Multiple sequence alignment - TraesCS3D01G296600

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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 TraesCS3D01G296600 chr3D 100.000 2283 0 0 1 2283 410519607 410517325 0.000000e+00 4217.0
1 TraesCS3D01G296600 chr3D 87.768 654 56 15 1638 2283 274673373 274674010 0.000000e+00 743.0
2 TraesCS3D01G296600 chr3D 87.538 650 60 13 1638 2282 274446834 274447467 0.000000e+00 732.0
3 TraesCS3D01G296600 chr3D 100.000 34 0 0 1099 1132 410518478 410518445 1.890000e-06 63.9
4 TraesCS3D01G296600 chr3D 100.000 34 0 0 1130 1163 410518509 410518476 1.890000e-06 63.9
5 TraesCS3D01G296600 chr3D 82.667 75 8 3 255 324 68079922 68079996 6.810000e-06 62.1
6 TraesCS3D01G296600 chr3A 89.888 623 33 17 526 1132 541225491 541226099 0.000000e+00 774.0
7 TraesCS3D01G296600 chr3A 93.052 403 17 5 1130 1527 541226066 541226462 1.520000e-161 579.0
8 TraesCS3D01G296600 chr3A 90.196 51 2 2 245 295 200126723 200126770 1.890000e-06 63.9
9 TraesCS3D01G296600 chr3A 84.058 69 6 4 261 324 80090209 80090141 6.810000e-06 62.1
10 TraesCS3D01G296600 chr5B 90.494 526 48 1 1760 2283 539245998 539245473 0.000000e+00 693.0
11 TraesCS3D01G296600 chr2A 85.263 665 72 12 1635 2283 192063546 192064200 0.000000e+00 662.0
12 TraesCS3D01G296600 chr2A 83.308 665 88 12 1636 2283 730588634 730589292 1.950000e-165 592.0
13 TraesCS3D01G296600 chr2A 100.000 34 0 0 296 329 541196548 541196515 1.890000e-06 63.9
14 TraesCS3D01G296600 chrUn 90.683 483 39 4 1803 2283 53429309 53429787 2.470000e-179 638.0
15 TraesCS3D01G296600 chrUn 78.832 137 22 6 1638 1769 326383299 326383165 4.040000e-13 86.1
16 TraesCS3D01G296600 chrUn 78.832 137 22 6 1638 1769 326404680 326404546 4.040000e-13 86.1
17 TraesCS3D01G296600 chrUn 78.832 137 22 6 1638 1769 355604183 355604317 4.040000e-13 86.1
18 TraesCS3D01G296600 chr5D 84.273 674 67 22 1624 2283 396458839 396459487 2.490000e-174 621.0
19 TraesCS3D01G296600 chr5D 83.976 674 64 20 1638 2283 502077072 502076415 6.970000e-170 606.0
20 TraesCS3D01G296600 chr5D 88.679 106 11 1 1638 1743 422336311 422336207 6.620000e-26 128.0
21 TraesCS3D01G296600 chr1D 84.041 683 69 22 1634 2283 248842510 248843185 2.490000e-174 621.0
22 TraesCS3D01G296600 chr1D 87.242 533 58 8 1754 2283 252911745 252911220 1.170000e-167 599.0
23 TraesCS3D01G296600 chr7B 89.770 479 43 5 1807 2283 746688523 746688997 1.940000e-170 608.0
24 TraesCS3D01G296600 chr3B 89.540 478 23 14 440 905 536429880 536429418 4.230000e-162 580.0
25 TraesCS3D01G296600 chr3B 94.636 261 9 2 1130 1386 536429263 536429004 1.270000e-107 399.0
26 TraesCS3D01G296600 chr3B 93.750 192 11 1 941 1132 536429420 536429230 1.030000e-73 287.0
27 TraesCS3D01G296600 chr3B 86.831 243 19 3 1 239 536433673 536433440 2.250000e-65 259.0
28 TraesCS3D01G296600 chr3B 92.908 141 6 1 1387 1527 536428862 536428726 3.850000e-48 202.0
29 TraesCS3D01G296600 chr3B 100.000 33 0 0 225 257 536433429 536433397 6.810000e-06 62.1
30 TraesCS3D01G296600 chr4B 82.396 676 77 20 1635 2283 386466785 386467445 3.310000e-153 551.0
31 TraesCS3D01G296600 chr4B 93.023 43 3 0 253 295 124737577 124737619 1.890000e-06 63.9
32 TraesCS3D01G296600 chr6D 87.162 148 17 2 986 1132 411767167 411767313 1.400000e-37 167.0
33 TraesCS3D01G296600 chr6D 85.965 57 4 2 271 324 275674461 275674406 8.810000e-05 58.4
34 TraesCS3D01G296600 chr6B 86.486 148 18 2 986 1132 619404730 619404876 6.530000e-36 161.0
35 TraesCS3D01G296600 chr7D 88.496 113 12 1 1634 1745 463954503 463954391 3.960000e-28 135.0
36 TraesCS3D01G296600 chr4D 86.607 112 13 2 1635 1745 358619016 358619126 3.080000e-24 122.0
37 TraesCS3D01G296600 chr4D 89.041 73 3 1 251 323 32346501 32346568 4.040000e-13 86.1
38 TraesCS3D01G296600 chr7A 93.333 75 5 0 250 324 492257339 492257265 6.670000e-21 111.0
39 TraesCS3D01G296600 chr5A 91.304 69 6 0 255 323 546897785 546897853 6.710000e-16 95.3
40 TraesCS3D01G296600 chr4A 92.982 57 3 1 268 323 694850955 694851011 5.230000e-12 82.4
41 TraesCS3D01G296600 chr1A 94.595 37 2 0 296 332 522462398 522462362 8.810000e-05 58.4


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 TraesCS3D01G296600 chr3D 410517325 410519607 2282 True 1448.266667 4217 100.000000 1 2283 3 chr3D.!!$R1 2282
1 TraesCS3D01G296600 chr3D 274673373 274674010 637 False 743.000000 743 87.768000 1638 2283 1 chr3D.!!$F3 645
2 TraesCS3D01G296600 chr3D 274446834 274447467 633 False 732.000000 732 87.538000 1638 2282 1 chr3D.!!$F2 644
3 TraesCS3D01G296600 chr3A 541225491 541226462 971 False 676.500000 774 91.470000 526 1527 2 chr3A.!!$F2 1001
4 TraesCS3D01G296600 chr5B 539245473 539245998 525 True 693.000000 693 90.494000 1760 2283 1 chr5B.!!$R1 523
5 TraesCS3D01G296600 chr2A 192063546 192064200 654 False 662.000000 662 85.263000 1635 2283 1 chr2A.!!$F1 648
6 TraesCS3D01G296600 chr2A 730588634 730589292 658 False 592.000000 592 83.308000 1636 2283 1 chr2A.!!$F2 647
7 TraesCS3D01G296600 chr5D 396458839 396459487 648 False 621.000000 621 84.273000 1624 2283 1 chr5D.!!$F1 659
8 TraesCS3D01G296600 chr5D 502076415 502077072 657 True 606.000000 606 83.976000 1638 2283 1 chr5D.!!$R2 645
9 TraesCS3D01G296600 chr1D 248842510 248843185 675 False 621.000000 621 84.041000 1634 2283 1 chr1D.!!$F1 649
10 TraesCS3D01G296600 chr1D 252911220 252911745 525 True 599.000000 599 87.242000 1754 2283 1 chr1D.!!$R1 529
11 TraesCS3D01G296600 chr3B 536428726 536433673 4947 True 298.183333 580 92.944167 1 1527 6 chr3B.!!$R1 1526
12 TraesCS3D01G296600 chr4B 386466785 386467445 660 False 551.000000 551 82.396000 1635 2283 1 chr4B.!!$F2 648

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
575 3965 0.03467 AAATGCTCCAGGAGACAGGC 60.035 55.0 21.89 5.6 36.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 5184 0.179078 GGCTGGAGATGCTCTCAGTG 60.179 60.0 13.06 0.0 45.12 3.66 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
64 65 1.422531 AGCCATTCTTTGCACCCAAA 58.577 45.000 0.00 0.00 38.56 3.28
65 66 1.070601 AGCCATTCTTTGCACCCAAAC 59.929 47.619 0.00 0.00 36.09 2.93
70 71 3.701532 TTCTTTGCACCCAAACTAACG 57.298 42.857 0.00 0.00 36.09 3.18
92 93 5.146460 CGAACATGTTCAATCACGTTCATT 58.854 37.500 32.06 0.00 39.46 2.57
98 99 8.296000 ACATGTTCAATCACGTTCATTTATTGA 58.704 29.630 0.00 0.00 35.39 2.57
112 113 7.465353 TCATTTATTGAAGGTCATTGCTTCA 57.535 32.000 0.00 0.00 35.60 3.02
113 114 7.894708 TCATTTATTGAAGGTCATTGCTTCAA 58.105 30.769 16.66 16.66 46.60 2.69
127 128 5.929697 TTGCTTCAAGGATAGCGATATTG 57.070 39.130 0.00 0.00 40.26 1.90
128 129 4.318332 TGCTTCAAGGATAGCGATATTGG 58.682 43.478 0.00 0.00 40.26 3.16
152 153 1.377594 CATGTGTAGCTGCTGGGCA 60.378 57.895 13.43 8.27 36.92 5.36
172 173 4.320494 GGCAATTATAATTCCTGCTCACCG 60.320 45.833 16.38 1.98 0.00 4.94
186 191 2.662866 CTCACCGGACCCTTCACTATA 58.337 52.381 9.46 0.00 0.00 1.31
192 197 4.472108 ACCGGACCCTTCACTATATTGAAA 59.528 41.667 9.46 0.00 35.07 2.69
199 204 6.833933 ACCCTTCACTATATTGAAATGGGAAC 59.166 38.462 25.14 0.00 40.88 3.62
208 213 4.664150 TTGAAATGGGAACTTGACCAAC 57.336 40.909 0.00 0.00 40.73 3.77
209 214 3.636679 TGAAATGGGAACTTGACCAACA 58.363 40.909 0.00 0.00 40.73 3.33
210 215 3.636300 TGAAATGGGAACTTGACCAACAG 59.364 43.478 0.00 0.00 40.73 3.16
211 216 3.593442 AATGGGAACTTGACCAACAGA 57.407 42.857 0.00 0.00 40.73 3.41
212 217 2.341846 TGGGAACTTGACCAACAGAC 57.658 50.000 0.00 0.00 32.89 3.51
214 219 1.226746 GGAACTTGACCAACAGACCG 58.773 55.000 0.00 0.00 0.00 4.79
216 221 2.135933 GAACTTGACCAACAGACCGAG 58.864 52.381 0.00 0.00 0.00 4.63
217 222 0.249911 ACTTGACCAACAGACCGAGC 60.250 55.000 0.00 0.00 0.00 5.03
218 223 0.951040 CTTGACCAACAGACCGAGCC 60.951 60.000 0.00 0.00 0.00 4.70
219 224 2.432628 GACCAACAGACCGAGCCG 60.433 66.667 0.00 0.00 0.00 5.52
220 225 3.222354 GACCAACAGACCGAGCCGT 62.222 63.158 0.00 0.00 0.00 5.68
221 226 2.432628 CCAACAGACCGAGCCGTC 60.433 66.667 0.00 0.00 0.00 4.79
222 227 2.432628 CAACAGACCGAGCCGTCC 60.433 66.667 0.00 0.00 32.91 4.79
223 228 2.915659 AACAGACCGAGCCGTCCA 60.916 61.111 0.00 0.00 32.91 4.02
259 281 8.849543 TTACCTACTGAAAATCATACTACCCT 57.150 34.615 0.00 0.00 0.00 4.34
260 282 7.362802 ACCTACTGAAAATCATACTACCCTC 57.637 40.000 0.00 0.00 0.00 4.30
261 283 7.133483 ACCTACTGAAAATCATACTACCCTCT 58.867 38.462 0.00 0.00 0.00 3.69
262 284 7.288158 ACCTACTGAAAATCATACTACCCTCTC 59.712 40.741 0.00 0.00 0.00 3.20
263 285 6.487299 ACTGAAAATCATACTACCCTCTCC 57.513 41.667 0.00 0.00 0.00 3.71
273 431 2.226170 ACTACCCTCTCCCTCCCAAAAT 60.226 50.000 0.00 0.00 0.00 1.82
277 435 2.580783 CCCTCTCCCTCCCAAAATGTAA 59.419 50.000 0.00 0.00 0.00 2.41
282 1949 2.640826 TCCCTCCCAAAATGTAAGACGT 59.359 45.455 0.00 0.00 0.00 4.34
284 1951 3.824443 CCCTCCCAAAATGTAAGACGTTT 59.176 43.478 0.00 0.00 38.84 3.60
308 3612 8.829514 TTTTTGACACTACGTCTTACATTTTG 57.170 30.769 0.00 0.00 45.60 2.44
310 3614 4.992319 TGACACTACGTCTTACATTTTGGG 59.008 41.667 0.00 0.00 45.60 4.12
311 3615 5.217978 ACACTACGTCTTACATTTTGGGA 57.782 39.130 0.00 0.00 0.00 4.37
315 3619 2.690786 CGTCTTACATTTTGGGACGGA 58.309 47.619 0.00 0.00 43.69 4.69
316 3620 2.671396 CGTCTTACATTTTGGGACGGAG 59.329 50.000 0.00 0.00 43.69 4.63
317 3621 3.007635 GTCTTACATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
318 3622 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
319 3623 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
320 3624 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
321 3625 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
323 3627 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
324 3628 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
325 3629 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
354 3736 8.502105 AACTAAAATATGCACTGGTAGTTACC 57.498 34.615 8.92 1.25 46.62 2.85
375 3757 9.018582 GTTACCAGAAGAGTTACCTAAGTTAGA 57.981 37.037 11.66 0.00 0.00 2.10
400 3782 9.991906 GACTAGCATACTTATTACATAAACCCA 57.008 33.333 0.00 0.00 0.00 4.51
412 3794 4.510571 ACATAAACCCAAGGCTAACGTAG 58.489 43.478 0.00 0.00 0.00 3.51
480 3862 9.778993 CTATATATGCAGTAACAATGCCATTTC 57.221 33.333 0.00 0.00 43.18 2.17
500 3882 5.689383 TTCGTCCTTGAAAATCTTTCTGG 57.311 39.130 1.22 3.88 0.00 3.86
574 3964 1.681166 CCAAATGCTCCAGGAGACAGG 60.681 57.143 21.89 11.04 38.62 4.00
575 3965 0.034670 AAATGCTCCAGGAGACAGGC 60.035 55.000 21.89 5.60 36.83 4.85
576 3966 1.203441 AATGCTCCAGGAGACAGGCA 61.203 55.000 21.89 11.83 36.83 4.75
577 3967 0.987081 ATGCTCCAGGAGACAGGCAT 60.987 55.000 21.89 13.72 36.83 4.40
578 3968 1.153208 GCTCCAGGAGACAGGCATG 60.153 63.158 21.89 0.00 36.83 4.06
583 3973 0.035725 CAGGAGACAGGCATGAGCAA 60.036 55.000 4.84 0.00 44.61 3.91
662 4052 1.649390 GGCACACAACGTCACCACAA 61.649 55.000 0.00 0.00 0.00 3.33
663 4053 0.380378 GCACACAACGTCACCACAAT 59.620 50.000 0.00 0.00 0.00 2.71
675 4065 4.331968 GTCACCACAATGAGGTCCAAATA 58.668 43.478 0.00 0.00 37.23 1.40
693 4087 6.547880 TCCAAATAACTAGCACAAGTGGAAAA 59.452 34.615 2.00 0.00 0.00 2.29
696 4090 2.914059 ACTAGCACAAGTGGAAAACGT 58.086 42.857 2.00 0.00 0.00 3.99
745 4139 2.034066 TCCTTCCCGGCAAAGCAG 59.966 61.111 0.00 0.00 0.00 4.24
761 4155 0.675837 GCAGCACAGCCAATCAGAGA 60.676 55.000 0.00 0.00 0.00 3.10
785 4179 1.815817 GATGCCCACCAAACCCACAC 61.816 60.000 0.00 0.00 0.00 3.82
832 4226 5.652452 ACCAGGTAAAAATAATCACAGCTCC 59.348 40.000 0.00 0.00 0.00 4.70
857 4251 2.113139 ACGAGCCAAACCCACAGG 59.887 61.111 0.00 0.00 40.04 4.00
861 4255 3.615709 GCCAAACCCACAGGCCAC 61.616 66.667 5.01 0.00 42.58 5.01
862 4256 2.123511 CCAAACCCACAGGCCACA 60.124 61.111 5.01 0.00 36.11 4.17
863 4257 2.202395 CCAAACCCACAGGCCACAG 61.202 63.158 5.01 0.00 36.11 3.66
868 4262 2.293318 CCCACAGGCCACAGCTCTA 61.293 63.158 5.01 0.00 39.73 2.43
884 4278 5.305644 ACAGCTCTATATAAACCCAGACTGG 59.694 44.000 15.15 15.15 37.25 4.00
930 4324 3.180584 CGATAGCACAAACGAGCTGATAC 59.819 47.826 0.00 0.00 41.97 2.24
938 4332 1.018148 ACGAGCTGATACCTCACGAG 58.982 55.000 0.00 0.00 0.00 4.18
939 4333 1.018148 CGAGCTGATACCTCACGAGT 58.982 55.000 0.00 0.00 0.00 4.18
959 4353 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
961 4355 0.676466 CACACACACACACACACCCT 60.676 55.000 0.00 0.00 0.00 4.34
962 4356 0.676466 ACACACACACACACACCCTG 60.676 55.000 0.00 0.00 0.00 4.45
984 4390 2.105134 ACACCCCTCGTTTGTTGACATA 59.895 45.455 0.00 0.00 0.00 2.29
1094 4500 2.166664 GTCTGGTGTACCTGATCCTCAC 59.833 54.545 12.82 0.00 44.15 3.51
1104 4510 1.821753 CTGATCCTCACCAACTCGTCT 59.178 52.381 0.00 0.00 0.00 4.18
1106 4512 1.819288 GATCCTCACCAACTCGTCTGA 59.181 52.381 0.00 0.00 0.00 3.27
1107 4513 0.959553 TCCTCACCAACTCGTCTGAC 59.040 55.000 0.00 0.00 0.00 3.51
1108 4514 0.387367 CCTCACCAACTCGTCTGACG 60.387 60.000 23.33 23.33 44.19 4.35
1109 4515 0.311165 CTCACCAACTCGTCTGACGT 59.689 55.000 27.16 8.74 43.14 4.34
1110 4516 0.309922 TCACCAACTCGTCTGACGTC 59.690 55.000 27.16 9.11 43.14 4.34
1111 4517 0.311165 CACCAACTCGTCTGACGTCT 59.689 55.000 27.16 12.42 43.14 4.18
1112 4518 1.030457 ACCAACTCGTCTGACGTCTT 58.970 50.000 27.16 17.06 43.14 3.01
1113 4519 1.001597 ACCAACTCGTCTGACGTCTTC 60.002 52.381 27.16 6.16 43.14 2.87
1114 4520 1.267261 CCAACTCGTCTGACGTCTTCT 59.733 52.381 27.16 8.32 43.14 2.85
1115 4521 2.576406 CAACTCGTCTGACGTCTTCTC 58.424 52.381 27.16 4.05 43.14 2.87
1116 4522 1.158434 ACTCGTCTGACGTCTTCTCC 58.842 55.000 27.16 0.00 43.14 3.71
1117 4523 1.157585 CTCGTCTGACGTCTTCTCCA 58.842 55.000 27.16 6.91 43.14 3.86
1118 4524 1.535896 CTCGTCTGACGTCTTCTCCAA 59.464 52.381 27.16 6.22 43.14 3.53
1119 4525 1.951602 TCGTCTGACGTCTTCTCCAAA 59.048 47.619 27.16 3.58 43.14 3.28
1120 4526 2.031069 TCGTCTGACGTCTTCTCCAAAG 60.031 50.000 27.16 2.92 43.14 2.77
1121 4527 2.031069 CGTCTGACGTCTTCTCCAAAGA 60.031 50.000 21.30 5.48 36.74 2.52
1122 4528 3.366476 CGTCTGACGTCTTCTCCAAAGAT 60.366 47.826 21.30 0.00 36.74 2.40
1123 4529 4.142665 CGTCTGACGTCTTCTCCAAAGATA 60.143 45.833 21.30 0.00 36.74 1.98
1124 4530 5.619309 CGTCTGACGTCTTCTCCAAAGATAA 60.619 44.000 21.30 0.00 36.74 1.75
1125 4531 5.802956 GTCTGACGTCTTCTCCAAAGATAAG 59.197 44.000 17.92 0.15 0.00 1.73
1126 4532 5.710567 TCTGACGTCTTCTCCAAAGATAAGA 59.289 40.000 17.92 2.75 33.98 2.10
1127 4533 6.208797 TCTGACGTCTTCTCCAAAGATAAGAA 59.791 38.462 17.92 0.00 37.08 2.52
1128 4534 6.390721 TGACGTCTTCTCCAAAGATAAGAAG 58.609 40.000 17.92 5.24 44.74 2.85
1129 4535 5.172205 ACGTCTTCTCCAAAGATAAGAAGC 58.828 41.667 6.50 2.50 43.63 3.86
1130 4536 5.046950 ACGTCTTCTCCAAAGATAAGAAGCT 60.047 40.000 6.50 0.00 43.63 3.74
1131 4537 5.518487 CGTCTTCTCCAAAGATAAGAAGCTC 59.482 44.000 6.50 2.82 43.63 4.09
1132 4538 5.518487 GTCTTCTCCAAAGATAAGAAGCTCG 59.482 44.000 6.50 0.00 43.63 5.03
1133 4539 5.186021 TCTTCTCCAAAGATAAGAAGCTCGT 59.814 40.000 6.50 0.00 43.63 4.18
1134 4540 5.000012 TCTCCAAAGATAAGAAGCTCGTC 58.000 43.478 0.00 0.00 0.00 4.20
1135 4541 4.707448 TCTCCAAAGATAAGAAGCTCGTCT 59.293 41.667 0.00 0.00 0.00 4.18
1136 4542 4.748892 TCCAAAGATAAGAAGCTCGTCTG 58.251 43.478 0.00 0.00 0.00 3.51
1183 4589 2.683933 TCCCTGAGCTTCCGGTCC 60.684 66.667 0.00 0.00 36.84 4.46
1375 4785 3.706594 AGTTCCTCTGTTCTGAGTTGTCA 59.293 43.478 6.10 0.00 32.50 3.58
1389 4940 6.317140 TCTGAGTTGTCATGGATTCTTATTGC 59.683 38.462 0.00 0.00 30.18 3.56
1426 4977 9.919416 TGAGAATCATATTTGAACTCCCATAAA 57.081 29.630 15.32 0.00 42.56 1.40
1429 4980 9.956720 GAATCATATTTGAACTCCCATAAAGTG 57.043 33.333 0.00 0.00 34.96 3.16
1434 4985 9.927081 ATATTTGAACTCCCATAAAGTGAGATT 57.073 29.630 0.00 0.00 0.00 2.40
1436 4987 8.792830 TTTGAACTCCCATAAAGTGAGATTAG 57.207 34.615 0.00 0.00 0.00 1.73
1437 4988 6.349300 TGAACTCCCATAAAGTGAGATTAGC 58.651 40.000 0.00 0.00 0.00 3.09
1454 5005 5.955355 AGATTAGCTAGGTGGGATCTGTATC 59.045 44.000 4.27 0.00 0.00 2.24
1528 5080 5.904362 AAAAAGTGTCTGCTCTCAGTTTT 57.096 34.783 11.98 11.98 44.05 2.43
1529 5081 5.904362 AAAAGTGTCTGCTCTCAGTTTTT 57.096 34.783 11.98 4.78 41.41 1.94
1548 5100 3.963383 TTTTTGAAACGGAGTCTGCTC 57.037 42.857 0.00 0.00 45.00 4.26
1549 5101 2.910688 TTTGAAACGGAGTCTGCTCT 57.089 45.000 0.00 0.00 45.00 4.09
1550 5102 2.440539 TTGAAACGGAGTCTGCTCTC 57.559 50.000 0.00 0.00 45.00 3.20
1551 5103 1.328279 TGAAACGGAGTCTGCTCTCA 58.672 50.000 0.00 0.00 45.00 3.27
1552 5104 1.270826 TGAAACGGAGTCTGCTCTCAG 59.729 52.381 0.00 5.13 45.00 3.35
1553 5105 1.271102 GAAACGGAGTCTGCTCTCAGT 59.729 52.381 0.00 5.63 45.00 3.41
1554 5106 1.333177 AACGGAGTCTGCTCTCAGTT 58.667 50.000 13.12 13.12 45.00 3.16
1555 5107 0.600557 ACGGAGTCTGCTCTCAGTTG 59.399 55.000 0.00 0.00 39.12 3.16
1556 5108 0.600557 CGGAGTCTGCTCTCAGTTGT 59.399 55.000 0.00 0.00 41.38 3.32
1557 5109 1.668337 CGGAGTCTGCTCTCAGTTGTG 60.668 57.143 0.00 0.00 41.38 3.33
1558 5110 1.615883 GGAGTCTGCTCTCAGTTGTGA 59.384 52.381 0.00 0.00 41.38 3.58
1559 5111 2.233431 GGAGTCTGCTCTCAGTTGTGAT 59.767 50.000 0.00 0.00 41.38 3.06
1560 5112 3.306641 GGAGTCTGCTCTCAGTTGTGATT 60.307 47.826 0.00 0.00 41.38 2.57
1561 5113 4.081972 GGAGTCTGCTCTCAGTTGTGATTA 60.082 45.833 0.00 0.00 41.38 1.75
1562 5114 5.395103 GGAGTCTGCTCTCAGTTGTGATTAT 60.395 44.000 0.00 0.00 41.38 1.28
1563 5115 5.417811 AGTCTGCTCTCAGTTGTGATTATG 58.582 41.667 0.00 0.00 41.10 1.90
1564 5116 4.569966 GTCTGCTCTCAGTTGTGATTATGG 59.430 45.833 0.00 0.00 41.10 2.74
1565 5117 4.223700 TCTGCTCTCAGTTGTGATTATGGT 59.776 41.667 0.00 0.00 41.10 3.55
1566 5118 5.422012 TCTGCTCTCAGTTGTGATTATGGTA 59.578 40.000 0.00 0.00 41.10 3.25
1567 5119 5.419542 TGCTCTCAGTTGTGATTATGGTAC 58.580 41.667 0.00 0.00 30.18 3.34
1568 5120 5.187772 TGCTCTCAGTTGTGATTATGGTACT 59.812 40.000 0.00 0.00 30.18 2.73
1569 5121 6.109359 GCTCTCAGTTGTGATTATGGTACTT 58.891 40.000 0.00 0.00 30.18 2.24
1570 5122 6.036517 GCTCTCAGTTGTGATTATGGTACTTG 59.963 42.308 0.00 0.00 30.18 3.16
1571 5123 7.239763 TCTCAGTTGTGATTATGGTACTTGA 57.760 36.000 0.00 0.00 30.18 3.02
1572 5124 7.323420 TCTCAGTTGTGATTATGGTACTTGAG 58.677 38.462 0.00 0.00 30.18 3.02
1573 5125 7.004555 TCAGTTGTGATTATGGTACTTGAGT 57.995 36.000 0.00 0.00 0.00 3.41
1574 5126 7.450074 TCAGTTGTGATTATGGTACTTGAGTT 58.550 34.615 0.00 0.00 0.00 3.01
1575 5127 7.936847 TCAGTTGTGATTATGGTACTTGAGTTT 59.063 33.333 0.00 0.00 0.00 2.66
1576 5128 8.567948 CAGTTGTGATTATGGTACTTGAGTTTT 58.432 33.333 0.00 0.00 0.00 2.43
1577 5129 9.131791 AGTTGTGATTATGGTACTTGAGTTTTT 57.868 29.630 0.00 0.00 0.00 1.94
1578 5130 9.180678 GTTGTGATTATGGTACTTGAGTTTTTG 57.819 33.333 0.00 0.00 0.00 2.44
1579 5131 8.458573 TGTGATTATGGTACTTGAGTTTTTGT 57.541 30.769 0.00 0.00 0.00 2.83
1580 5132 8.908903 TGTGATTATGGTACTTGAGTTTTTGTT 58.091 29.630 0.00 0.00 0.00 2.83
1581 5133 9.744468 GTGATTATGGTACTTGAGTTTTTGTTT 57.256 29.630 0.00 0.00 0.00 2.83
1582 5134 9.959749 TGATTATGGTACTTGAGTTTTTGTTTC 57.040 29.630 0.00 0.00 0.00 2.78
1583 5135 9.959749 GATTATGGTACTTGAGTTTTTGTTTCA 57.040 29.630 0.00 0.00 0.00 2.69
1587 5139 8.472683 TGGTACTTGAGTTTTTGTTTCATTTG 57.527 30.769 0.00 0.00 0.00 2.32
1588 5140 8.091449 TGGTACTTGAGTTTTTGTTTCATTTGT 58.909 29.630 0.00 0.00 0.00 2.83
1589 5141 9.575783 GGTACTTGAGTTTTTGTTTCATTTGTA 57.424 29.630 0.00 0.00 0.00 2.41
1617 5169 6.644248 ACTTTAATTCCTGGTTAACACACC 57.356 37.500 8.10 0.00 37.34 4.16
1618 5170 6.130569 ACTTTAATTCCTGGTTAACACACCA 58.869 36.000 8.10 0.00 45.13 4.17
1619 5171 6.780522 ACTTTAATTCCTGGTTAACACACCAT 59.219 34.615 8.10 0.00 46.16 3.55
1620 5172 7.945664 ACTTTAATTCCTGGTTAACACACCATA 59.054 33.333 8.10 0.00 46.16 2.74
1621 5173 8.887264 TTTAATTCCTGGTTAACACACCATAT 57.113 30.769 8.10 0.00 46.16 1.78
1622 5174 6.773976 AATTCCTGGTTAACACACCATATG 57.226 37.500 8.10 0.00 46.16 1.78
1623 5175 3.616219 TCCTGGTTAACACACCATATGC 58.384 45.455 8.10 0.00 46.16 3.14
1624 5176 2.687935 CCTGGTTAACACACCATATGCC 59.312 50.000 8.10 0.00 46.16 4.40
1625 5177 3.351740 CTGGTTAACACACCATATGCCA 58.648 45.455 8.10 0.00 46.16 4.92
1626 5178 3.761218 CTGGTTAACACACCATATGCCAA 59.239 43.478 8.10 0.00 46.16 4.52
1627 5179 4.348486 TGGTTAACACACCATATGCCAAT 58.652 39.130 8.10 0.00 42.27 3.16
1628 5180 5.510430 TGGTTAACACACCATATGCCAATA 58.490 37.500 8.10 0.00 42.27 1.90
1629 5181 5.358442 TGGTTAACACACCATATGCCAATAC 59.642 40.000 8.10 0.00 42.27 1.89
1630 5182 5.358442 GGTTAACACACCATATGCCAATACA 59.642 40.000 8.10 0.00 36.73 2.29
1631 5183 6.127591 GGTTAACACACCATATGCCAATACAA 60.128 38.462 8.10 0.00 36.73 2.41
1632 5184 4.981806 ACACACCATATGCCAATACAAC 57.018 40.909 0.00 0.00 0.00 3.32
1707 5259 2.648454 GGCGTGCCGGTGAAAAAT 59.352 55.556 1.90 0.00 0.00 1.82
1716 5268 0.236187 CGGTGAAAAATTCGGCGTGA 59.764 50.000 6.85 0.00 0.00 4.35
1769 5340 1.136774 GATTTCGGCCCACTTTCGC 59.863 57.895 0.00 0.00 0.00 4.70
1997 5647 4.074259 ACATCTTGCTGCAGTTGTTGATA 58.926 39.130 16.64 0.00 0.00 2.15
2018 5668 1.352352 CACCTGTGGGTCTTGGATCTT 59.648 52.381 0.00 0.00 45.41 2.40
2024 5674 2.303022 GTGGGTCTTGGATCTTCTGACA 59.697 50.000 0.00 0.00 0.00 3.58
2038 5688 6.857437 TCTTCTGACACATATTGAGGAAGA 57.143 37.500 0.00 0.00 36.40 2.87
2194 5844 4.202556 TGACCTCCCACATTTGATCTTTCA 60.203 41.667 0.00 0.00 0.00 2.69
2238 5888 4.084066 CGGACAACAACAAATCGAGATTGA 60.084 41.667 17.68 0.00 0.00 2.57
2261 5911 0.322816 ACACCAAATGCCTGCTCGAT 60.323 50.000 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.561373 GCTTTGAAACCCTCCGCG 59.439 61.111 0.00 0.00 0.00 6.46
10 11 2.561373 CGCTTTGAAACCCTCCGC 59.439 61.111 0.00 0.00 0.00 5.54
46 47 1.070601 AGTTTGGGTGCAAAGAATGGC 59.929 47.619 0.00 0.00 0.00 4.40
50 51 3.280295 TCGTTAGTTTGGGTGCAAAGAA 58.720 40.909 0.00 0.00 0.00 2.52
53 54 2.753452 TGTTCGTTAGTTTGGGTGCAAA 59.247 40.909 0.00 0.00 0.00 3.68
64 65 4.748102 ACGTGATTGAACATGTTCGTTAGT 59.252 37.500 28.55 20.64 42.28 2.24
65 66 5.264060 ACGTGATTGAACATGTTCGTTAG 57.736 39.130 28.55 20.11 42.28 2.34
98 99 3.950395 GCTATCCTTGAAGCAATGACCTT 59.050 43.478 0.00 0.00 38.63 3.50
101 102 3.198068 TCGCTATCCTTGAAGCAATGAC 58.802 45.455 0.00 0.00 38.70 3.06
112 113 3.815401 GTGCAACCAATATCGCTATCCTT 59.185 43.478 0.00 0.00 0.00 3.36
113 114 3.181455 TGTGCAACCAATATCGCTATCCT 60.181 43.478 0.00 0.00 34.36 3.24
127 128 0.109597 GCAGCTACACATGTGCAACC 60.110 55.000 25.68 11.44 35.91 3.77
128 129 0.877071 AGCAGCTACACATGTGCAAC 59.123 50.000 25.68 14.37 38.44 4.17
152 153 5.063880 GTCCGGTGAGCAGGAATTATAATT 58.936 41.667 10.51 10.51 40.54 1.40
172 173 5.770162 CCCATTTCAATATAGTGAAGGGTCC 59.230 44.000 22.84 0.00 37.84 4.46
186 191 4.653341 TGTTGGTCAAGTTCCCATTTCAAT 59.347 37.500 0.00 0.00 0.00 2.57
192 197 2.489073 GGTCTGTTGGTCAAGTTCCCAT 60.489 50.000 0.00 0.00 0.00 4.00
199 204 0.951040 GGCTCGGTCTGTTGGTCAAG 60.951 60.000 0.00 0.00 0.00 3.02
208 213 1.592400 TACTTGGACGGCTCGGTCTG 61.592 60.000 7.37 2.49 37.12 3.51
209 214 1.303888 TACTTGGACGGCTCGGTCT 60.304 57.895 7.37 0.00 37.12 3.85
210 215 1.139095 CTACTTGGACGGCTCGGTC 59.861 63.158 0.00 0.00 36.18 4.79
211 216 2.348888 CCTACTTGGACGGCTCGGT 61.349 63.158 0.00 0.00 38.35 4.69
212 217 2.348888 ACCTACTTGGACGGCTCGG 61.349 63.158 0.00 0.00 39.71 4.63
214 219 0.824759 ATCACCTACTTGGACGGCTC 59.175 55.000 0.00 0.00 39.71 4.70
216 221 2.109425 AAATCACCTACTTGGACGGC 57.891 50.000 0.00 0.00 39.71 5.68
217 222 3.528532 GGTAAATCACCTACTTGGACGG 58.471 50.000 0.00 0.00 44.79 4.79
257 279 3.523564 TCTTACATTTTGGGAGGGAGAGG 59.476 47.826 0.00 0.00 0.00 3.69
258 280 4.518249 GTCTTACATTTTGGGAGGGAGAG 58.482 47.826 0.00 0.00 0.00 3.20
259 281 3.055385 CGTCTTACATTTTGGGAGGGAGA 60.055 47.826 0.00 0.00 0.00 3.71
260 282 3.270877 CGTCTTACATTTTGGGAGGGAG 58.729 50.000 0.00 0.00 0.00 4.30
261 283 2.640826 ACGTCTTACATTTTGGGAGGGA 59.359 45.455 0.00 0.00 0.00 4.20
262 284 3.067684 ACGTCTTACATTTTGGGAGGG 57.932 47.619 0.00 0.00 0.00 4.30
263 285 5.447624 AAAACGTCTTACATTTTGGGAGG 57.552 39.130 0.00 0.00 0.00 4.30
296 1963 3.007635 CCTCCGTCCCAAAATGTAAGAC 58.992 50.000 0.00 0.00 0.00 3.01
308 3612 2.149973 TTTAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
310 3614 7.573968 TTAGTTATTTAGTACTCCCTCCGTC 57.426 40.000 0.00 0.00 0.00 4.79
311 3615 7.961326 TTTAGTTATTTAGTACTCCCTCCGT 57.039 36.000 0.00 0.00 0.00 4.69
448 3830 9.371136 GCATTGTTACTGCATATATAGAGCTAA 57.629 33.333 10.29 1.51 39.46 3.09
449 3831 7.981789 GGCATTGTTACTGCATATATAGAGCTA 59.018 37.037 10.29 0.00 41.47 3.32
450 3832 6.820656 GGCATTGTTACTGCATATATAGAGCT 59.179 38.462 10.29 0.00 41.47 4.09
451 3833 6.595326 TGGCATTGTTACTGCATATATAGAGC 59.405 38.462 0.00 3.63 41.47 4.09
452 3834 8.728337 ATGGCATTGTTACTGCATATATAGAG 57.272 34.615 0.00 0.00 41.47 2.43
453 3835 9.519191 AAATGGCATTGTTACTGCATATATAGA 57.481 29.630 14.47 0.00 41.47 1.98
454 3836 9.778993 GAAATGGCATTGTTACTGCATATATAG 57.221 33.333 14.47 0.00 41.47 1.31
455 3837 8.450180 CGAAATGGCATTGTTACTGCATATATA 58.550 33.333 14.47 0.00 41.47 0.86
456 3838 7.040478 ACGAAATGGCATTGTTACTGCATATAT 60.040 33.333 14.47 0.00 41.47 0.86
480 3862 3.366374 GCCCAGAAAGATTTTCAAGGACG 60.366 47.826 11.69 0.00 0.00 4.79
574 3964 0.450983 GGAGTTGCTCTTGCTCATGC 59.549 55.000 0.00 0.00 40.48 4.06
575 3965 1.817357 TGGAGTTGCTCTTGCTCATG 58.183 50.000 0.00 0.00 40.48 3.07
576 3966 2.366533 CATGGAGTTGCTCTTGCTCAT 58.633 47.619 0.00 0.00 40.48 2.90
577 3967 1.612462 CCATGGAGTTGCTCTTGCTCA 60.612 52.381 5.56 0.00 40.48 4.26
578 3968 1.093159 CCATGGAGTTGCTCTTGCTC 58.907 55.000 5.56 0.00 40.48 4.26
583 3973 1.271597 GGTTGACCATGGAGTTGCTCT 60.272 52.381 21.47 0.00 35.64 4.09
654 4044 3.524095 ATTTGGACCTCATTGTGGTGA 57.476 42.857 14.84 0.00 38.03 4.02
662 4052 5.435686 TGTGCTAGTTATTTGGACCTCAT 57.564 39.130 0.00 0.00 0.00 2.90
663 4053 4.901197 TGTGCTAGTTATTTGGACCTCA 57.099 40.909 0.00 0.00 0.00 3.86
675 4065 3.064820 CACGTTTTCCACTTGTGCTAGTT 59.935 43.478 0.00 0.00 0.00 2.24
693 4087 1.407979 AGAAGTCGTTGGTCTTCACGT 59.592 47.619 7.48 0.00 41.46 4.49
696 4090 2.432874 TGGAAGAAGTCGTTGGTCTTCA 59.567 45.455 13.08 0.00 45.97 3.02
745 4139 0.390340 TCGTCTCTGATTGGCTGTGC 60.390 55.000 0.00 0.00 0.00 4.57
761 4155 0.893727 GGTTTGGTGGGCATCTTCGT 60.894 55.000 0.00 0.00 0.00 3.85
832 4226 3.283684 TTTGGCTCGTGCGGTTGG 61.284 61.111 3.02 0.00 40.82 3.77
857 4251 4.040461 TCTGGGTTTATATAGAGCTGTGGC 59.960 45.833 0.00 0.00 39.06 5.01
858 4252 5.305644 AGTCTGGGTTTATATAGAGCTGTGG 59.694 44.000 0.00 0.00 0.00 4.17
859 4253 6.219473 CAGTCTGGGTTTATATAGAGCTGTG 58.781 44.000 0.00 0.00 0.00 3.66
860 4254 5.305644 CCAGTCTGGGTTTATATAGAGCTGT 59.694 44.000 11.46 0.00 32.67 4.40
861 4255 5.540337 TCCAGTCTGGGTTTATATAGAGCTG 59.460 44.000 19.11 0.00 38.32 4.24
862 4256 5.716979 TCCAGTCTGGGTTTATATAGAGCT 58.283 41.667 19.11 0.00 38.32 4.09
863 4257 6.267928 TCTTCCAGTCTGGGTTTATATAGAGC 59.732 42.308 19.11 0.00 38.32 4.09
868 4262 7.071321 CCTTACTCTTCCAGTCTGGGTTTATAT 59.929 40.741 19.11 2.17 38.32 0.86
884 4278 3.427773 CGGTAGTGTCTGCCTTACTCTTC 60.428 52.174 2.81 0.00 34.05 2.87
930 4324 0.102300 TGTGTGTGTGACTCGTGAGG 59.898 55.000 1.43 0.00 0.00 3.86
938 4332 1.136085 GTGTGTGTGTGTGTGTGTGAC 60.136 52.381 0.00 0.00 0.00 3.67
939 4333 1.152510 GTGTGTGTGTGTGTGTGTGA 58.847 50.000 0.00 0.00 0.00 3.58
959 4353 0.179029 AACAAACGAGGGGTGTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
961 4355 0.542333 TCAACAAACGAGGGGTGTCA 59.458 50.000 0.00 0.00 0.00 3.58
962 4356 0.942252 GTCAACAAACGAGGGGTGTC 59.058 55.000 0.00 0.00 0.00 3.67
1094 4500 1.267261 AGAAGACGTCAGACGAGTTGG 59.733 52.381 29.53 0.00 46.05 3.77
1104 4510 5.977489 TCTTATCTTTGGAGAAGACGTCA 57.023 39.130 19.50 0.00 42.57 4.35
1106 4512 5.046950 AGCTTCTTATCTTTGGAGAAGACGT 60.047 40.000 14.55 0.00 45.67 4.34
1107 4513 5.415221 AGCTTCTTATCTTTGGAGAAGACG 58.585 41.667 14.55 6.15 45.67 4.18
1108 4514 5.518487 CGAGCTTCTTATCTTTGGAGAAGAC 59.482 44.000 14.55 7.32 45.67 3.01
1109 4515 5.186021 ACGAGCTTCTTATCTTTGGAGAAGA 59.814 40.000 14.55 4.64 45.79 2.87
1110 4516 5.415221 ACGAGCTTCTTATCTTTGGAGAAG 58.585 41.667 7.73 7.73 45.72 2.85
1111 4517 5.186021 AGACGAGCTTCTTATCTTTGGAGAA 59.814 40.000 0.00 0.00 35.07 2.87
1112 4518 4.707448 AGACGAGCTTCTTATCTTTGGAGA 59.293 41.667 0.00 0.00 36.09 3.71
1113 4519 4.803088 CAGACGAGCTTCTTATCTTTGGAG 59.197 45.833 0.00 0.00 0.00 3.86
1114 4520 4.462834 TCAGACGAGCTTCTTATCTTTGGA 59.537 41.667 0.00 0.00 0.00 3.53
1115 4521 4.564769 GTCAGACGAGCTTCTTATCTTTGG 59.435 45.833 0.00 0.00 0.00 3.28
1116 4522 4.264145 CGTCAGACGAGCTTCTTATCTTTG 59.736 45.833 18.63 0.00 46.05 2.77
1117 4523 4.082679 ACGTCAGACGAGCTTCTTATCTTT 60.083 41.667 29.53 0.00 46.05 2.52
1118 4524 3.440872 ACGTCAGACGAGCTTCTTATCTT 59.559 43.478 29.53 0.00 46.05 2.40
1119 4525 3.011119 ACGTCAGACGAGCTTCTTATCT 58.989 45.455 29.53 0.00 46.05 1.98
1120 4526 3.064271 AGACGTCAGACGAGCTTCTTATC 59.936 47.826 29.53 12.55 46.05 1.75
1121 4527 3.011119 AGACGTCAGACGAGCTTCTTAT 58.989 45.455 29.53 3.07 46.05 1.73
1122 4528 2.424557 AGACGTCAGACGAGCTTCTTA 58.575 47.619 29.53 0.00 46.05 2.10
1123 4529 1.240256 AGACGTCAGACGAGCTTCTT 58.760 50.000 29.53 4.69 46.05 2.52
1124 4530 1.198178 GAAGACGTCAGACGAGCTTCT 59.802 52.381 32.31 22.91 46.05 2.85
1125 4531 1.198178 AGAAGACGTCAGACGAGCTTC 59.802 52.381 32.43 32.43 46.05 3.86
1126 4532 1.198178 GAGAAGACGTCAGACGAGCTT 59.802 52.381 29.53 26.89 46.05 3.74
1127 4533 0.800012 GAGAAGACGTCAGACGAGCT 59.200 55.000 29.53 20.96 46.05 4.09
1128 4534 0.179184 GGAGAAGACGTCAGACGAGC 60.179 60.000 29.53 19.14 46.05 5.03
1129 4535 1.157585 TGGAGAAGACGTCAGACGAG 58.842 55.000 29.53 1.57 46.05 4.18
1130 4536 1.601166 TTGGAGAAGACGTCAGACGA 58.399 50.000 29.53 0.88 46.05 4.20
1131 4537 3.366476 ATCTTTGGAGAAGACGTCAGACG 60.366 47.826 21.62 21.62 40.69 4.18
1132 4538 3.644884 TCTTTGGAGAAGACGTCAGAC 57.355 47.619 19.50 8.36 0.00 3.51
1133 4539 5.710567 TCTTATCTTTGGAGAAGACGTCAGA 59.289 40.000 19.50 9.34 42.57 3.27
1134 4540 5.955488 TCTTATCTTTGGAGAAGACGTCAG 58.045 41.667 19.50 3.51 42.57 3.51
1135 4541 5.977489 TCTTATCTTTGGAGAAGACGTCA 57.023 39.130 19.50 0.00 42.57 4.35
1136 4542 5.289917 GCTTCTTATCTTTGGAGAAGACGTC 59.710 44.000 7.70 7.70 45.67 4.34
1183 4589 2.512286 ACGCTCATGGACCGCATG 60.512 61.111 0.00 0.00 0.00 4.06
1375 4785 4.780815 TCTCAACCGCAATAAGAATCCAT 58.219 39.130 0.00 0.00 0.00 3.41
1389 4940 8.615211 TCAAATATGATTCTCAAATCTCAACCG 58.385 33.333 0.41 0.00 41.63 4.44
1424 4975 4.362677 TCCCACCTAGCTAATCTCACTTT 58.637 43.478 0.00 0.00 0.00 2.66
1426 4977 3.689872 TCCCACCTAGCTAATCTCACT 57.310 47.619 0.00 0.00 0.00 3.41
1429 4980 4.156477 ACAGATCCCACCTAGCTAATCTC 58.844 47.826 0.00 0.00 0.00 2.75
1434 4985 4.106502 ACAGATACAGATCCCACCTAGCTA 59.893 45.833 0.00 0.00 31.81 3.32
1435 4986 3.116939 ACAGATACAGATCCCACCTAGCT 60.117 47.826 0.00 0.00 31.81 3.32
1436 4987 3.235200 ACAGATACAGATCCCACCTAGC 58.765 50.000 0.00 0.00 31.81 3.42
1437 4988 5.882040 TCTACAGATACAGATCCCACCTAG 58.118 45.833 0.00 0.00 31.81 3.02
1528 5080 3.541632 AGAGCAGACTCCGTTTCAAAAA 58.458 40.909 0.00 0.00 44.65 1.94
1529 5081 3.131396 GAGAGCAGACTCCGTTTCAAAA 58.869 45.455 0.00 0.00 44.65 2.44
1530 5082 2.102420 TGAGAGCAGACTCCGTTTCAAA 59.898 45.455 0.00 0.00 44.65 2.69
1531 5083 1.686587 TGAGAGCAGACTCCGTTTCAA 59.313 47.619 0.00 0.00 44.65 2.69
1532 5084 1.270826 CTGAGAGCAGACTCCGTTTCA 59.729 52.381 0.00 0.00 45.17 2.69
1533 5085 1.271102 ACTGAGAGCAGACTCCGTTTC 59.729 52.381 0.00 0.00 45.17 2.78
1534 5086 1.333177 ACTGAGAGCAGACTCCGTTT 58.667 50.000 0.00 0.00 45.17 3.60
1535 5087 1.000283 CAACTGAGAGCAGACTCCGTT 60.000 52.381 0.00 0.00 45.17 4.44
1536 5088 0.600557 CAACTGAGAGCAGACTCCGT 59.399 55.000 0.00 0.00 45.17 4.69
1537 5089 0.600557 ACAACTGAGAGCAGACTCCG 59.399 55.000 0.00 0.00 45.17 4.63
1538 5090 1.615883 TCACAACTGAGAGCAGACTCC 59.384 52.381 0.00 0.00 45.17 3.85
1539 5091 3.591196 ATCACAACTGAGAGCAGACTC 57.409 47.619 0.00 0.00 45.17 3.36
1540 5092 5.417811 CATAATCACAACTGAGAGCAGACT 58.582 41.667 0.00 0.00 45.17 3.24
1541 5093 4.569966 CCATAATCACAACTGAGAGCAGAC 59.430 45.833 0.00 0.00 45.17 3.51
1542 5094 4.223700 ACCATAATCACAACTGAGAGCAGA 59.776 41.667 0.00 0.00 45.17 4.26
1544 5096 4.558226 ACCATAATCACAACTGAGAGCA 57.442 40.909 0.00 0.00 0.00 4.26
1545 5097 5.665459 AGTACCATAATCACAACTGAGAGC 58.335 41.667 0.00 0.00 0.00 4.09
1546 5098 7.323420 TCAAGTACCATAATCACAACTGAGAG 58.677 38.462 0.00 0.00 0.00 3.20
1547 5099 7.039011 ACTCAAGTACCATAATCACAACTGAGA 60.039 37.037 0.00 0.00 0.00 3.27
1548 5100 7.099764 ACTCAAGTACCATAATCACAACTGAG 58.900 38.462 0.00 0.00 0.00 3.35
1549 5101 7.004555 ACTCAAGTACCATAATCACAACTGA 57.995 36.000 0.00 0.00 0.00 3.41
1550 5102 7.672983 AACTCAAGTACCATAATCACAACTG 57.327 36.000 0.00 0.00 0.00 3.16
1551 5103 8.691661 AAAACTCAAGTACCATAATCACAACT 57.308 30.769 0.00 0.00 0.00 3.16
1552 5104 9.180678 CAAAAACTCAAGTACCATAATCACAAC 57.819 33.333 0.00 0.00 0.00 3.32
1553 5105 8.908903 ACAAAAACTCAAGTACCATAATCACAA 58.091 29.630 0.00 0.00 0.00 3.33
1554 5106 8.458573 ACAAAAACTCAAGTACCATAATCACA 57.541 30.769 0.00 0.00 0.00 3.58
1555 5107 9.744468 AAACAAAAACTCAAGTACCATAATCAC 57.256 29.630 0.00 0.00 0.00 3.06
1556 5108 9.959749 GAAACAAAAACTCAAGTACCATAATCA 57.040 29.630 0.00 0.00 0.00 2.57
1557 5109 9.959749 TGAAACAAAAACTCAAGTACCATAATC 57.040 29.630 0.00 0.00 0.00 1.75
1561 5113 9.097257 CAAATGAAACAAAAACTCAAGTACCAT 57.903 29.630 0.00 0.00 0.00 3.55
1562 5114 8.091449 ACAAATGAAACAAAAACTCAAGTACCA 58.909 29.630 0.00 0.00 0.00 3.25
1563 5115 8.474006 ACAAATGAAACAAAAACTCAAGTACC 57.526 30.769 0.00 0.00 0.00 3.34
1591 5143 8.631797 GGTGTGTTAACCAGGAATTAAAGTTTA 58.368 33.333 2.48 0.00 40.22 2.01
1592 5144 7.124448 TGGTGTGTTAACCAGGAATTAAAGTTT 59.876 33.333 2.48 0.00 45.43 2.66
1593 5145 6.608002 TGGTGTGTTAACCAGGAATTAAAGTT 59.392 34.615 2.48 0.00 45.43 2.66
1594 5146 6.130569 TGGTGTGTTAACCAGGAATTAAAGT 58.869 36.000 2.48 0.00 45.43 2.66
1595 5147 6.642707 TGGTGTGTTAACCAGGAATTAAAG 57.357 37.500 2.48 0.00 45.43 1.85
1606 5158 5.358442 TGTATTGGCATATGGTGTGTTAACC 59.642 40.000 4.56 0.00 40.94 2.85
1607 5159 6.443934 TGTATTGGCATATGGTGTGTTAAC 57.556 37.500 4.56 0.00 0.00 2.01
1608 5160 6.434340 TGTTGTATTGGCATATGGTGTGTTAA 59.566 34.615 4.56 0.00 0.00 2.01
1609 5161 5.946377 TGTTGTATTGGCATATGGTGTGTTA 59.054 36.000 4.56 0.00 0.00 2.41
1610 5162 4.769488 TGTTGTATTGGCATATGGTGTGTT 59.231 37.500 4.56 0.00 0.00 3.32
1611 5163 4.157656 GTGTTGTATTGGCATATGGTGTGT 59.842 41.667 4.56 0.00 0.00 3.72
1612 5164 4.398988 AGTGTTGTATTGGCATATGGTGTG 59.601 41.667 4.56 0.00 0.00 3.82
1613 5165 4.398988 CAGTGTTGTATTGGCATATGGTGT 59.601 41.667 4.56 0.00 0.00 4.16
1614 5166 4.639755 TCAGTGTTGTATTGGCATATGGTG 59.360 41.667 4.56 0.00 0.00 4.17
1615 5167 4.854173 TCAGTGTTGTATTGGCATATGGT 58.146 39.130 4.56 0.00 0.00 3.55
1616 5168 5.125356 TCTCAGTGTTGTATTGGCATATGG 58.875 41.667 4.56 0.00 0.00 2.74
1617 5169 5.277683 GCTCTCAGTGTTGTATTGGCATATG 60.278 44.000 0.00 0.00 0.00 1.78
1618 5170 4.818546 GCTCTCAGTGTTGTATTGGCATAT 59.181 41.667 0.00 0.00 0.00 1.78
1619 5171 4.191544 GCTCTCAGTGTTGTATTGGCATA 58.808 43.478 0.00 0.00 0.00 3.14
1620 5172 3.012518 GCTCTCAGTGTTGTATTGGCAT 58.987 45.455 0.00 0.00 0.00 4.40
1621 5173 2.224499 TGCTCTCAGTGTTGTATTGGCA 60.224 45.455 0.00 0.00 0.00 4.92
1622 5174 2.426522 TGCTCTCAGTGTTGTATTGGC 58.573 47.619 0.00 0.00 0.00 4.52
1623 5175 4.511527 AGATGCTCTCAGTGTTGTATTGG 58.488 43.478 0.00 0.00 0.00 3.16
1624 5176 4.569966 GGAGATGCTCTCAGTGTTGTATTG 59.430 45.833 13.06 0.00 45.12 1.90
1625 5177 4.223700 TGGAGATGCTCTCAGTGTTGTATT 59.776 41.667 13.06 0.00 45.12 1.89
1626 5178 3.771479 TGGAGATGCTCTCAGTGTTGTAT 59.229 43.478 13.06 0.00 45.12 2.29
1627 5179 3.165071 TGGAGATGCTCTCAGTGTTGTA 58.835 45.455 13.06 0.00 45.12 2.41
1628 5180 1.973515 TGGAGATGCTCTCAGTGTTGT 59.026 47.619 13.06 0.00 45.12 3.32
1629 5181 2.619147 CTGGAGATGCTCTCAGTGTTG 58.381 52.381 13.06 0.00 45.12 3.33
1630 5182 1.066286 GCTGGAGATGCTCTCAGTGTT 60.066 52.381 13.06 0.00 45.12 3.32
1631 5183 0.536260 GCTGGAGATGCTCTCAGTGT 59.464 55.000 13.06 0.00 45.12 3.55
1632 5184 0.179078 GGCTGGAGATGCTCTCAGTG 60.179 60.000 13.06 0.00 45.12 3.66
1662 5214 0.393077 GCGCTATTTCTAGCCCCTGA 59.607 55.000 0.00 0.00 46.41 3.86
1769 5340 0.670239 GAAAGTGGGCCAATTTGCGG 60.670 55.000 33.85 0.00 31.79 5.69
1976 5626 3.570926 ATCAACAACTGCAGCAAGATG 57.429 42.857 15.27 8.96 0.00 2.90
2018 5668 5.481824 ACTGTCTTCCTCAATATGTGTCAGA 59.518 40.000 0.00 0.00 0.00 3.27
2024 5674 4.163078 CCTGGACTGTCTTCCTCAATATGT 59.837 45.833 7.85 0.00 36.51 2.29
2038 5688 1.827399 CTACCGGCAACCTGGACTGT 61.827 60.000 0.00 0.00 0.00 3.55
2117 5767 1.252175 TGAGAGCGAGCAGAAAGAGT 58.748 50.000 0.00 0.00 0.00 3.24
2194 5844 2.741878 TACCCCGCTCAGACCTGGTT 62.742 60.000 0.00 0.00 0.00 3.67
2238 5888 1.117142 AGCAGGCATTTGGTGTGCTT 61.117 50.000 0.00 0.00 41.72 3.91
2261 5911 0.839946 GGAGGCTTGCAGGAAGGATA 59.160 55.000 0.00 0.00 31.56 2.59


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

AutoCloner maintained by Alex Coulton.