Multiple sequence alignment - TraesCS1D01G211000

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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 TraesCS1D01G211000 chr1D 100.000 9753 0 0 1 9753 296989204 296979452 0.000000e+00 18011.0
1 TraesCS1D01G211000 chr1D 85.321 436 34 5 1589 1996 453046896 453047329 3.260000e-114 424.0
2 TraesCS1D01G211000 chr1D 83.451 284 25 12 9453 9734 46477006 46477269 2.720000e-60 244.0
3 TraesCS1D01G211000 chr1D 93.506 77 4 1 1995 2070 453047306 453047382 8.010000e-21 113.0
4 TraesCS1D01G211000 chr1B 96.017 3440 77 23 2310 5715 398152973 398149560 0.000000e+00 5539.0
5 TraesCS1D01G211000 chr1B 96.399 1833 49 9 6350 8171 398148693 398146867 0.000000e+00 3003.0
6 TraesCS1D01G211000 chr1B 90.286 1606 90 34 8169 9753 398146509 398144949 0.000000e+00 2041.0
7 TraesCS1D01G211000 chr1B 97.048 1118 26 4 1196 2313 398154138 398153028 0.000000e+00 1875.0
8 TraesCS1D01G211000 chr1B 95.789 380 15 1 5700 6079 398149505 398149127 6.470000e-171 612.0
9 TraesCS1D01G211000 chr1B 92.507 347 13 3 876 1209 398154509 398154163 1.470000e-132 484.0
10 TraesCS1D01G211000 chr1B 95.324 278 10 1 6075 6352 398149048 398148774 1.160000e-118 438.0
11 TraesCS1D01G211000 chr1B 83.297 461 65 9 4572 5028 530998252 530998704 1.960000e-111 414.0
12 TraesCS1D01G211000 chr1B 85.714 203 14 6 669 870 398154739 398154551 5.970000e-47 200.0
13 TraesCS1D01G211000 chr1A 94.201 3018 129 11 2740 5715 369509762 369506749 0.000000e+00 4562.0
14 TraesCS1D01G211000 chr1A 97.374 2475 48 8 5700 8171 369506694 369504234 0.000000e+00 4194.0
15 TraesCS1D01G211000 chr1A 87.881 1246 79 36 1 1209 369514594 369513384 0.000000e+00 1399.0
16 TraesCS1D01G211000 chr1A 90.798 978 55 17 8170 9128 369503803 369502842 0.000000e+00 1275.0
17 TraesCS1D01G211000 chr1A 87.769 605 22 13 1735 2313 369512481 369511903 0.000000e+00 660.0
18 TraesCS1D01G211000 chr1A 91.423 478 36 5 1196 1672 369513359 369512886 0.000000e+00 651.0
19 TraesCS1D01G211000 chr1A 93.355 301 19 1 2406 2705 369511516 369511216 2.500000e-120 444.0
20 TraesCS1D01G211000 chr1A 96.129 155 6 0 9599 9753 369497645 369497491 4.520000e-63 254.0
21 TraesCS1D01G211000 chr1A 94.845 97 4 1 2313 2408 369511845 369511749 6.100000e-32 150.0
22 TraesCS1D01G211000 chr1A 94.667 75 4 0 1664 1738 369512861 369512787 6.190000e-22 117.0
23 TraesCS1D01G211000 chrUn 85.253 434 36 5 1589 1996 90483022 90482591 1.170000e-113 422.0
24 TraesCS1D01G211000 chrUn 84.028 432 34 5 1589 1996 90402460 90402040 5.530000e-102 383.0
25 TraesCS1D01G211000 chrUn 93.590 78 4 1 1995 2071 90402063 90401986 2.230000e-21 115.0
26 TraesCS1D01G211000 chrUn 95.161 62 2 1 2011 2071 90482598 90482537 8.060000e-16 97.1
27 TraesCS1D01G211000 chr5A 84.043 282 27 7 9453 9734 299616892 299616629 1.260000e-63 255.0
28 TraesCS1D01G211000 chr4D 83.039 283 28 12 9453 9734 462822409 462822146 1.270000e-58 239.0
29 TraesCS1D01G211000 chr4D 84.615 234 29 7 4534 4763 312979396 312979626 9.860000e-55 226.0
30 TraesCS1D01G211000 chr3D 83.099 284 26 12 9453 9734 12137748 12137485 1.270000e-58 239.0
31 TraesCS1D01G211000 chr7A 82.671 277 28 9 9459 9734 46898306 46898049 2.740000e-55 228.0
32 TraesCS1D01G211000 chr2D 82.394 284 28 10 9453 9734 36499291 36499554 2.740000e-55 228.0
33 TraesCS1D01G211000 chr7D 81.272 283 33 9 9453 9734 32509881 32509618 2.760000e-50 211.0


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 TraesCS1D01G211000 chr1D 296979452 296989204 9752 True 18011.000000 18011 100.000000 1 9753 1 chr1D.!!$R1 9752
1 TraesCS1D01G211000 chr1B 398144949 398154739 9790 True 1774.000000 5539 93.635500 669 9753 8 chr1B.!!$R1 9084
2 TraesCS1D01G211000 chr1A 369502842 369514594 11752 True 1494.666667 4562 92.479222 1 9128 9 chr1A.!!$R2 9127

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
772 812 2.040606 TTTCCCTCCTCCCCTCCG 59.959 66.667 0.00 0.00 0.00 4.63 F
773 813 2.531483 CTTTCCCTCCTCCCCTCCGA 62.531 65.000 0.00 0.00 0.00 4.55 F
1271 1403 2.970974 GCGGCCTGTTTCTGTCTGC 61.971 63.158 0.00 0.00 0.00 4.26 F
1868 2341 4.437682 AGGTCTTGGTTCAATGAGTCAA 57.562 40.909 0.00 1.70 0.00 3.18 F
3712 5935 2.744741 TGTGCTGTTTTCACTTTCGACA 59.255 40.909 0.00 0.00 35.58 4.35 F
3827 6050 0.811281 CCCGGGTCTTTGCTTTGATC 59.189 55.000 14.18 0.00 0.00 2.92 F
5050 7281 1.194098 GCTCGAAGCATTGATCCATCG 59.806 52.381 2.53 0.00 41.89 3.84 F
5217 7448 1.328279 AAAGGGCTGGTGCAGTAAAC 58.672 50.000 0.00 0.00 41.91 2.01 F
5383 7642 1.401539 GGAACAATTGCAGCTCGTTCC 60.402 52.381 17.96 17.96 46.27 3.62 F
5475 7735 2.057137 TATTGGCCACTTCATGCTCC 57.943 50.000 3.88 0.00 0.00 4.70 F
6456 8951 2.286872 CGGCATGATGAAGCTCTTTCT 58.713 47.619 0.00 0.00 36.71 2.52 F
7761 10259 0.400594 ACTGAGGTTGGCTGGGTAAC 59.599 55.000 0.00 0.00 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 2341 0.608640 GTGATCCCTGGTCGAACAGT 59.391 55.000 27.88 10.87 36.75 3.55 R
2320 2877 1.538512 CACAGAACATTCACCAGCAGG 59.461 52.381 0.00 0.00 42.21 4.85 R
2363 2920 3.510388 AGTACACCAGATCATGTCACG 57.490 47.619 0.00 0.00 0.00 4.35 R
3810 6033 1.438651 TCGATCAAAGCAAAGACCCG 58.561 50.000 0.00 0.00 0.00 5.28 R
5106 7337 0.831307 AGCGAAAGATGTAGGGGGTC 59.169 55.000 0.00 0.00 0.00 4.46 R
5721 8050 1.352352 ACAGCCTGTCTTACAGCCATT 59.648 47.619 0.00 0.00 44.63 3.16 R
6883 9381 1.609841 GGTAAGACAAACCACCCTCGG 60.610 57.143 0.00 0.00 36.96 4.63 R
6990 9488 4.536364 ACGAAAGGCAACATTATGATCG 57.464 40.909 0.00 0.00 41.41 3.69 R
7309 9807 1.134431 AGTTTGCCAACCAAAGCCAAG 60.134 47.619 0.00 0.00 43.67 3.61 R
7414 9912 3.429207 GGTACTTCTCTTCACGTGCTTTC 59.571 47.826 11.67 0.00 0.00 2.62 R
7788 10286 1.204704 CATCAGAGCCACGGTTCACTA 59.795 52.381 2.60 0.00 0.00 2.74 R
9063 12111 0.106819 GTTGAGCTGGGATGCTGGAT 60.107 55.000 0.00 0.00 44.17 3.41 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 7.114866 TGTGCCATCAATTGAACATGAATAT 57.885 32.000 13.09 0.00 0.00 1.28
31 32 8.136800 TGTGCCATCAATTGAACATGAATATAC 58.863 33.333 13.09 2.41 0.00 1.47
33 34 7.287235 TGCCATCAATTGAACATGAATATACCA 59.713 33.333 13.09 0.00 0.00 3.25
56 57 2.945447 TGGCTTAGTTCATTGCATGC 57.055 45.000 11.82 11.82 0.00 4.06
63 64 2.366533 AGTTCATTGCATGCTCTCTGG 58.633 47.619 20.33 2.78 0.00 3.86
160 162 5.308237 AGGAACTCTGACAATTGGTAGAACT 59.692 40.000 10.83 6.13 0.00 3.01
161 163 6.497259 AGGAACTCTGACAATTGGTAGAACTA 59.503 38.462 10.83 0.00 0.00 2.24
195 197 9.838339 ATTTTAGATGGTAGCACTATATATGGC 57.162 33.333 0.00 0.00 0.00 4.40
245 247 4.733077 TTACTGGTTTTGATGGAAGGGA 57.267 40.909 0.00 0.00 0.00 4.20
252 254 4.459337 GGTTTTGATGGAAGGGAACTACTG 59.541 45.833 0.00 0.00 42.68 2.74
284 286 9.942850 AATTAAGAAAATGAAATGGTTTCGGAT 57.057 25.926 0.00 0.00 42.55 4.18
341 343 5.335269 GCAAGGCCTACTCTTTTCTTCTTTC 60.335 44.000 5.16 0.00 0.00 2.62
343 345 6.194285 AGGCCTACTCTTTTCTTCTTTCTT 57.806 37.500 1.29 0.00 0.00 2.52
373 379 5.505181 TTTGCTTCCTCCTGAAAGATACT 57.495 39.130 0.00 0.00 34.07 2.12
386 392 7.390718 TCCTGAAAGATACTTAAGAACTTTGGC 59.609 37.037 20.90 13.14 34.07 4.52
389 395 7.227910 TGAAAGATACTTAAGAACTTTGGCGTT 59.772 33.333 20.90 6.04 32.20 4.84
392 398 8.788325 AGATACTTAAGAACTTTGGCGTTTAT 57.212 30.769 10.09 0.00 0.00 1.40
393 399 8.880750 AGATACTTAAGAACTTTGGCGTTTATC 58.119 33.333 10.09 1.60 0.00 1.75
394 400 5.923665 ACTTAAGAACTTTGGCGTTTATCG 58.076 37.500 10.09 0.00 43.12 2.92
395 401 5.467735 ACTTAAGAACTTTGGCGTTTATCGT 59.532 36.000 10.09 0.00 42.13 3.73
401 407 4.284485 ACTTTGGCGTTTATCGTGTTTTC 58.716 39.130 0.00 0.00 42.13 2.29
420 426 6.127083 TGTTTTCATTTGCTCTTCTTTCCCTT 60.127 34.615 0.00 0.00 0.00 3.95
458 464 7.995289 TGACTTGTTGGGTTAGCATATATTTG 58.005 34.615 0.00 0.00 0.00 2.32
478 484 9.751542 ATATTTGTCTCGATACTTAACTCTTGG 57.248 33.333 2.42 0.00 0.00 3.61
493 499 3.237746 CTCTTGGATGGGCTAGAGATGA 58.762 50.000 0.00 0.00 37.00 2.92
519 525 5.959618 AAGTTGTTACATCAGCCCTAAAC 57.040 39.130 0.00 0.00 0.00 2.01
531 537 5.451354 TCAGCCCTAAACAAAAGTTAAGGT 58.549 37.500 0.00 0.00 0.00 3.50
542 548 7.119709 ACAAAAGTTAAGGTTGGCAAAGTAT 57.880 32.000 0.00 0.00 0.00 2.12
557 563 6.062095 GGCAAAGTATAGCTCCCTCAAATAA 58.938 40.000 0.00 0.00 0.00 1.40
558 564 6.717084 GGCAAAGTATAGCTCCCTCAAATAAT 59.283 38.462 0.00 0.00 0.00 1.28
559 565 7.231519 GGCAAAGTATAGCTCCCTCAAATAATT 59.768 37.037 0.00 0.00 0.00 1.40
560 566 9.284968 GCAAAGTATAGCTCCCTCAAATAATTA 57.715 33.333 0.00 0.00 0.00 1.40
564 570 9.608718 AGTATAGCTCCCTCAAATAATTACTCT 57.391 33.333 0.00 0.00 0.00 3.24
602 608 4.993705 TTTCAGGGTTACATCACTTCCT 57.006 40.909 0.00 0.00 0.00 3.36
603 609 4.993705 TTCAGGGTTACATCACTTCCTT 57.006 40.909 0.00 0.00 0.00 3.36
604 610 4.993705 TCAGGGTTACATCACTTCCTTT 57.006 40.909 0.00 0.00 0.00 3.11
605 611 5.319043 TCAGGGTTACATCACTTCCTTTT 57.681 39.130 0.00 0.00 0.00 2.27
606 612 5.701224 TCAGGGTTACATCACTTCCTTTTT 58.299 37.500 0.00 0.00 0.00 1.94
627 633 4.664150 TTTTGGGAAACACATCACTTCC 57.336 40.909 0.00 0.00 38.33 3.46
628 634 3.593442 TTGGGAAACACATCACTTCCT 57.407 42.857 0.00 0.00 38.94 3.36
629 635 3.593442 TGGGAAACACATCACTTCCTT 57.407 42.857 0.00 0.00 38.94 3.36
683 723 4.040829 TGAAGAACTCTGTCCACACATCAT 59.959 41.667 0.00 0.00 0.00 2.45
691 731 4.124970 CTGTCCACACATCATATGTCCAG 58.875 47.826 1.90 0.00 42.70 3.86
763 803 3.487372 ACAGTGCTTTTACTTTCCCTCC 58.513 45.455 0.00 0.00 0.00 4.30
772 812 2.040606 TTTCCCTCCTCCCCTCCG 59.959 66.667 0.00 0.00 0.00 4.63
773 813 2.531483 CTTTCCCTCCTCCCCTCCGA 62.531 65.000 0.00 0.00 0.00 4.55
830 872 4.760047 CACCACCGCCCCGAAGAG 62.760 72.222 0.00 0.00 0.00 2.85
942 1021 4.874977 GCTCGGCGGAGTACCAGC 62.875 72.222 20.92 2.32 42.53 4.85
1245 1377 3.276846 GTTTGCTCGCGGTGGTGT 61.277 61.111 6.13 0.00 0.00 4.16
1271 1403 2.970974 GCGGCCTGTTTCTGTCTGC 61.971 63.158 0.00 0.00 0.00 4.26
1368 1500 4.704833 GAGGCTGCCGGCAAGTCA 62.705 66.667 32.09 6.96 44.01 3.41
1445 1577 5.626955 GTGACAGCTGCTTTTACTCATTTTC 59.373 40.000 15.27 0.00 0.00 2.29
1561 1694 7.200434 TCCTAATTTTGAGTCTATGGAAGCT 57.800 36.000 0.00 0.00 0.00 3.74
1628 1761 6.495181 CCTGTAGAGATTAGATAGGGAAGCAA 59.505 42.308 0.00 0.00 0.00 3.91
1636 1769 9.706529 AGATTAGATAGGGAAGCAAGAATTTTT 57.293 29.630 0.00 0.00 0.00 1.94
1868 2341 4.437682 AGGTCTTGGTTCAATGAGTCAA 57.562 40.909 0.00 1.70 0.00 3.18
2081 2578 5.521735 GCTGAATAGGTGATGTACAACTCTG 59.478 44.000 0.00 0.00 43.93 3.35
2097 2594 6.035843 ACAACTCTGCAAGTAATGTTTGTTG 58.964 36.000 0.00 0.00 37.17 3.33
2318 2875 5.408604 CCGATATAATCCAAACAGTAGTGCC 59.591 44.000 0.00 0.00 0.00 5.01
2320 2877 6.366332 CGATATAATCCAAACAGTAGTGCCTC 59.634 42.308 0.00 0.00 0.00 4.70
2363 2920 7.604927 TGTGTAACTACCATCCTGAAATACAAC 59.395 37.037 0.00 0.00 38.04 3.32
2936 5157 3.384789 GGCTTGTCCTTTTCACCTTTTCT 59.615 43.478 0.00 0.00 0.00 2.52
2939 5160 6.406512 GGCTTGTCCTTTTCACCTTTTCTAAA 60.407 38.462 0.00 0.00 0.00 1.85
2940 5161 7.039270 GCTTGTCCTTTTCACCTTTTCTAAAA 58.961 34.615 0.00 0.00 0.00 1.52
3244 5467 7.149307 GTCTATCCTTCAATGACTAGGCTTAC 58.851 42.308 0.00 0.00 0.00 2.34
3304 5527 4.801330 TCTTGAATCAAGGAGCTACGAA 57.199 40.909 21.35 0.00 41.33 3.85
3396 5619 8.389779 TGTGATTATCTTTTCTGTAAACTGCA 57.610 30.769 0.00 0.00 0.00 4.41
3554 5777 9.016623 GGTGCGTGTTTTATTTCCTTATATTTC 57.983 33.333 0.00 0.00 0.00 2.17
3555 5778 9.016623 GTGCGTGTTTTATTTCCTTATATTTCC 57.983 33.333 0.00 0.00 0.00 3.13
3590 5813 3.061322 TGAAACCCAAGTCATACGTTCG 58.939 45.455 0.00 0.00 0.00 3.95
3711 5934 3.098636 GTGTGCTGTTTTCACTTTCGAC 58.901 45.455 0.00 0.00 35.58 4.20
3712 5935 2.744741 TGTGCTGTTTTCACTTTCGACA 59.255 40.909 0.00 0.00 35.58 4.35
3827 6050 0.811281 CCCGGGTCTTTGCTTTGATC 59.189 55.000 14.18 0.00 0.00 2.92
3918 6141 5.250774 ACCTTCAGTTGTGTTGGATACCTAT 59.749 40.000 0.00 0.00 0.00 2.57
4639 6870 6.496565 CCATGGAGGAGAATAACTCTGTAGAT 59.503 42.308 5.56 0.00 44.37 1.98
4931 7162 1.993956 TGCAGTTATTGGTTGCCTGT 58.006 45.000 0.00 0.00 37.03 4.00
4935 7166 3.243704 GCAGTTATTGGTTGCCTGTTTGA 60.244 43.478 0.00 0.00 31.79 2.69
5050 7281 1.194098 GCTCGAAGCATTGATCCATCG 59.806 52.381 2.53 0.00 41.89 3.84
5106 7337 4.303086 ACGATCACCAATCTAGGTAACG 57.697 45.455 0.00 0.00 40.77 3.18
5122 7353 3.431346 GGTAACGACCCCCTACATCTTTC 60.431 52.174 0.00 0.00 40.23 2.62
5131 7362 3.600388 CCCTACATCTTTCGCTGAAAGT 58.400 45.455 21.84 12.13 46.22 2.66
5150 7381 6.012333 TGAAAGTCAAAAAGGCCCCTATACTA 60.012 38.462 0.00 0.00 0.00 1.82
5160 7391 2.297597 GCCCCTATACTACTGCACTCAG 59.702 54.545 0.00 0.00 45.71 3.35
5217 7448 1.328279 AAAGGGCTGGTGCAGTAAAC 58.672 50.000 0.00 0.00 41.91 2.01
5232 7463 6.145696 GTGCAGTAAACGAGTCTTATGAAAGT 59.854 38.462 0.00 0.00 34.13 2.66
5263 7494 4.219115 AGCTGTGCAGATACTACCTGTAT 58.781 43.478 3.02 0.00 43.94 2.29
5383 7642 1.401539 GGAACAATTGCAGCTCGTTCC 60.402 52.381 17.96 17.96 46.27 3.62
5475 7735 2.057137 TATTGGCCACTTCATGCTCC 57.943 50.000 3.88 0.00 0.00 4.70
5579 7839 3.383620 TGAATTGTTGGCATTGTCACC 57.616 42.857 0.00 0.00 0.00 4.02
5591 7851 3.610114 GCATTGTCACCAAGTTAGTGCTG 60.610 47.826 0.00 0.00 35.14 4.41
5636 7896 9.720769 ACATGTTTATACCTATGCCTACATAAC 57.279 33.333 0.00 0.00 38.29 1.89
5719 8048 6.027749 GCAATGCTTTATGTTGTGTAGGTAC 58.972 40.000 0.00 0.00 0.00 3.34
5721 8050 7.065324 GCAATGCTTTATGTTGTGTAGGTACTA 59.935 37.037 0.00 0.00 41.75 1.82
6132 8544 3.979501 ATTCCCCATAAGCACTTCCAT 57.020 42.857 0.00 0.00 0.00 3.41
6456 8951 2.286872 CGGCATGATGAAGCTCTTTCT 58.713 47.619 0.00 0.00 36.71 2.52
6504 8999 7.610865 ACTTATCTAATATGAAGCAGGAGAGC 58.389 38.462 0.00 0.00 0.00 4.09
6883 9381 4.556233 GAATCAAACAACTGTTTAGGGGC 58.444 43.478 7.48 0.00 45.54 5.80
7006 9504 7.840931 TGACTATATCGATCATAATGTTGCCT 58.159 34.615 0.00 0.00 0.00 4.75
7234 9732 3.955650 TGTGAAGACCAGTACCTAAGC 57.044 47.619 0.00 0.00 0.00 3.09
7414 9912 3.248266 GCTTGTGCTTGCTATTTTCCAG 58.752 45.455 0.00 0.00 36.03 3.86
7594 10092 4.811024 TCTGATGACTATGAAAACGGCATC 59.189 41.667 0.00 0.00 33.24 3.91
7761 10259 0.400594 ACTGAGGTTGGCTGGGTAAC 59.599 55.000 0.00 0.00 0.00 2.50
7853 10351 3.700538 TGCATTGAAAGGAATGGTAGCT 58.299 40.909 0.00 0.00 34.42 3.32
7854 10352 4.088634 TGCATTGAAAGGAATGGTAGCTT 58.911 39.130 0.00 0.00 34.42 3.74
7879 10377 3.665745 TCAAAATGGGCTGCTCTTTTC 57.334 42.857 13.01 0.00 0.00 2.29
8014 10512 4.116747 TGGTAAGCCAGTTTGTTGTTTG 57.883 40.909 0.00 0.00 40.46 2.93
8030 10531 5.235186 TGTTGTTTGTTCTGTTTGTTGGTTG 59.765 36.000 0.00 0.00 0.00 3.77
8062 10563 5.930837 AATTGTCAGTTTTCCCTGAAACA 57.069 34.783 3.68 0.00 42.81 2.83
8122 10623 5.655488 ACTCGATTGTTCTGTTATCTCCAG 58.345 41.667 0.00 0.00 0.00 3.86
8126 10627 6.602009 TCGATTGTTCTGTTATCTCCAGTAGA 59.398 38.462 0.00 0.00 39.02 2.59
8154 10662 2.890808 TCACAGTATCCCGCAATCTC 57.109 50.000 0.00 0.00 0.00 2.75
8286 11314 0.473755 TGCATATGGAGATTGCCCGT 59.526 50.000 4.56 0.00 35.51 5.28
8547 11576 9.143631 CATTTTATCTGATTGTTTCCTGGTTTC 57.856 33.333 0.00 0.00 0.00 2.78
8593 11622 3.338249 TGAGCTCTACTTCCAAATGCAC 58.662 45.455 16.19 0.00 0.00 4.57
8707 11748 0.815734 CGATACACCAGAACCCGTCT 59.184 55.000 0.00 0.00 36.88 4.18
8714 11755 1.371183 CAGAACCCGTCTTGCTCCA 59.629 57.895 0.00 0.00 32.70 3.86
8783 11830 2.741092 GCCGGAAGTCAGTCACCA 59.259 61.111 5.05 0.00 0.00 4.17
8809 11856 2.547640 TAGCTGAGACGGGCGTACCT 62.548 60.000 0.00 0.00 36.97 3.08
8817 11864 1.216977 CGGGCGTACCTGAATCACA 59.783 57.895 0.00 0.00 46.41 3.58
8829 11877 6.156748 ACCTGAATCACATGTAGCGTATTA 57.843 37.500 0.00 0.00 0.00 0.98
8988 12036 5.829924 ACATGATGATGGTCCTTTTGGATAC 59.170 40.000 0.00 0.00 40.91 2.24
9033 12081 1.664016 GCGTCAGTGCAACATTTGAGG 60.664 52.381 0.00 0.00 41.43 3.86
9049 12097 3.593442 TGAGGAAGGAAAAAGGAAGCA 57.407 42.857 0.00 0.00 0.00 3.91
9054 12102 4.082125 GGAAGGAAAAAGGAAGCATCAGA 58.918 43.478 0.00 0.00 0.00 3.27
9055 12103 4.524328 GGAAGGAAAAAGGAAGCATCAGAA 59.476 41.667 0.00 0.00 0.00 3.02
9057 12105 5.911378 AGGAAAAAGGAAGCATCAGAATC 57.089 39.130 0.00 0.00 0.00 2.52
9059 12107 4.439289 GGAAAAAGGAAGCATCAGAATCCG 60.439 45.833 0.00 0.00 37.05 4.18
9060 12108 1.673168 AAGGAAGCATCAGAATCCGC 58.327 50.000 0.00 0.00 37.05 5.54
9061 12109 0.835941 AGGAAGCATCAGAATCCGCT 59.164 50.000 0.00 0.00 37.05 5.52
9062 12110 1.211457 AGGAAGCATCAGAATCCGCTT 59.789 47.619 0.00 0.00 46.90 4.68
9063 12111 2.435805 AGGAAGCATCAGAATCCGCTTA 59.564 45.455 0.00 0.00 44.40 3.09
9064 12112 3.072184 AGGAAGCATCAGAATCCGCTTAT 59.928 43.478 0.00 0.00 44.40 1.73
9065 12113 3.434984 GGAAGCATCAGAATCCGCTTATC 59.565 47.826 0.00 0.00 44.40 1.75
9066 12114 3.051081 AGCATCAGAATCCGCTTATCC 57.949 47.619 0.00 0.00 0.00 2.59
9067 12115 2.369860 AGCATCAGAATCCGCTTATCCA 59.630 45.455 0.00 0.00 0.00 3.41
9068 12116 2.740981 GCATCAGAATCCGCTTATCCAG 59.259 50.000 0.00 0.00 0.00 3.86
9069 12117 2.533266 TCAGAATCCGCTTATCCAGC 57.467 50.000 0.00 0.00 46.31 4.85
9082 12130 0.106819 ATCCAGCATCCCAGCTCAAC 60.107 55.000 0.00 0.00 44.54 3.18
9102 12157 3.000727 ACCAGCCTAATTTCGTTCGAAG 58.999 45.455 0.00 0.00 0.00 3.79
9121 12176 0.179100 GCAAGCGCCATCTGTAGAGA 60.179 55.000 2.29 0.00 0.00 3.10
9122 12177 1.850377 CAAGCGCCATCTGTAGAGAG 58.150 55.000 2.29 0.00 0.00 3.20
9123 12178 0.103937 AAGCGCCATCTGTAGAGAGC 59.896 55.000 2.29 0.00 0.00 4.09
9126 12181 1.543802 GCGCCATCTGTAGAGAGCTAT 59.456 52.381 0.00 0.00 0.00 2.97
9127 12182 2.750166 GCGCCATCTGTAGAGAGCTATA 59.250 50.000 0.00 0.00 0.00 1.31
9128 12183 3.380004 GCGCCATCTGTAGAGAGCTATAT 59.620 47.826 0.00 0.00 0.00 0.86
9131 12186 6.428465 GCGCCATCTGTAGAGAGCTATATATA 59.572 42.308 0.00 0.00 0.00 0.86
9133 12188 8.664798 CGCCATCTGTAGAGAGCTATATATATC 58.335 40.741 0.00 0.00 0.00 1.63
9134 12189 9.513906 GCCATCTGTAGAGAGCTATATATATCA 57.486 37.037 0.00 0.00 0.00 2.15
9160 12215 5.023533 TCTCCTTTTGGGAATCATCTACG 57.976 43.478 0.00 0.00 44.58 3.51
9161 12216 4.469945 TCTCCTTTTGGGAATCATCTACGT 59.530 41.667 0.00 0.00 44.58 3.57
9162 12217 5.659525 TCTCCTTTTGGGAATCATCTACGTA 59.340 40.000 0.00 0.00 44.58 3.57
9163 12218 5.667466 TCCTTTTGGGAATCATCTACGTAC 58.333 41.667 0.00 0.00 41.91 3.67
9173 12228 7.222999 GGGAATCATCTACGTACTCTTCTTTTG 59.777 40.741 0.00 0.00 0.00 2.44
9178 12233 7.328737 TCATCTACGTACTCTTCTTTTGCTTTC 59.671 37.037 0.00 0.00 0.00 2.62
9179 12234 5.924825 TCTACGTACTCTTCTTTTGCTTTCC 59.075 40.000 0.00 0.00 0.00 3.13
9180 12235 3.493503 ACGTACTCTTCTTTTGCTTTCCG 59.506 43.478 0.00 0.00 0.00 4.30
9184 12239 5.363979 ACTCTTCTTTTGCTTTCCGAATC 57.636 39.130 0.00 0.00 0.00 2.52
9199 12254 5.321959 TCCGAATCATCTATCATCTGCTC 57.678 43.478 0.00 0.00 0.00 4.26
9203 12258 5.336610 CGAATCATCTATCATCTGCTCCAGT 60.337 44.000 0.00 0.00 32.61 4.00
9226 12281 1.435256 AGTGGAGTGCCTACTTGGTT 58.565 50.000 0.00 0.00 37.25 3.67
9227 12282 1.348036 AGTGGAGTGCCTACTTGGTTC 59.652 52.381 0.00 0.00 37.25 3.62
9228 12283 1.348036 GTGGAGTGCCTACTTGGTTCT 59.652 52.381 0.00 0.00 37.25 3.01
9229 12284 2.565834 GTGGAGTGCCTACTTGGTTCTA 59.434 50.000 0.00 0.00 37.25 2.10
9230 12285 3.007614 GTGGAGTGCCTACTTGGTTCTAA 59.992 47.826 0.00 0.00 37.25 2.10
9231 12286 3.649023 TGGAGTGCCTACTTGGTTCTAAA 59.351 43.478 0.00 0.00 37.25 1.85
9232 12287 4.254492 GGAGTGCCTACTTGGTTCTAAAG 58.746 47.826 0.00 0.00 37.25 1.85
9257 12313 4.830826 AAACCTCGAATCACCTTGTTTC 57.169 40.909 0.00 0.00 0.00 2.78
9263 12319 4.373527 TCGAATCACCTTGTTTCGAGAAA 58.626 39.130 14.85 0.00 46.88 2.52
9314 12370 1.284982 CTCCGTGCAAGTCCGTGAAG 61.285 60.000 0.00 0.00 0.00 3.02
9368 12424 2.125350 CTGTTCCTCGCAGGCTCC 60.125 66.667 0.00 0.00 34.61 4.70
9388 12444 2.352814 CCGAGGCCAGTAAGATAATCCG 60.353 54.545 5.01 0.00 0.00 4.18
9389 12445 2.557056 CGAGGCCAGTAAGATAATCCGA 59.443 50.000 5.01 0.00 0.00 4.55
9392 12448 3.067833 GGCCAGTAAGATAATCCGAAGC 58.932 50.000 0.00 0.00 0.00 3.86
9393 12449 2.731976 GCCAGTAAGATAATCCGAAGCG 59.268 50.000 0.00 0.00 0.00 4.68
9469 12525 2.125512 CACCGCTCGCCTTAAGCT 60.126 61.111 0.00 0.00 40.39 3.74
9513 12569 1.271102 GAAACCGCTCACTCACTCTCT 59.729 52.381 0.00 0.00 0.00 3.10
9517 12573 1.138671 GCTCACTCACTCTCTCGCC 59.861 63.158 0.00 0.00 0.00 5.54
9555 12611 4.130281 GTACCGCACGCTCGCAAC 62.130 66.667 0.00 0.00 0.00 4.17
9559 12615 3.838795 CGCACGCTCGCAACCTAC 61.839 66.667 0.00 0.00 0.00 3.18
9560 12616 3.488090 GCACGCTCGCAACCTACC 61.488 66.667 0.00 0.00 0.00 3.18
9561 12617 3.179265 CACGCTCGCAACCTACCG 61.179 66.667 0.00 0.00 0.00 4.02
9566 12622 3.695022 CTCGCAACCTACCGACCGG 62.695 68.421 6.94 6.94 42.03 5.28
9569 12625 4.807039 CAACCTACCGACCGGCCG 62.807 72.222 21.04 21.04 39.32 6.13
9608 12664 3.186047 CGTTCACCGCCGATGTCC 61.186 66.667 0.00 0.00 0.00 4.02
9731 12787 2.094130 GCACCACCACTACTACCTCTTC 60.094 54.545 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.287235 TGGTATATTCATGTTCAATTGATGGCA 59.713 33.333 9.40 9.36 0.00 4.92
29 30 4.217550 GCAATGAACTAAGCCAAACTGGTA 59.782 41.667 0.00 0.00 40.46 3.25
31 32 3.005684 TGCAATGAACTAAGCCAAACTGG 59.994 43.478 0.00 0.00 41.55 4.00
71 72 8.260270 TGATCAAATGATAATCACGATGGATC 57.740 34.615 0.00 0.00 34.37 3.36
72 73 8.803397 ATGATCAAATGATAATCACGATGGAT 57.197 30.769 0.00 0.00 34.37 3.41
73 74 8.625786 AATGATCAAATGATAATCACGATGGA 57.374 30.769 0.00 0.00 34.37 3.41
169 171 9.838339 GCCATATATAGTGCTACCATCTAAAAT 57.162 33.333 0.27 0.00 0.00 1.82
195 197 3.731867 GCCATCGCTGGTAATCTTTTGTG 60.732 47.826 7.21 0.00 45.10 3.33
221 223 5.480073 TCCCTTCCATCAAAACCAGTAAATG 59.520 40.000 0.00 0.00 0.00 2.32
222 224 5.650283 TCCCTTCCATCAAAACCAGTAAAT 58.350 37.500 0.00 0.00 0.00 1.40
297 299 4.566004 TGCGGATATGCTAAGATTACACC 58.434 43.478 0.00 0.00 35.36 4.16
302 304 3.077359 GCCTTGCGGATATGCTAAGATT 58.923 45.455 8.87 0.00 35.36 2.40
304 306 1.270839 GGCCTTGCGGATATGCTAAGA 60.271 52.381 0.00 0.00 35.36 2.10
315 317 1.087501 GAAAAGAGTAGGCCTTGCGG 58.912 55.000 12.58 0.00 0.00 5.69
354 356 6.879400 TCTTAAGTATCTTTCAGGAGGAAGC 58.121 40.000 1.63 0.00 36.72 3.86
355 357 8.536175 AGTTCTTAAGTATCTTTCAGGAGGAAG 58.464 37.037 1.63 0.00 36.72 3.46
357 359 8.437274 AAGTTCTTAAGTATCTTTCAGGAGGA 57.563 34.615 1.63 0.00 0.00 3.71
359 361 8.940952 CCAAAGTTCTTAAGTATCTTTCAGGAG 58.059 37.037 1.63 1.51 0.00 3.69
363 369 6.708949 ACGCCAAAGTTCTTAAGTATCTTTCA 59.291 34.615 1.63 0.00 0.00 2.69
373 379 5.236911 ACACGATAAACGCCAAAGTTCTTAA 59.763 36.000 0.00 0.00 46.94 1.85
389 395 7.202016 AGAAGAGCAAATGAAAACACGATAA 57.798 32.000 0.00 0.00 0.00 1.75
392 398 5.499139 AAGAAGAGCAAATGAAAACACGA 57.501 34.783 0.00 0.00 0.00 4.35
393 399 5.173854 GGAAAGAAGAGCAAATGAAAACACG 59.826 40.000 0.00 0.00 0.00 4.49
394 400 5.463392 GGGAAAGAAGAGCAAATGAAAACAC 59.537 40.000 0.00 0.00 0.00 3.32
395 401 5.363580 AGGGAAAGAAGAGCAAATGAAAACA 59.636 36.000 0.00 0.00 0.00 2.83
401 407 4.919754 CGAAAAGGGAAAGAAGAGCAAATG 59.080 41.667 0.00 0.00 0.00 2.32
420 426 7.097834 ACCCAACAAGTCAAAATTTAACGAAA 58.902 30.769 0.00 0.00 0.00 3.46
458 464 6.210078 CCATCCAAGAGTTAAGTATCGAGAC 58.790 44.000 0.86 0.86 0.00 3.36
470 476 3.121929 TCTCTAGCCCATCCAAGAGTT 57.878 47.619 0.00 0.00 37.37 3.01
478 484 3.570550 ACTTACGTCATCTCTAGCCCATC 59.429 47.826 0.00 0.00 0.00 3.51
493 499 3.007614 AGGGCTGATGTAACAACTTACGT 59.992 43.478 0.00 0.00 35.84 3.57
519 525 7.328493 GCTATACTTTGCCAACCTTAACTTTTG 59.672 37.037 0.00 0.00 0.00 2.44
531 537 2.843730 TGAGGGAGCTATACTTTGCCAA 59.156 45.455 0.00 0.00 0.00 4.52
581 587 4.993705 AGGAAGTGATGTAACCCTGAAA 57.006 40.909 0.00 0.00 0.00 2.69
605 611 4.714308 AGGAAGTGATGTGTTTCCCAAAAA 59.286 37.500 0.00 0.00 41.00 1.94
606 612 4.285863 AGGAAGTGATGTGTTTCCCAAAA 58.714 39.130 0.00 0.00 41.00 2.44
607 613 3.909732 AGGAAGTGATGTGTTTCCCAAA 58.090 40.909 0.00 0.00 41.00 3.28
608 614 3.593442 AGGAAGTGATGTGTTTCCCAA 57.407 42.857 0.00 0.00 41.00 4.12
609 615 3.593442 AAGGAAGTGATGTGTTTCCCA 57.407 42.857 0.00 0.00 41.00 4.37
610 616 4.937201 AAAAGGAAGTGATGTGTTTCCC 57.063 40.909 0.00 0.00 41.00 3.97
661 667 3.995199 TGATGTGTGGACAGAGTTCTTC 58.005 45.455 0.00 0.00 34.87 2.87
671 677 2.874701 GCTGGACATATGATGTGTGGAC 59.125 50.000 10.38 0.00 45.03 4.02
708 748 0.696501 GGAACTTTAGGCCCAGGTCA 59.303 55.000 13.00 0.00 0.00 4.02
830 872 1.414866 GGAGGCTGAGGGAGGGATTC 61.415 65.000 0.00 0.00 0.00 2.52
1189 1283 2.282110 CAATGCACACACCCCGGA 60.282 61.111 0.73 0.00 0.00 5.14
1198 1292 3.433709 CAACAAACGACTTCAATGCACA 58.566 40.909 0.00 0.00 0.00 4.57
1245 1377 1.686052 AGAAACAGGCCGCATCAAAAA 59.314 42.857 0.00 0.00 0.00 1.94
1271 1403 2.359602 CCTGCACTCACCAGCCAG 60.360 66.667 0.00 0.00 0.00 4.85
1445 1577 6.669278 CCATGATCACTTCATCAAGCAATAG 58.331 40.000 0.00 0.00 43.40 1.73
1480 1613 6.690530 TCGAAATGAATCCTTCAAATTTGCT 58.309 32.000 13.54 0.00 43.95 3.91
1509 1642 3.490761 CGGCCCAATTCAAATGTATCCAC 60.491 47.826 0.00 0.00 0.00 4.02
1582 1715 3.008049 GGACAAAGGCCTGAAGTTCTCTA 59.992 47.826 5.69 0.00 0.00 2.43
1660 1793 5.041287 CCTCGTCGCTGATTTATAGAAACA 58.959 41.667 0.00 0.00 0.00 2.83
1661 1794 5.041940 ACCTCGTCGCTGATTTATAGAAAC 58.958 41.667 0.00 0.00 0.00 2.78
1868 2341 0.608640 GTGATCCCTGGTCGAACAGT 59.391 55.000 27.88 10.87 36.75 3.55
2097 2594 3.757745 ACACACACAGCAACAAGTAAC 57.242 42.857 0.00 0.00 0.00 2.50
2318 2875 2.082231 CAGAACATTCACCAGCAGGAG 58.918 52.381 0.35 0.00 38.69 3.69
2320 2877 1.538512 CACAGAACATTCACCAGCAGG 59.461 52.381 0.00 0.00 42.21 4.85
2363 2920 3.510388 AGTACACCAGATCATGTCACG 57.490 47.619 0.00 0.00 0.00 4.35
3554 5777 4.099266 TGGGTTTCATCAACTTTGACAAGG 59.901 41.667 0.00 0.00 40.49 3.61
3555 5778 5.261209 TGGGTTTCATCAACTTTGACAAG 57.739 39.130 0.00 0.00 40.49 3.16
3590 5813 9.744468 AAACCAAATACATTGTAAAGACAGAAC 57.256 29.630 0.00 0.00 36.76 3.01
3810 6033 1.438651 TCGATCAAAGCAAAGACCCG 58.561 50.000 0.00 0.00 0.00 5.28
3918 6141 4.219115 TGGTCTTTGCTAATCAAAACCCA 58.781 39.130 13.65 9.56 43.44 4.51
4918 7149 4.098914 AGAGTCAAACAGGCAACCAATA 57.901 40.909 0.00 0.00 37.17 1.90
4919 7150 2.949447 AGAGTCAAACAGGCAACCAAT 58.051 42.857 0.00 0.00 37.17 3.16
4931 7162 8.931568 ACCTTCCTACTAGTAAAAAGAGTCAAA 58.068 33.333 18.80 0.00 0.00 2.69
4935 7166 9.599056 AGTTACCTTCCTACTAGTAAAAAGAGT 57.401 33.333 18.80 16.63 0.00 3.24
5106 7337 0.831307 AGCGAAAGATGTAGGGGGTC 59.169 55.000 0.00 0.00 0.00 4.46
5122 7353 1.602920 GGGCCTTTTTGACTTTCAGCG 60.603 52.381 0.84 0.00 0.00 5.18
5131 7362 4.384868 GCAGTAGTATAGGGGCCTTTTTGA 60.385 45.833 0.84 0.00 0.00 2.69
5217 7448 5.635280 TCTCAAGCAACTTTCATAAGACTCG 59.365 40.000 0.00 0.00 35.30 4.18
5263 7494 9.944663 CTAAGCAAAAACTCAGTAAATTGTACA 57.055 29.630 0.00 0.00 0.00 2.90
5393 7652 4.908601 TTGAACATACCTGAGGTGACAT 57.091 40.909 15.83 0.00 36.19 3.06
5579 7839 2.430465 ACCATCTGCAGCACTAACTTG 58.570 47.619 9.47 0.00 0.00 3.16
5591 7851 1.740025 GTGCCTAGTGAAACCATCTGC 59.260 52.381 0.00 0.00 37.80 4.26
5636 7896 1.995376 ACCCAAACCCAAGCACTAAG 58.005 50.000 0.00 0.00 0.00 2.18
5693 7953 4.158394 CCTACACAACATAAAGCATTGCCT 59.842 41.667 4.70 0.00 0.00 4.75
5694 7954 4.082245 ACCTACACAACATAAAGCATTGCC 60.082 41.667 4.70 0.00 0.00 4.52
5719 8048 3.201290 CAGCCTGTCTTACAGCCATTAG 58.799 50.000 1.43 0.00 44.63 1.73
5721 8050 1.352352 ACAGCCTGTCTTACAGCCATT 59.648 47.619 0.00 0.00 44.63 3.16
6100 8512 7.289084 GTGCTTATGGGGAATTAAAGGGATAAA 59.711 37.037 0.00 0.00 0.00 1.40
6107 8519 5.656416 TGGAAGTGCTTATGGGGAATTAAAG 59.344 40.000 0.00 0.00 0.00 1.85
6456 8951 6.653320 AGTTTTCAGCCAAGTTTCGTGATATA 59.347 34.615 0.00 0.00 0.00 0.86
6504 8999 3.762247 CCCAATGCCCCAGTTGCG 61.762 66.667 0.00 0.00 0.00 4.85
6883 9381 1.609841 GGTAAGACAAACCACCCTCGG 60.610 57.143 0.00 0.00 36.96 4.63
6990 9488 4.536364 ACGAAAGGCAACATTATGATCG 57.464 40.909 0.00 0.00 41.41 3.69
7234 9732 6.218019 CAGGTTGCATATTCCATTGTATTGG 58.782 40.000 0.00 0.00 38.18 3.16
7309 9807 1.134431 AGTTTGCCAACCAAAGCCAAG 60.134 47.619 0.00 0.00 43.67 3.61
7414 9912 3.429207 GGTACTTCTCTTCACGTGCTTTC 59.571 47.826 11.67 0.00 0.00 2.62
7788 10286 1.204704 CATCAGAGCCACGGTTCACTA 59.795 52.381 2.60 0.00 0.00 2.74
7870 10368 4.142534 GCACATGCTAGATTGAAAAGAGCA 60.143 41.667 0.00 0.00 41.97 4.26
7871 10369 4.349501 GCACATGCTAGATTGAAAAGAGC 58.650 43.478 0.00 0.00 38.21 4.09
7957 10455 2.947652 GCAGCTATCAGCATCCTTTTCA 59.052 45.455 0.38 0.00 45.56 2.69
8014 10512 2.959507 AGCCAACCAACAAACAGAAC 57.040 45.000 0.00 0.00 0.00 3.01
8030 10531 8.094548 AGGGAAAACTGACAATTAAAATAAGCC 58.905 33.333 0.00 0.00 0.00 4.35
8097 10598 6.796426 TGGAGATAACAGAACAATCGAGTAG 58.204 40.000 0.00 0.00 0.00 2.57
8122 10623 6.393990 GGGATACTGTGATCATGATGTCTAC 58.606 44.000 14.30 7.40 0.00 2.59
8126 10627 4.263018 CGGGATACTGTGATCATGATGT 57.737 45.455 14.30 7.28 38.54 3.06
8154 10662 3.939592 CGCCCCTTCTAAGTTTCTTAAGG 59.060 47.826 1.85 0.00 37.13 2.69
8185 11211 5.487488 ACTCATCTAACTAATGTTGGTCCCA 59.513 40.000 0.00 0.00 37.59 4.37
8191 11217 8.725148 AGAAGCAAACTCATCTAACTAATGTTG 58.275 33.333 0.00 0.00 37.59 3.33
8286 11314 2.461300 ACTGAGGAGCTGCATACCTA 57.539 50.000 8.35 2.94 33.89 3.08
8295 11323 2.826725 GCGGGTTATATACTGAGGAGCT 59.173 50.000 0.00 0.00 0.00 4.09
8492 11520 5.646577 ACGTTTTATCTGAGTAGTGCTCT 57.353 39.130 9.77 0.00 44.41 4.09
8495 11523 6.648725 ATGAACGTTTTATCTGAGTAGTGC 57.351 37.500 0.46 0.00 0.00 4.40
8533 11562 2.031508 GCGAATCGAAACCAGGAAACAA 60.032 45.455 6.91 0.00 0.00 2.83
8534 11563 1.533731 GCGAATCGAAACCAGGAAACA 59.466 47.619 6.91 0.00 0.00 2.83
8547 11576 2.020559 GCAGTTCTGCGCGAATCG 59.979 61.111 12.10 0.00 42.12 3.34
8683 11724 0.179081 GGTTCTGGTGTATCGCCCTC 60.179 60.000 0.00 0.00 32.22 4.30
8714 11755 1.068121 AGCAAAGCCTTCCAGTACCT 58.932 50.000 0.00 0.00 0.00 3.08
8783 11830 1.178276 CCCGTCTCAGCTACAAGACT 58.822 55.000 16.56 0.00 39.80 3.24
8809 11856 8.432110 ACAAATAATACGCTACATGTGATTCA 57.568 30.769 9.11 0.00 0.00 2.57
8817 11864 7.528481 TCGACAAACAAATAATACGCTACAT 57.472 32.000 0.00 0.00 0.00 2.29
8829 11877 2.297701 AGGTGTGCTCGACAAACAAAT 58.702 42.857 9.53 0.00 38.37 2.32
8988 12036 4.091509 CGTTCTCCGTACCATTTTCTTCTG 59.908 45.833 0.00 0.00 0.00 3.02
9033 12081 5.712152 TTCTGATGCTTCCTTTTTCCTTC 57.288 39.130 0.00 0.00 0.00 3.46
9049 12097 3.051081 GCTGGATAAGCGGATTCTGAT 57.949 47.619 0.00 0.00 43.45 2.90
9060 12108 1.419012 TGAGCTGGGATGCTGGATAAG 59.581 52.381 0.00 0.00 44.17 1.73
9061 12109 1.510492 TGAGCTGGGATGCTGGATAA 58.490 50.000 0.00 0.00 44.17 1.75
9062 12110 1.141657 GTTGAGCTGGGATGCTGGATA 59.858 52.381 0.00 0.00 44.17 2.59
9063 12111 0.106819 GTTGAGCTGGGATGCTGGAT 60.107 55.000 0.00 0.00 44.17 3.41
9064 12112 1.300963 GTTGAGCTGGGATGCTGGA 59.699 57.895 0.00 0.00 44.17 3.86
9065 12113 1.751927 GGTTGAGCTGGGATGCTGG 60.752 63.158 0.00 0.00 44.17 4.85
9066 12114 1.001764 TGGTTGAGCTGGGATGCTG 60.002 57.895 0.00 0.00 44.17 4.41
9067 12115 2.833604 GCTGGTTGAGCTGGGATGCT 62.834 60.000 0.00 0.00 45.21 3.79
9068 12116 2.413142 GCTGGTTGAGCTGGGATGC 61.413 63.158 0.00 0.00 45.21 3.91
9069 12117 3.915575 GCTGGTTGAGCTGGGATG 58.084 61.111 0.00 0.00 45.21 3.51
9082 12130 2.223044 GCTTCGAACGAAATTAGGCTGG 60.223 50.000 10.68 0.00 33.34 4.85
9102 12157 0.179100 TCTCTACAGATGGCGCTTGC 60.179 55.000 7.64 0.00 38.11 4.01
9122 12177 9.995003 CCAAAAGGAGAGGATGATATATATAGC 57.005 37.037 0.87 0.87 0.00 2.97
9140 12195 4.837093 ACGTAGATGATTCCCAAAAGGA 57.163 40.909 0.00 0.00 45.68 3.36
9141 12196 5.671493 AGTACGTAGATGATTCCCAAAAGG 58.329 41.667 0.00 0.00 0.00 3.11
9142 12197 6.574350 AGAGTACGTAGATGATTCCCAAAAG 58.426 40.000 0.00 0.00 0.00 2.27
9160 12215 5.668558 TTCGGAAAGCAAAAGAAGAGTAC 57.331 39.130 0.00 0.00 0.00 2.73
9161 12216 5.995282 TGATTCGGAAAGCAAAAGAAGAGTA 59.005 36.000 0.00 0.00 0.00 2.59
9162 12217 4.821805 TGATTCGGAAAGCAAAAGAAGAGT 59.178 37.500 0.00 0.00 0.00 3.24
9163 12218 5.362556 TGATTCGGAAAGCAAAAGAAGAG 57.637 39.130 0.00 0.00 0.00 2.85
9173 12228 5.163874 GCAGATGATAGATGATTCGGAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
9178 12233 4.081807 TGGAGCAGATGATAGATGATTCGG 60.082 45.833 0.00 0.00 0.00 4.30
9179 12234 5.069501 TGGAGCAGATGATAGATGATTCG 57.930 43.478 0.00 0.00 0.00 3.34
9180 12235 6.040209 ACTGGAGCAGATGATAGATGATTC 57.960 41.667 0.00 0.00 35.18 2.52
9184 12239 5.718724 TGTACTGGAGCAGATGATAGATG 57.281 43.478 0.00 0.00 35.18 2.90
9199 12254 0.687354 AGGCACTCCACTTGTACTGG 59.313 55.000 0.00 0.00 33.74 4.00
9203 12258 2.301870 CCAAGTAGGCACTCCACTTGTA 59.698 50.000 17.15 0.00 42.88 2.41
9226 12281 6.436532 AGGTGATTCGAGGTTTAGACTTTAGA 59.563 38.462 0.00 0.00 0.00 2.10
9227 12282 6.631962 AGGTGATTCGAGGTTTAGACTTTAG 58.368 40.000 0.00 0.00 0.00 1.85
9228 12283 6.600882 AGGTGATTCGAGGTTTAGACTTTA 57.399 37.500 0.00 0.00 0.00 1.85
9229 12284 5.485209 AGGTGATTCGAGGTTTAGACTTT 57.515 39.130 0.00 0.00 0.00 2.66
9230 12285 5.221661 ACAAGGTGATTCGAGGTTTAGACTT 60.222 40.000 0.00 0.00 0.00 3.01
9231 12286 4.283722 ACAAGGTGATTCGAGGTTTAGACT 59.716 41.667 0.00 0.00 0.00 3.24
9232 12287 4.566987 ACAAGGTGATTCGAGGTTTAGAC 58.433 43.478 0.00 0.00 0.00 2.59
9368 12424 2.557056 TCGGATTATCTTACTGGCCTCG 59.443 50.000 3.32 0.00 0.00 4.63
9492 12548 0.318762 AGAGTGAGTGAGCGGTTTCC 59.681 55.000 0.00 0.00 0.00 3.13
9495 12551 0.885196 GAGAGAGTGAGTGAGCGGTT 59.115 55.000 0.00 0.00 0.00 4.44
9499 12555 1.138671 GGCGAGAGAGTGAGTGAGC 59.861 63.158 0.00 0.00 0.00 4.26
9500 12556 0.884514 TTGGCGAGAGAGTGAGTGAG 59.115 55.000 0.00 0.00 0.00 3.51
9546 12602 2.879462 GTCGGTAGGTTGCGAGCG 60.879 66.667 0.00 0.00 37.89 5.03
9552 12608 4.807039 CGGCCGGTCGGTAGGTTG 62.807 72.222 23.57 0.00 37.65 3.77
9586 12642 3.064987 ATCGGCGGTGAACGGAGAG 62.065 63.158 7.21 0.00 44.51 3.20
9587 12643 3.066190 ATCGGCGGTGAACGGAGA 61.066 61.111 7.21 0.00 44.51 3.71
9588 12644 2.885644 CATCGGCGGTGAACGGAG 60.886 66.667 16.62 0.00 44.51 4.63
9592 12648 3.186047 CGGACATCGGCGGTGAAC 61.186 66.667 29.09 18.97 34.75 3.18
9731 12787 1.467734 GTGTTGAGCTGCTTGATGGAG 59.532 52.381 2.53 0.00 37.17 3.86


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

AutoCloner maintained by Alex Coulton.