTAATCAAC 59.645 44.000 0.00 0.00 0.00 3.18
7810 10562 6.886459 ACCATGATCCAATATGTTACCATAGC 59.114 38.462 0.00 0.00 36.99 2.97
7981 10776 2.947852 AGTGACTGCTACTTAACTGCG 58.052 47.619 0.00 0.00 0.00 5.18
8214 11009 0.692476 TTGTATGGTCTGGCAGCAGT 59.308 50.000 10.34 0.00 35.45 4.40
8355 11156 1.663388 TACGTGTGCTGGTTCTGCG 60.663 57.895 0.00 0.00 0.00 5.18
8419 11284 5.414789 TCTCGGTGAGAACAATAATGGAA 57.585 39.130 0.00 0.00 35.59 3.53
8420 11285 5.175859 TCTCGGTGAGAACAATAATGGAAC 58.824 41.667 0.00 0.00 35.59 3.62
8421 11286 5.046591 TCTCGGTGAGAACAATAATGGAACT 60.047 40.000 0.00 0.00 35.59 3.01
8458 11325 4.022935 CAGCCTGCTGACAAAATTTACTGA 60.023 41.667 13.85 0.00 46.30 3.41
8470 11337 7.360361 ACAAAATTTACTGAATTCTCGGTGAC 58.640 34.615 7.05 0.00 41.49 3.67
8482 11349 4.280436 TCTCGGTGACAACAATAATGGT 57.720 40.909 0.00 0.00 0.00 3.55
8502 11369 3.492102 TGCTATCCTAAGGCACAATCC 57.508 47.619 0.00 0.00 0.00 3.01
8520 11387 4.776795 ATCCGGTGTGACAAAATTTACC 57.223 40.909 0.00 0.00 0.00 2.85
8587 11553 3.804325 ACAATAATGGAGCGATCTCGTTG 59.196 43.478 0.00 2.36 40.26 4.10
8693 11663 1.236616 CGTTGCCTGCATGAAGTCCA 61.237 55.000 0.00 0.00 0.00 4.02
8743 14415 4.025401 GTCGCTTTGCACCCCGTG 62.025 66.667 0.00 0.00 36.51 4.94
8752 14425 0.110678 TGCACCCCGTGGTTTGAATA 59.889 50.000 0.00 0.00 44.75 1.75
8904 17731 2.967887 AGACGGTTACAAACACCCTACT 59.032 45.455 0.00 0.00 0.00 2.57
8919 17746 8.946797 AACACCCTACTAGAGTTTAAAGACTA 57.053 34.615 0.00 0.00 0.00 2.59
8928 17755 8.189460 ACTAGAGTTTAAAGACTACAATAGGCG 58.811 37.037 0.00 0.00 39.39 5.52
8970 17797 9.913451 GAGATTTAGAAATCACTGAAAGAATCG 57.087 33.333 15.51 0.00 45.59 3.34
8988 17815 1.227853 GTTGGTTGGAGCGTCACCT 60.228 57.895 0.00 0.00 0.00 4.00
9104 17932 1.514678 CGCACAAGTAGCCAGCCAAA 61.515 55.000 0.00 0.00 0.00 3.28
9125 17953 5.627182 AATGCTCTCCTTGATAGACACAT 57.373 39.130 0.00 0.00 0.00 3.21
9210 18038 0.107214 ACGCCGGATTGGACATCATT 60.107 50.000 5.05 0.00 42.00 2.57
9227 18055 2.126882 CATTGATGTAGGGAGGGGTCA 58.873 52.381 0.00 0.00 0.00 4.02
9254 18082 6.931281 AGTGACCTTATTCCAATATGTCATCG 59.069 38.462 12.04 0.00 36.39 3.84
9255 18083 6.147821 GTGACCTTATTCCAATATGTCATCGG 59.852 42.308 12.04 0.00 36.39 4.18
9293 18126 5.479027 GCCACCAGGAAAATAAAACCTAAGA 59.521 40.000 0.00 0.00 36.89 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.448540 GAGGAGGTGGATGTGCACG 60.449 63.158 13.13 0.00 0.00 5.34
21 22 2.024273 CCAAGGTAGTAGAGGAGGTGGA 60.024 54.545 0.00 0.00 0.00 4.02
51 52 1.148273 TGCAAGGAGGAAGCGTTGT 59.852 52.632 0.00 0.00 36.37 3.32
58 59 4.716784 ACTATCATAGTGTGCAAGGAGGAA 59.283 41.667 0.00 0.00 37.69 3.36
69 70 4.022762 CGCCTTCAGCTACTATCATAGTGT 60.023 45.833 7.66 0.00 40.39 3.55
145 146 1.944676 GCCATCGCGGACTTAGTCG 60.945 63.158 6.13 3.35 36.56 4.18
334 335 1.071471 CCTTCTGGCGGTGACAGTT 59.929 57.895 0.00 0.00 40.10 3.16
381 385 4.643784 AGTCTTCGGATATAGTTGTTCGGT 59.356 41.667 0.00 0.00 0.00 4.69
393 397 3.947910 ACAACGGAAAGTCTTCGGATA 57.052 42.857 0.00 0.00 36.15 2.59
404 408 2.421751 TGTCCTTCCAACAACGGAAA 57.578 45.000 0.00 0.00 44.42 3.13
423 427 2.140717 GTCCCTTTCGTCAACATCGTT 58.859 47.619 0.00 0.00 0.00 3.85
609 614 6.737254 AAGACGGACGAAATTCATGTAAAT 57.263 33.333 0.00 0.00 0.00 1.40
638 645 9.725019 TGAATATTCACACTAGTTCAAATGAGT 57.275 29.630 14.23 0.00 31.01 3.41
668 676 0.692476 CCTGACCATCCAACCACAGA 59.308 55.000 0.00 0.00 0.00 3.41
669 677 0.401738 ACCTGACCATCCAACCACAG 59.598 55.000 0.00 0.00 0.00 3.66
687 695 0.874607 AACGCGGTTGACAGTGAGAC 60.875 55.000 12.47 0.00 0.00 3.36
692 700 2.590575 CCCAACGCGGTTGACAGT 60.591 61.111 12.47 0.00 45.28 3.55
724 732 2.289002 GAGCCGAACATCCAATCATGAC 59.711 50.000 0.00 0.00 0.00 3.06
730 760 1.278985 TGTGAGAGCCGAACATCCAAT 59.721 47.619 0.00 0.00 0.00 3.16
738 768 2.325583 AAAACAGTGTGAGAGCCGAA 57.674 45.000 0.00 0.00 0.00 4.30
766 801 6.015918 ACCATCCAACCATGATCAAGTAAAA 58.984 36.000 0.00 0.00 0.00 1.52
774 809 1.134098 ACCGACCATCCAACCATGATC 60.134 52.381 0.00 0.00 0.00 2.92
780 815 0.613777 AGAGAACCGACCATCCAACC 59.386 55.000 0.00 0.00 0.00 3.77
784 819 0.895530 TGACAGAGAACCGACCATCC 59.104 55.000 0.00 0.00 0.00 3.51
794 829 5.677319 ATTCTAATCCGGTTGACAGAGAA 57.323 39.130 0.00 2.95 0.00 2.87
827 863 1.549170 GTGATGTCGTGGAGTAAGGGT 59.451 52.381 0.00 0.00 0.00 4.34
893 986 2.852413 CGCGGATCTTTGTAGTGTAGTG 59.148 50.000 0.00 0.00 0.00 2.74
894 987 2.159282 CCGCGGATCTTTGTAGTGTAGT 60.159 50.000 24.07 0.00 0.00 2.73
895 988 2.159282 ACCGCGGATCTTTGTAGTGTAG 60.159 50.000 35.90 0.00 0.00 2.74
896 989 1.820519 ACCGCGGATCTTTGTAGTGTA 59.179 47.619 35.90 0.00 0.00 2.90
897 990 0.606604 ACCGCGGATCTTTGTAGTGT 59.393 50.000 35.90 0.00 0.00 3.55
1447 1584 9.226345 GCTATATATCTTGTCTTGTTTTGTTGC 57.774 33.333 0.00 0.00 0.00 4.17
1450 1587 9.672673 AGTGCTATATATCTTGTCTTGTTTTGT 57.327 29.630 0.00 0.00 0.00 2.83
1624 3614 8.999431 TCAGAAAAGTGGTATGATTGTACTTTC 58.001 33.333 0.00 0.00 39.78 2.62
2000 4024 2.805671 CAAAATGTGTACCTGCGTCTCA 59.194 45.455 0.00 0.00 0.00 3.27
2021 4045 4.762251 ACAACTCTTCCATCAACCTAAAGC 59.238 41.667 0.00 0.00 0.00 3.51
2022 4046 5.335191 GCACAACTCTTCCATCAACCTAAAG 60.335 44.000 0.00 0.00 0.00 1.85
2083 4108 2.952978 CGAGAGGCTGGTAACTCTACAT 59.047 50.000 0.00 0.00 43.71 2.29
2245 4270 9.167311 AGAGATTTTAGTCGCAATTACTTGATT 57.833 29.630 0.00 0.00 34.04 2.57
2391 4416 0.107066 ATGCATTGTCATCTCCCGCA 60.107 50.000 0.00 0.00 0.00 5.69
2634 4659 2.548480 CTGTGCATATGACATGCTCCTG 59.452 50.000 6.97 2.58 44.79 3.86
2700 4725 1.400142 CGTGAAAGTTGCAAGGACACA 59.600 47.619 18.79 7.58 0.00 3.72
2808 4833 2.227388 CCTTGAACTGTCAACCATCTGC 59.773 50.000 0.00 0.00 38.88 4.26
2821 4846 8.611654 TTATTAAGCTCGTTTAACCTTGAACT 57.388 30.769 0.00 0.00 0.00 3.01
3063 5088 8.449423 AATAACACCCCAAGATATATAGCTGA 57.551 34.615 0.28 0.00 0.00 4.26
3164 5189 9.219603 CCATTAGGATGATATTTATGACGTGTT 57.780 33.333 0.00 0.00 36.89 3.32
3166 5191 7.280876 CCCCATTAGGATGATATTTATGACGTG 59.719 40.741 0.00 0.00 38.24 4.49
3200 5227 5.010012 ACAATCAATTTCACAGAGTTGGTCC 59.990 40.000 0.00 0.00 0.00 4.46
3218 5245 1.814394 GACTGCATGCAAGGACAATCA 59.186 47.619 22.88 0.00 0.00 2.57
3357 5385 7.208064 ACATATTAAGAGAAAGGGCCACTTA 57.792 36.000 6.18 4.81 38.85 2.24
3598 5789 4.933400 GCCTCAATTACTTCGGTGTCTTAA 59.067 41.667 0.00 0.00 0.00 1.85
3599 5790 4.501071 GCCTCAATTACTTCGGTGTCTTA 58.499 43.478 0.00 0.00 0.00 2.10
3669 5922 7.557719 ACTGATTATCCAATGTGTTTAAGGGAG 59.442 37.037 0.00 0.00 0.00 4.30
3706 5959 7.148255 TGGGAATATGAGCGTTAATCAATATGC 60.148 37.037 0.00 0.00 0.00 3.14
4028 6290 4.766373 TGCTACAAATGGCAAGAGAATCAA 59.234 37.500 0.00 0.00 39.73 2.57
4349 6663 3.452627 AGAACACACTGTTTCCAGAGACT 59.547 43.478 0.00 0.00 41.28 3.24
4362 6676 5.828871 ACTATACAGGGTAGAGAACACACT 58.171 41.667 5.16 0.00 31.97 3.55
4384 6698 6.560253 AAACTATGTTGGAACACTCATGAC 57.440 37.500 0.00 0.00 42.51 3.06
4387 6701 8.157476 AGTAGAAAACTATGTTGGAACACTCAT 58.843 33.333 0.00 0.00 42.51 2.90
4462 6776 5.575987 GCTAGGAGTAGGATCCAAGGCTATA 60.576 48.000 15.82 0.00 42.26 1.31
4500 6814 6.054941 TCACTGCTATTTCTTTGTTGTCAGA 58.945 36.000 0.00 0.00 0.00 3.27
4637 6951 9.339958 CTAAGCCTTTAGTCCCAAACAAGTTGG 62.340 44.444 7.96 0.00 42.29 3.77
4638 6952 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
4639 6953 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
4640 6954 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
4641 6955 5.313712 TCTAAGCCTTTAGTCCCAAACAAG 58.686 41.667 0.00 0.00 37.97 3.16
4642 6956 5.313280 TCTAAGCCTTTAGTCCCAAACAA 57.687 39.130 0.00 0.00 37.97 2.83
4643 6957 4.986054 TCTAAGCCTTTAGTCCCAAACA 57.014 40.909 0.00 0.00 37.97 2.83
4644 6958 6.489022 TCTTTTCTAAGCCTTTAGTCCCAAAC 59.511 38.462 0.00 0.00 37.97 2.93
4645 6959 6.607019 TCTTTTCTAAGCCTTTAGTCCCAAA 58.393 36.000 0.00 0.00 37.97 3.28
4646 6960 6.195600 TCTTTTCTAAGCCTTTAGTCCCAA 57.804 37.500 0.00 0.00 37.97 4.12
4647 6961 5.836024 TCTTTTCTAAGCCTTTAGTCCCA 57.164 39.130 0.00 0.00 37.97 4.37
4648 6962 7.447545 TCTTTTCTTTTCTAAGCCTTTAGTCCC 59.552 37.037 0.00 0.00 37.97 4.46
4649 6963 8.392372 TCTTTTCTTTTCTAAGCCTTTAGTCC 57.608 34.615 0.00 0.00 37.97 3.85
4650 6964 9.274206 TCTCTTTTCTTTTCTAAGCCTTTAGTC 57.726 33.333 0.00 0.00 37.97 2.59
4651 6965 9.278978 CTCTCTTTTCTTTTCTAAGCCTTTAGT 57.721 33.333 0.00 0.00 37.97 2.24
4652 6966 9.495572 TCTCTCTTTTCTTTTCTAAGCCTTTAG 57.504 33.333 0.00 0.00 38.09 1.85
4654 6968 8.791675 CATCTCTCTTTTCTTTTCTAAGCCTTT 58.208 33.333 0.00 0.00 0.00 3.11
4655 6969 7.941790 ACATCTCTCTTTTCTTTTCTAAGCCTT 59.058 33.333 0.00 0.00 0.00 4.35
4656 6970 7.457561 ACATCTCTCTTTTCTTTTCTAAGCCT 58.542 34.615 0.00 0.00 0.00 4.58
4657 6971 7.680442 ACATCTCTCTTTTCTTTTCTAAGCC 57.320 36.000 0.00 0.00 0.00 4.35
4658 6972 9.209175 TGTACATCTCTCTTTTCTTTTCTAAGC 57.791 33.333 0.00 0.00 0.00 3.09
4662 6976 9.213799 GACATGTACATCTCTCTTTTCTTTTCT 57.786 33.333 5.07 0.00 0.00 2.52
4663 6977 9.213799 AGACATGTACATCTCTCTTTTCTTTTC 57.786 33.333 5.07 0.00 0.00 2.29
4672 6986 9.806448 ACAGATTATAGACATGTACATCTCTCT 57.194 33.333 15.90 12.88 0.00 3.10
4674 6988 9.019656 GGACAGATTATAGACATGTACATCTCT 57.980 37.037 16.54 16.54 0.00 3.10
4675 6989 8.247562 GGGACAGATTATAGACATGTACATCTC 58.752 40.741 5.07 3.96 0.00 2.75
4676 6990 7.952930 AGGGACAGATTATAGACATGTACATCT 59.047 37.037 5.07 4.72 0.00 2.90
4677 6991 8.128322 AGGGACAGATTATAGACATGTACATC 57.872 38.462 5.07 0.00 0.00 3.06
4678 6992 8.497910 AAGGGACAGATTATAGACATGTACAT 57.502 34.615 1.41 1.41 0.00 2.29
4679 6993 7.914427 AAGGGACAGATTATAGACATGTACA 57.086 36.000 0.00 0.00 0.00 2.90
4680 6994 8.421784 TCAAAGGGACAGATTATAGACATGTAC 58.578 37.037 0.00 0.00 0.00 2.90
4681 6995 8.421784 GTCAAAGGGACAGATTATAGACATGTA 58.578 37.037 0.00 0.00 46.19 2.29
4682 6996 7.275920 GTCAAAGGGACAGATTATAGACATGT 58.724 38.462 0.00 0.00 46.19 3.21
4683 6997 7.721286 GTCAAAGGGACAGATTATAGACATG 57.279 40.000 0.00 0.00 46.19 3.21
4706 7020 3.945285 CGACCTTTGTATTGCTATTGGGT 59.055 43.478 0.00 0.00 0.00 4.51
4752 7066 5.886960 AGATTGGTCTTTTTCAATCCTCG 57.113 39.130 11.07 0.00 46.09 4.63
4759 7073 5.596361 TGCCTTGTTAGATTGGTCTTTTTCA 59.404 36.000 0.00 0.00 35.87 2.69
4764 7078 6.948309 ACTAATTGCCTTGTTAGATTGGTCTT 59.052 34.615 0.00 0.00 35.87 3.01
4867 7195 3.636153 AGTGAGGAAAAGCCCTATCAC 57.364 47.619 0.00 0.00 38.82 3.06
4876 7204 7.442364 TGACACTAAGAATGAAGTGAGGAAAAG 59.558 37.037 9.30 0.00 44.79 2.27
4877 7205 7.226720 GTGACACTAAGAATGAAGTGAGGAAAA 59.773 37.037 9.30 0.00 44.79 2.29
4886 7214 7.430793 CGATACTCAGTGACACTAAGAATGAAG 59.569 40.741 12.96 0.00 0.00 3.02
5081 7409 9.268268 TGTTTAAACACGAAGTAGAATTCATCT 57.732 29.630 17.01 2.47 41.61 2.90
5430 7760 8.780249 TGCTTAAAGGTGATACAAGAAAGTAAC 58.220 33.333 0.00 0.00 0.00 2.50
5489 7819 0.025001 CAAGCGGCGACAGTAATTCG 59.975 55.000 12.98 0.00 39.56 3.34
5588 7918 7.004086 TGCCTTATCCCTCATATTTGGTTTAG 58.996 38.462 0.00 0.00 0.00 1.85
5716 8055 5.880054 AAAGGTAGATGAACCAACAATCG 57.120 39.130 0.00 0.00 42.40 3.34
5770 8109 6.533730 TCACCATATATTCACAACATCCTCC 58.466 40.000 0.00 0.00 0.00 4.30
6048 8389 4.705386 CAGATGCTTTCTTGCCATCGGC 62.705 54.545 0.00 0.00 40.32 5.54
6050 8391 1.741706 ACAGATGCTTTCTTGCCATCG 59.258 47.619 0.00 0.00 29.93 3.84
6086 8427 9.334947 ACTTCTCTAATAATTGACATGTCCATG 57.665 33.333 22.85 5.74 44.15 3.66
6155 8496 8.836413 CCTGTCTCTTTCAACAACAGTAAATAA 58.164 33.333 0.00 0.00 36.46 1.40
6182 8523 8.627403 ACCAAAGTATCTGCATATTCAATGAAG 58.373 33.333 1.10 0.00 0.00 3.02
6381 8723 0.619255 TTATCGGTGGGAGCCTTGGA 60.619 55.000 0.00 0.00 0.00 3.53
6469 8811 4.525487 ACTGAACAGACCAATGCAAATCAT 59.475 37.500 8.87 0.00 36.87 2.45
6516 8859 4.440663 GGATCCTTAAAATCTTGTGCCTGC 60.441 45.833 3.84 0.00 0.00 4.85
6659 9002 4.041444 TGCCCTTTTGATATGCCAAAAAGT 59.959 37.500 0.00 0.00 43.04 2.66
6796 9139 4.498682 GCAAGATCAAGTAACCATCATGGC 60.499 45.833 2.52 0.00 42.67 4.40
6803 9147 3.691118 GCTCATGCAAGATCAAGTAACCA 59.309 43.478 0.00 0.00 39.41 3.67
7109 9456 4.804597 GCACCCCCGTTCCAAAAATAAAAT 60.805 41.667 0.00 0.00 0.00 1.82
7114 9461 0.471022 AGCACCCCCGTTCCAAAAAT 60.471 50.000 0.00 0.00 0.00 1.82
7121 9468 0.893727 ATTGTTGAGCACCCCCGTTC 60.894 55.000 0.00 0.00 0.00 3.95
7144 9492 8.956426 CATTAAACCTTGCTATCCTTCTACAAA 58.044 33.333 0.00 0.00 0.00 2.83
7299 9648 1.907936 TGAAAGAAAATGGCCATGGGG 59.092 47.619 21.63 0.00 37.18 4.96
7360 9709 1.242989 TGCAAGCAAACCGCATAAGA 58.757 45.000 0.00 0.00 46.13 2.10
7535 9903 6.047511 ACACAATAGAGAGAATTCAGTGCT 57.952 37.500 8.44 2.13 0.00 4.40
7577 9947 4.445448 GCCATCTTCCATGAAGTAGACCAT 60.445 45.833 0.00 0.00 40.24 3.55
7719 10470 2.410469 GAATGGTGGATGCGCTGC 59.590 61.111 9.73 0.00 0.00 5.25
7810 10562 6.912082 TGTGTCACAATTCAAGGTAATCATG 58.088 36.000 2.31 0.00 0.00 3.07
7981 10776 4.091365 TGTGATGTTTGTGAATCGATCGTC 59.909 41.667 15.94 6.90 0.00 4.20
8355 11156 5.975939 GCAACAGATAATGCCTTCAGATTTC 59.024 40.000 0.00 0.00 36.56 2.17
8442 11307 7.535258 CACCGAGAATTCAGTAAATTTTGTCAG 59.465 37.037 8.44 0.00 37.70 3.51
8458 11325 5.710099 ACCATTATTGTTGTCACCGAGAATT 59.290 36.000 0.00 0.00 0.00 2.17
8470 11337 6.294176 GCCTTAGGATAGCACCATTATTGTTG 60.294 42.308 0.69 0.00 0.00 3.33
8482 11349 2.224281 CGGATTGTGCCTTAGGATAGCA 60.224 50.000 0.69 0.00 0.00 3.49
8587 11553 2.095415 AGTTTAATCGGCGCAAAGGTTC 60.095 45.455 10.83 0.00 0.00 3.62
8655 11625 3.336468 ACGAACATGCACCCGTTATTTA 58.664 40.909 0.00 0.00 30.41 1.40
8666 11636 2.192187 TGCAGGCAACGAACATGCA 61.192 52.632 11.13 11.13 45.60 3.96
8752 14425 9.438163 AGATTTGAATGATAATTGGGTTGGTAT 57.562 29.630 0.00 0.00 0.00 2.73
8904 17731 6.976925 GCGCCTATTGTAGTCTTTAAACTCTA 59.023 38.462 0.00 0.00 0.00 2.43
8964 17791 0.034896 ACGCTCCAACCAACGATTCT 59.965 50.000 0.00 0.00 0.00 2.40
8970 17797 0.034337 TAGGTGACGCTCCAACCAAC 59.966 55.000 0.00 0.00 0.00 3.77
8988 17815 1.908344 TGCAAGCCTGTTCTGCATTA 58.092 45.000 0.00 0.00 0.00 1.90
9104 17932 4.652881 TGATGTGTCTATCAAGGAGAGCAT 59.347 41.667 0.00 0.00 34.32 3.79
9125 17953 4.341487 TCTCTTCGGATCTTGGTAGTTGA 58.659 43.478 0.00 0.00 0.00 3.18
9210 18038 1.015609 TCTGACCCCTCCCTACATCA 58.984 55.000 0.00 0.00 0.00 3.07
9227 18055 7.437713 TGACATATTGGAATAAGGTCACTCT 57.562 36.000 10.73 0.00 35.84 3.24
9293 18126 7.119116 AGCCTCGTTTGTTTTGATTTTCTTTTT 59.881 29.630 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.