Multiple sequence alignment - TraesCS4B01G055000

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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 TraesCS4B01G055000 chr4B 100.000 4074 0 0 1 4074 43749714 43753787 0.000000e+00 7524.0
1 TraesCS4B01G055000 chr4B 80.311 772 114 27 1898 2658 43766717 43767461 2.140000e-152 549.0
2 TraesCS4B01G055000 chr4B 85.631 515 65 3 2745 3252 43758723 43759235 2.160000e-147 532.0
3 TraesCS4B01G055000 chr4B 85.794 359 49 2 2760 3118 43767684 43768040 2.970000e-101 379.0
4 TraesCS4B01G055000 chr4B 87.762 286 35 0 2387 2672 43758339 43758624 6.520000e-88 335.0
5 TraesCS4B01G055000 chr4A 90.378 2432 164 32 1351 3760 572551646 572549263 0.000000e+00 3131.0
6 TraesCS4B01G055000 chr4A 81.039 770 104 22 1909 2658 572542919 572542172 3.530000e-160 575.0
7 TraesCS4B01G055000 chr4A 84.682 581 82 2 2751 3326 572542046 572541468 1.270000e-159 573.0
8 TraesCS4B01G055000 chr4A 79.771 786 117 30 1898 2664 572536334 572535572 2.160000e-147 532.0
9 TraesCS4B01G055000 chr4A 88.835 412 32 7 341 743 572552591 572552185 1.020000e-135 494.0
10 TraesCS4B01G055000 chr4A 86.000 450 41 17 744 1179 572552148 572551707 2.870000e-126 462.0
11 TraesCS4B01G055000 chr4A 90.000 200 17 3 105 303 572552791 572552594 5.230000e-64 255.0
12 TraesCS4B01G055000 chr4A 97.500 80 1 1 1 79 572552864 572552785 7.100000e-28 135.0
13 TraesCS4B01G055000 chr4D 90.084 1674 112 26 1465 3116 30420863 30422504 0.000000e+00 2122.0
14 TraesCS4B01G055000 chr4D 88.742 1288 99 29 105 1365 30419389 30420657 0.000000e+00 1533.0
15 TraesCS4B01G055000 chr4D 84.266 1144 145 28 2086 3211 30413050 30414176 0.000000e+00 1083.0
16 TraesCS4B01G055000 chr4D 81.404 769 110 23 1898 2658 30503466 30504209 7.540000e-167 597.0
17 TraesCS4B01G055000 chr4D 80.307 716 110 20 1950 2658 30509439 30510130 2.810000e-141 512.0
18 TraesCS4B01G055000 chr4D 91.931 347 15 4 3196 3536 30422530 30422869 1.330000e-129 473.0
19 TraesCS4B01G055000 chr4D 83.463 514 72 8 2745 3252 30504314 30504820 2.220000e-127 466.0
20 TraesCS4B01G055000 chr4D 90.230 348 26 4 3535 3882 30425070 30425409 8.030000e-122 448.0
21 TraesCS4B01G055000 chr4D 85.294 374 53 2 2745 3118 30510231 30510602 6.390000e-103 385.0
22 TraesCS4B01G055000 chr4D 77.888 502 72 23 906 1398 30412467 30412938 4.010000e-70 276.0
23 TraesCS4B01G055000 chr4D 93.182 88 4 2 1 86 30419315 30419402 1.190000e-25 128.0
24 TraesCS4B01G055000 chr7B 81.148 732 101 25 1909 2630 104260596 104259892 1.650000e-153 553.0
25 TraesCS4B01G055000 chr7B 83.099 497 75 5 2751 3242 104259085 104258593 1.040000e-120 444.0
26 TraesCS4B01G055000 chr7B 92.701 137 10 0 3938 4074 512748071 512748207 8.930000e-47 198.0
27 TraesCS4B01G055000 chr1B 93.056 144 10 0 3931 4074 13267913 13267770 1.150000e-50 211.0
28 TraesCS4B01G055000 chr6B 88.235 68 5 3 273 339 533998683 533998748 1.210000e-10 78.7
29 TraesCS4B01G055000 chr6B 87.879 66 5 3 274 338 401410815 401410878 1.570000e-09 75.0
30 TraesCS4B01G055000 chr2A 88.060 67 5 3 273 338 172556596 172556532 4.370000e-10 76.8
31 TraesCS4B01G055000 chr2A 88.060 67 5 3 273 338 646837850 646837786 4.370000e-10 76.8


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 TraesCS4B01G055000 chr4B 43749714 43753787 4073 False 7524.0 7524 100.0000 1 4074 1 chr4B.!!$F1 4073
1 TraesCS4B01G055000 chr4B 43766717 43768040 1323 False 464.0 549 83.0525 1898 3118 2 chr4B.!!$F3 1220
2 TraesCS4B01G055000 chr4B 43758339 43759235 896 False 433.5 532 86.6965 2387 3252 2 chr4B.!!$F2 865
3 TraesCS4B01G055000 chr4A 572549263 572552864 3601 True 895.4 3131 90.5426 1 3760 5 chr4A.!!$R3 3759
4 TraesCS4B01G055000 chr4A 572541468 572542919 1451 True 574.0 575 82.8605 1909 3326 2 chr4A.!!$R2 1417
5 TraesCS4B01G055000 chr4A 572535572 572536334 762 True 532.0 532 79.7710 1898 2664 1 chr4A.!!$R1 766
6 TraesCS4B01G055000 chr4D 30419315 30425409 6094 False 940.8 2122 90.8338 1 3882 5 chr4D.!!$F2 3881
7 TraesCS4B01G055000 chr4D 30412467 30414176 1709 False 679.5 1083 81.0770 906 3211 2 chr4D.!!$F1 2305
8 TraesCS4B01G055000 chr4D 30503466 30504820 1354 False 531.5 597 82.4335 1898 3252 2 chr4D.!!$F3 1354
9 TraesCS4B01G055000 chr4D 30509439 30510602 1163 False 448.5 512 82.8005 1950 3118 2 chr4D.!!$F4 1168
10 TraesCS4B01G055000 chr7B 104258593 104260596 2003 True 498.5 553 82.1235 1909 3242 2 chr7B.!!$R1 1333

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
131 134 0.179029 TAATAAAGGCCGCCCTCTGC 60.179 55.0 5.55 0.00 41.9 4.26 F
1765 1967 0.104620 ATAGCCCCCTTCCGTACCAT 60.105 55.0 0.00 0.00 0.0 3.55 F
2119 2325 0.107945 CAGTTAGCAGGCCTGAGGAC 60.108 60.0 37.21 26.67 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2012 0.109723 TTGCTTACGGGCTTCCACTT 59.890 50.0 0.00 0.0 0.00 3.16 R
2658 3578 0.103026 TGATCGATGTTCAGAGGCGG 59.897 55.0 0.54 0.0 0.00 6.13 R
3952 7245 0.107654 GGTGCAGATAAGCTCGGGTT 60.108 55.0 0.00 0.0 34.99 4.11 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
76 79 2.615447 GGCCGCCCTAACAATTAACTAC 59.385 50.000 0.00 0.00 0.00 2.73
77 80 3.538591 GCCGCCCTAACAATTAACTACT 58.461 45.455 0.00 0.00 0.00 2.57
78 81 4.443315 GGCCGCCCTAACAATTAACTACTA 60.443 45.833 0.00 0.00 0.00 1.82
79 82 4.748600 GCCGCCCTAACAATTAACTACTAG 59.251 45.833 0.00 0.00 0.00 2.57
80 83 5.683249 GCCGCCCTAACAATTAACTACTAGT 60.683 44.000 0.00 0.00 0.00 2.57
81 84 6.461509 GCCGCCCTAACAATTAACTACTAGTA 60.462 42.308 1.89 1.89 0.00 1.82
82 85 7.664758 CCGCCCTAACAATTAACTACTAGTAT 58.335 38.462 2.33 0.00 0.00 2.12
83 86 8.146412 CCGCCCTAACAATTAACTACTAGTATT 58.854 37.037 2.33 0.00 0.00 1.89
127 130 4.596212 ACTAGTATTAATAAAGGCCGCCCT 59.404 41.667 5.55 0.00 45.77 5.19
128 131 4.017177 AGTATTAATAAAGGCCGCCCTC 57.983 45.455 5.55 0.00 41.90 4.30
129 132 3.651423 AGTATTAATAAAGGCCGCCCTCT 59.349 43.478 5.55 0.00 41.90 3.69
130 133 2.341846 TTAATAAAGGCCGCCCTCTG 57.658 50.000 5.55 0.00 41.90 3.35
131 134 0.179029 TAATAAAGGCCGCCCTCTGC 60.179 55.000 5.55 0.00 41.90 4.26
179 183 1.201429 AACAGGGATTCCTCCACGCT 61.201 55.000 2.01 0.00 44.08 5.07
238 242 2.650608 GTGAAACCTCACGCACATTTC 58.349 47.619 0.00 0.00 42.54 2.17
281 285 3.313526 CAGATGTTTTTAGGCCGATCTGG 59.686 47.826 0.00 0.00 42.50 3.86
283 287 3.149005 TGTTTTTAGGCCGATCTGGTT 57.851 42.857 0.00 0.00 41.21 3.67
284 288 3.078837 TGTTTTTAGGCCGATCTGGTTC 58.921 45.455 0.00 0.27 41.21 3.62
285 289 2.018542 TTTTAGGCCGATCTGGTTCG 57.981 50.000 0.00 0.00 41.21 3.95
323 327 0.438830 GTCGTAGCTTTGCTTGTCCG 59.561 55.000 0.00 0.00 40.44 4.79
325 329 1.291877 CGTAGCTTTGCTTGTCCGCT 61.292 55.000 0.00 0.00 40.44 5.52
327 331 0.250295 TAGCTTTGCTTGTCCGCTGT 60.250 50.000 0.00 0.00 40.44 4.40
328 332 1.370900 GCTTTGCTTGTCCGCTGTG 60.371 57.895 0.00 0.00 0.00 3.66
331 335 1.195448 CTTTGCTTGTCCGCTGTGTAG 59.805 52.381 0.00 0.00 0.00 2.74
332 336 1.227999 TTGCTTGTCCGCTGTGTAGC 61.228 55.000 0.00 0.00 46.62 3.58
392 400 1.991121 TGGAGTACGGTCACTTGTCT 58.009 50.000 0.00 0.00 0.00 3.41
475 484 7.391554 CACTTTTCTGACCCTCTTAATTGATGA 59.608 37.037 0.00 0.00 0.00 2.92
480 489 6.385176 TCTGACCCTCTTAATTGATGAGTGAT 59.615 38.462 0.00 0.00 0.00 3.06
485 494 6.261826 CCCTCTTAATTGATGAGTGATGGAAC 59.738 42.308 0.00 0.00 0.00 3.62
503 512 3.372025 GGAACATAAGGGGAAGATGCACT 60.372 47.826 0.00 0.00 0.00 4.40
559 573 5.969423 AGCAAATGCACTTATGTATGCTTT 58.031 33.333 8.28 0.00 45.16 3.51
560 574 5.808540 AGCAAATGCACTTATGTATGCTTTG 59.191 36.000 8.28 12.60 45.16 2.77
561 575 5.501252 GCAAATGCACTTATGTATGCTTTGC 60.501 40.000 19.88 19.88 46.20 3.68
562 576 5.587388 AATGCACTTATGTATGCTTTGCT 57.413 34.783 0.00 0.00 42.55 3.91
563 577 5.587388 ATGCACTTATGTATGCTTTGCTT 57.413 34.783 0.00 0.00 42.55 3.91
564 578 4.735985 TGCACTTATGTATGCTTTGCTTG 58.264 39.130 0.00 0.00 42.55 4.01
565 579 4.218200 TGCACTTATGTATGCTTTGCTTGT 59.782 37.500 0.00 0.00 42.55 3.16
566 580 5.163513 GCACTTATGTATGCTTTGCTTGTT 58.836 37.500 0.00 0.00 38.84 2.83
567 581 5.287035 GCACTTATGTATGCTTTGCTTGTTC 59.713 40.000 0.00 0.00 38.84 3.18
568 582 6.380995 CACTTATGTATGCTTTGCTTGTTCA 58.619 36.000 0.00 0.00 0.00 3.18
569 583 6.525628 CACTTATGTATGCTTTGCTTGTTCAG 59.474 38.462 0.00 0.00 0.00 3.02
582 596 4.016444 GCTTGTTCAGATGGGTCCAAATA 58.984 43.478 0.00 0.00 0.00 1.40
686 700 6.370994 AGAGCTGACTTATGTTGTTCATTCTG 59.629 38.462 0.00 0.00 37.91 3.02
690 704 6.671190 TGACTTATGTTGTTCATTCTGCAAG 58.329 36.000 0.00 0.00 37.91 4.01
769 822 7.503521 TTGTCATTTTGTAGTGTTATCTGCA 57.496 32.000 0.00 0.00 0.00 4.41
782 835 7.940850 AGTGTTATCTGCAAACTGTTGTAATT 58.059 30.769 0.00 0.00 37.06 1.40
783 836 8.413229 AGTGTTATCTGCAAACTGTTGTAATTT 58.587 29.630 0.00 0.00 37.06 1.82
785 838 7.651304 TGTTATCTGCAAACTGTTGTAATTTGG 59.349 33.333 0.00 0.00 37.06 3.28
786 839 4.367450 TCTGCAAACTGTTGTAATTTGGC 58.633 39.130 0.00 0.00 37.06 4.52
787 840 4.118410 CTGCAAACTGTTGTAATTTGGCA 58.882 39.130 0.00 0.00 37.06 4.92
788 841 4.118410 TGCAAACTGTTGTAATTTGGCAG 58.882 39.130 0.00 0.00 37.06 4.85
795 848 6.581712 ACTGTTGTAATTTGGCAGAAAACAT 58.418 32.000 0.00 0.00 0.00 2.71
797 850 8.367156 ACTGTTGTAATTTGGCAGAAAACATAT 58.633 29.630 0.00 0.00 0.00 1.78
798 851 9.853555 CTGTTGTAATTTGGCAGAAAACATATA 57.146 29.630 0.00 0.00 0.00 0.86
837 890 3.131755 CACTACATGATCTCTGACCTGCA 59.868 47.826 0.00 0.00 0.00 4.41
838 891 2.687700 ACATGATCTCTGACCTGCAC 57.312 50.000 0.00 0.00 0.00 4.57
840 893 1.208776 CATGATCTCTGACCTGCACCA 59.791 52.381 0.00 0.00 0.00 4.17
842 895 1.002430 TGATCTCTGACCTGCACCAAC 59.998 52.381 0.00 0.00 0.00 3.77
843 896 1.277557 GATCTCTGACCTGCACCAACT 59.722 52.381 0.00 0.00 0.00 3.16
860 919 5.874261 CACCAACTTGATTTGAAACCACTTT 59.126 36.000 0.00 0.00 0.00 2.66
867 926 6.624352 TGATTTGAAACCACTTTCTCTCAG 57.376 37.500 0.00 0.00 37.30 3.35
871 930 4.130118 TGAAACCACTTTCTCTCAGAAGC 58.870 43.478 0.00 0.00 35.37 3.86
876 936 3.583806 CACTTTCTCTCAGAAGCACGAT 58.416 45.455 0.00 0.00 35.37 3.73
880 940 4.462508 TTCTCTCAGAAGCACGATGAAT 57.537 40.909 0.00 0.00 29.50 2.57
888 948 7.964559 TCTCAGAAGCACGATGAATTTATTTTG 59.035 33.333 0.00 0.00 0.00 2.44
889 949 7.815641 TCAGAAGCACGATGAATTTATTTTGA 58.184 30.769 0.00 0.00 0.00 2.69
891 951 8.581263 CAGAAGCACGATGAATTTATTTTGAAG 58.419 33.333 0.00 0.00 0.00 3.02
892 952 8.299570 AGAAGCACGATGAATTTATTTTGAAGT 58.700 29.630 0.00 0.00 0.00 3.01
894 954 8.452989 AGCACGATGAATTTATTTTGAAGTTC 57.547 30.769 0.00 0.00 0.00 3.01
895 955 8.081633 AGCACGATGAATTTATTTTGAAGTTCA 58.918 29.630 0.08 0.08 38.79 3.18
896 956 8.368126 GCACGATGAATTTATTTTGAAGTTCAG 58.632 33.333 5.56 0.00 38.12 3.02
898 961 9.612620 ACGATGAATTTATTTTGAAGTTCAGAC 57.387 29.630 5.56 0.00 38.12 3.51
963 1030 8.724153 CGTGTGTGTTAATTTATCATCATTTCG 58.276 33.333 0.00 0.00 0.00 3.46
981 1048 0.597568 CGCATTTGAAGGTTGAGCCA 59.402 50.000 0.00 0.00 40.61 4.75
1005 1072 7.293745 CACAGTAAGTTGAAGACATCATGTTC 58.706 38.462 0.00 0.00 38.03 3.18
1298 1373 8.983789 ACATGGGAAAGGTAAAGAAAAACTTAA 58.016 29.630 0.00 0.00 37.93 1.85
1329 1404 5.739161 CAGTGTGACAACTTCAGCTTTTTAC 59.261 40.000 0.00 0.00 33.71 2.01
1343 1418 4.738124 GCTTTTTACCAAGCTTCCATCTC 58.262 43.478 0.00 0.00 45.03 2.75
1391 1499 4.241681 TGTGCAAAACTTTGAACCTGAAC 58.758 39.130 10.21 0.00 44.47 3.18
1440 1558 5.183140 TGGCTTAGTAAATGAAGACCAAAGC 59.817 40.000 0.00 0.00 35.70 3.51
1447 1565 5.904362 AAATGAAGACCAAAGCCAGATAC 57.096 39.130 0.00 0.00 0.00 2.24
1456 1574 6.156256 AGACCAAAGCCAGATACATGTAAGTA 59.844 38.462 10.14 0.00 0.00 2.24
1463 1581 5.701290 GCCAGATACATGTAAGTAATCACCC 59.299 44.000 10.14 0.00 0.00 4.61
1511 1702 7.181125 AGACAAATAGTTTGACATACTCCCTCT 59.819 37.037 9.21 0.00 43.26 3.69
1567 1758 8.928448 AGGAATGATACTGTGACAATATGTACT 58.072 33.333 0.00 0.00 0.00 2.73
1568 1759 8.982685 GGAATGATACTGTGACAATATGTACTG 58.017 37.037 0.00 0.00 0.00 2.74
1569 1760 9.534565 GAATGATACTGTGACAATATGTACTGT 57.465 33.333 0.00 0.00 0.00 3.55
1576 1767 9.944376 ACTGTGACAATATGTACTGTATCTTTT 57.056 29.630 0.00 0.00 0.00 2.27
1609 1800 3.270877 GTGGCCGTTCAGATCTTACATT 58.729 45.455 0.00 0.00 0.00 2.71
1623 1814 9.591792 CAGATCTTACATTGACTACTGAATGAA 57.408 33.333 0.00 0.00 34.31 2.57
1646 1837 3.895232 TTAGTTTTGCACAAAAGCCCA 57.105 38.095 8.73 0.00 40.53 5.36
1651 1842 5.375773 AGTTTTGCACAAAAGCCCATAATT 58.624 33.333 8.73 0.00 40.53 1.40
1676 1874 6.655078 AGCATTTTTAGGAGTGTGAAATGT 57.345 33.333 8.38 0.00 38.99 2.71
1677 1875 6.681777 AGCATTTTTAGGAGTGTGAAATGTC 58.318 36.000 8.38 2.82 38.99 3.06
1678 1876 6.491403 AGCATTTTTAGGAGTGTGAAATGTCT 59.509 34.615 8.38 4.53 38.99 3.41
1679 1877 6.583806 GCATTTTTAGGAGTGTGAAATGTCTG 59.416 38.462 8.38 0.00 38.99 3.51
1680 1878 7.522073 GCATTTTTAGGAGTGTGAAATGTCTGA 60.522 37.037 8.38 0.00 38.99 3.27
1681 1879 6.861065 TTTTAGGAGTGTGAAATGTCTGAC 57.139 37.500 0.00 0.00 0.00 3.51
1737 1939 9.162764 ACAAATGTATGTTGTAACTGATAGTCC 57.837 33.333 0.00 0.00 37.44 3.85
1738 1940 8.328146 CAAATGTATGTTGTAACTGATAGTCCG 58.672 37.037 0.00 0.00 0.00 4.79
1739 1941 6.762702 TGTATGTTGTAACTGATAGTCCGA 57.237 37.500 0.00 0.00 0.00 4.55
1740 1942 7.342769 TGTATGTTGTAACTGATAGTCCGAT 57.657 36.000 0.00 0.00 0.00 4.18
1741 1943 8.454570 TGTATGTTGTAACTGATAGTCCGATA 57.545 34.615 0.00 0.00 0.00 2.92
1762 1964 0.835276 AACATAGCCCCCTTCCGTAC 59.165 55.000 0.00 0.00 0.00 3.67
1764 1966 1.052124 CATAGCCCCCTTCCGTACCA 61.052 60.000 0.00 0.00 0.00 3.25
1765 1967 0.104620 ATAGCCCCCTTCCGTACCAT 60.105 55.000 0.00 0.00 0.00 3.55
1771 1973 1.481802 CCCCTTCCGTACCATAGCCTA 60.482 57.143 0.00 0.00 0.00 3.93
1775 1977 1.991121 TCCGTACCATAGCCTACAGG 58.009 55.000 0.00 0.00 38.53 4.00
1780 1982 2.182516 ACCATAGCCTACAGGAGCTT 57.817 50.000 0.00 0.00 40.56 3.74
1782 1984 2.436173 ACCATAGCCTACAGGAGCTTTC 59.564 50.000 0.00 0.00 40.56 2.62
1791 1993 5.825151 GCCTACAGGAGCTTTCTTATGAATT 59.175 40.000 0.00 0.00 37.39 2.17
1834 2036 2.171659 TGGAAGCCCGTAAGCAATATCA 59.828 45.455 0.00 0.00 34.29 2.15
1837 2039 5.001232 GGAAGCCCGTAAGCAATATCAATA 58.999 41.667 0.00 0.00 34.23 1.90
1838 2040 5.648092 GGAAGCCCGTAAGCAATATCAATAT 59.352 40.000 0.00 0.00 34.23 1.28
1839 2041 6.403636 GGAAGCCCGTAAGCAATATCAATATG 60.404 42.308 0.00 0.00 34.23 1.78
1840 2042 4.943705 AGCCCGTAAGCAATATCAATATGG 59.056 41.667 0.00 0.00 34.23 2.74
1842 2044 5.414454 GCCCGTAAGCAATATCAATATGGAA 59.586 40.000 0.00 0.00 0.00 3.53
1843 2045 6.403636 GCCCGTAAGCAATATCAATATGGAAG 60.404 42.308 0.00 0.00 0.00 3.46
1844 2046 6.403636 CCCGTAAGCAATATCAATATGGAAGC 60.404 42.308 0.00 0.00 0.00 3.86
1845 2047 6.403636 CCGTAAGCAATATCAATATGGAAGCC 60.404 42.308 0.00 0.00 0.00 4.35
1846 2048 5.990120 AAGCAATATCAATATGGAAGCCC 57.010 39.130 0.00 0.00 0.00 5.19
1847 2049 4.012374 AGCAATATCAATATGGAAGCCCG 58.988 43.478 0.00 0.00 34.29 6.13
1864 2066 2.479275 GCCCGTAGTTCTTGTCAAAGAC 59.521 50.000 0.00 0.00 42.20 3.01
1885 2087 6.238648 AGACAAAACTACCCTTTGGTATCTG 58.761 40.000 0.89 0.00 46.04 2.90
1893 2095 4.273318 ACCCTTTGGTATCTGCATCTTTC 58.727 43.478 0.00 0.00 45.45 2.62
2041 2247 0.901827 TGGCAAGGTATCTCGAAGCA 59.098 50.000 0.00 0.00 0.00 3.91
2054 2260 1.075542 CGAAGCACGCAACTGGAATA 58.924 50.000 0.00 0.00 34.51 1.75
2119 2325 0.107945 CAGTTAGCAGGCCTGAGGAC 60.108 60.000 37.21 26.67 0.00 3.85
2139 2350 2.548057 ACATTCGCTGGGTAAATATGCG 59.452 45.455 0.00 0.00 46.71 4.73
2174 2392 5.603596 TGCAATGCTCAAGTGATTTCTTTT 58.396 33.333 6.82 0.00 0.00 2.27
2179 2397 7.941795 ATGCTCAAGTGATTTCTTTTCAAAG 57.058 32.000 0.00 0.00 37.36 2.77
2182 2400 6.974622 GCTCAAGTGATTTCTTTTCAAAGACA 59.025 34.615 1.28 0.00 44.18 3.41
2183 2401 7.167136 GCTCAAGTGATTTCTTTTCAAAGACAG 59.833 37.037 1.28 0.00 44.18 3.51
2345 2571 2.224314 GCAGGTAAGCACTCACTGTTTC 59.776 50.000 0.00 0.00 0.00 2.78
2385 2634 5.484715 TCCTTAACCTTGAATTCACCTACG 58.515 41.667 7.89 0.00 0.00 3.51
2555 2815 1.762708 ATGCAACCCCCATAAAGACG 58.237 50.000 0.00 0.00 0.00 4.18
2658 3578 2.423577 TCGAGGCTTTCTTTAAGGTGC 58.576 47.619 0.00 0.00 34.26 5.01
2673 3597 2.125552 TGCCGCCTCTGAACATCG 60.126 61.111 0.00 0.00 0.00 3.84
2713 3663 5.844004 TCTGGTTCTGTTCAGAAAGACTAC 58.156 41.667 15.44 4.59 37.11 2.73
2723 3679 4.557205 TCAGAAAGACTACCGAAAAGAGC 58.443 43.478 0.00 0.00 0.00 4.09
2724 3680 4.281182 TCAGAAAGACTACCGAAAAGAGCT 59.719 41.667 0.00 0.00 0.00 4.09
2725 3681 5.475909 TCAGAAAGACTACCGAAAAGAGCTA 59.524 40.000 0.00 0.00 0.00 3.32
2726 3682 5.573669 CAGAAAGACTACCGAAAAGAGCTAC 59.426 44.000 0.00 0.00 0.00 3.58
2727 3683 3.761311 AGACTACCGAAAAGAGCTACG 57.239 47.619 0.00 0.00 0.00 3.51
2728 3684 3.341823 AGACTACCGAAAAGAGCTACGA 58.658 45.455 0.00 0.00 0.00 3.43
2783 3850 6.923928 AATGTTTCAAATGGTTTCAGGTTG 57.076 33.333 0.00 0.00 0.00 3.77
3049 4117 0.379669 AGGTTATACCGCAGTCGTCG 59.620 55.000 0.00 0.00 44.90 5.12
3055 4123 2.877360 TACCGCAGTCGTCGCCAATC 62.877 60.000 0.00 0.00 0.00 2.67
3083 4151 5.391416 GCTAAAGCAAGTTGAGGAACATCTC 60.391 44.000 7.16 0.00 41.59 2.75
3084 4152 2.693069 AGCAAGTTGAGGAACATCTCG 58.307 47.619 7.16 0.00 36.61 4.04
3085 4153 2.300152 AGCAAGTTGAGGAACATCTCGA 59.700 45.455 7.16 0.00 36.61 4.04
3180 4264 9.738832 GCTCTAAAAGAGGAATATATCGATACC 57.261 37.037 7.41 4.46 42.54 2.73
3273 4357 6.248569 ACTAGTATATCCCCAAACAAGTGG 57.751 41.667 0.00 0.00 38.51 4.00
3362 4451 9.905713 TTATTTAGCTGTCTTCCATCTGTATTT 57.094 29.630 0.00 0.00 0.00 1.40
3398 4487 3.447918 AATATGCAGCTGCCATTTCAC 57.552 42.857 34.64 6.50 41.18 3.18
3460 4549 6.909158 CCCAAGTAACTCCATATATATCCCCT 59.091 42.308 0.00 0.00 0.00 4.79
3505 4596 8.859236 ATATATGAAAAGATGATGGTCACAGG 57.141 34.615 0.00 0.00 0.00 4.00
3614 6907 1.468914 CTCGTGATCTTGTCGGAGTGA 59.531 52.381 0.00 0.00 0.00 3.41
3615 6908 7.607990 AATCTCGTGATCTTGTCGGAGTGAC 62.608 48.000 0.00 0.00 38.89 3.67
3620 6913 2.873094 TCTTGTCGGAGTGACTAGGA 57.127 50.000 6.64 0.00 46.41 2.94
3670 6963 1.599576 GAGCCAAGAGAGGGGACAC 59.400 63.158 0.00 0.00 0.00 3.67
3703 6996 0.393077 AAGGACAGAAGTGGGTGTCG 59.607 55.000 0.00 0.00 43.45 4.35
3707 7000 1.374758 CAGAAGTGGGTGTCGAGGC 60.375 63.158 0.00 0.00 0.00 4.70
3736 7029 3.260884 TGTTCATTGGTGTCTCCTAGACC 59.739 47.826 4.69 0.00 44.44 3.85
3746 7039 8.209802 TGGTGTCTCCTAGACCTAAAATTTAA 57.790 34.615 4.69 0.00 44.44 1.52
3794 7087 0.373370 CCGTTGATGTGCACATACCG 59.627 55.000 31.45 28.18 36.57 4.02
3803 7096 1.330521 GTGCACATACCGCATAGTTGG 59.669 52.381 13.17 0.00 42.32 3.77
3821 7114 7.261742 ATAGTTGGAGCTATATGGGAGACCTG 61.262 46.154 0.00 0.00 39.52 4.00
3832 7125 1.341156 GGAGACCTGGCCATAGCTGT 61.341 60.000 5.51 0.00 39.73 4.40
3833 7126 0.543749 GAGACCTGGCCATAGCTGTT 59.456 55.000 5.51 0.00 39.73 3.16
3834 7127 1.762957 GAGACCTGGCCATAGCTGTTA 59.237 52.381 5.51 0.00 39.73 2.41
3835 7128 1.765314 AGACCTGGCCATAGCTGTTAG 59.235 52.381 5.51 0.00 39.73 2.34
3836 7129 0.181350 ACCTGGCCATAGCTGTTAGC 59.819 55.000 5.51 0.00 42.84 3.09
3837 7130 0.536006 CCTGGCCATAGCTGTTAGCC 60.536 60.000 5.51 12.92 43.77 3.93
3838 7131 0.471617 CTGGCCATAGCTGTTAGCCT 59.528 55.000 18.62 0.00 43.77 4.58
3839 7132 1.694150 CTGGCCATAGCTGTTAGCCTA 59.306 52.381 18.62 7.62 43.77 3.93
3882 7175 0.108567 GGAGGAAGACGAAGAGTGGC 60.109 60.000 0.00 0.00 0.00 5.01
3883 7176 0.892063 GAGGAAGACGAAGAGTGGCT 59.108 55.000 0.00 0.00 0.00 4.75
3884 7177 1.273886 GAGGAAGACGAAGAGTGGCTT 59.726 52.381 0.00 0.00 40.25 4.35
3885 7178 1.001406 AGGAAGACGAAGAGTGGCTTG 59.999 52.381 0.00 0.00 36.83 4.01
3886 7179 1.433534 GAAGACGAAGAGTGGCTTGG 58.566 55.000 0.00 0.00 36.83 3.61
3887 7180 0.603975 AAGACGAAGAGTGGCTTGGC 60.604 55.000 0.00 0.00 36.83 4.52
3888 7181 1.004440 GACGAAGAGTGGCTTGGCT 60.004 57.895 0.00 0.00 36.83 4.75
3889 7182 0.246635 GACGAAGAGTGGCTTGGCTA 59.753 55.000 0.00 0.00 36.83 3.93
3890 7183 0.247736 ACGAAGAGTGGCTTGGCTAG 59.752 55.000 0.00 0.00 36.83 3.42
3900 7193 1.954927 GCTTGGCTAGCGGATTTACT 58.045 50.000 9.00 0.00 40.71 2.24
3901 7194 3.107642 GCTTGGCTAGCGGATTTACTA 57.892 47.619 9.00 0.00 40.71 1.82
3902 7195 3.060602 GCTTGGCTAGCGGATTTACTAG 58.939 50.000 9.00 0.53 40.71 2.57
3903 7196 3.492829 GCTTGGCTAGCGGATTTACTAGT 60.493 47.826 9.00 0.00 40.71 2.57
3904 7197 4.694339 CTTGGCTAGCGGATTTACTAGTT 58.306 43.478 9.00 0.00 38.50 2.24
3905 7198 4.748277 TGGCTAGCGGATTTACTAGTTT 57.252 40.909 9.00 0.00 38.50 2.66
3906 7199 5.093849 TGGCTAGCGGATTTACTAGTTTT 57.906 39.130 9.00 0.00 38.50 2.43
3907 7200 5.493809 TGGCTAGCGGATTTACTAGTTTTT 58.506 37.500 9.00 0.00 38.50 1.94
3935 7228 3.439857 TTTTGATAGCAAGGGACTGCT 57.560 42.857 3.29 3.29 43.13 4.24
3936 7229 2.408271 TTGATAGCAAGGGACTGCTG 57.592 50.000 8.32 0.00 41.41 4.41
3937 7230 0.543277 TGATAGCAAGGGACTGCTGG 59.457 55.000 8.32 0.00 41.41 4.85
3938 7231 0.833287 GATAGCAAGGGACTGCTGGA 59.167 55.000 8.32 0.00 41.41 3.86
3939 7232 1.210478 GATAGCAAGGGACTGCTGGAA 59.790 52.381 8.32 0.00 41.41 3.53
3940 7233 1.064003 TAGCAAGGGACTGCTGGAAA 58.936 50.000 8.32 0.00 41.41 3.13
3941 7234 0.185901 AGCAAGGGACTGCTGGAAAA 59.814 50.000 0.00 0.00 40.26 2.29
3942 7235 1.203100 AGCAAGGGACTGCTGGAAAAT 60.203 47.619 0.00 0.00 40.26 1.82
3943 7236 1.620323 GCAAGGGACTGCTGGAAAATT 59.380 47.619 0.00 0.00 40.86 1.82
3944 7237 2.353109 GCAAGGGACTGCTGGAAAATTC 60.353 50.000 0.00 0.00 40.86 2.17
3945 7238 1.826385 AGGGACTGCTGGAAAATTCG 58.174 50.000 0.00 0.00 37.18 3.34
3946 7239 1.351017 AGGGACTGCTGGAAAATTCGA 59.649 47.619 0.00 0.00 37.18 3.71
3947 7240 2.159382 GGGACTGCTGGAAAATTCGAA 58.841 47.619 0.00 0.00 0.00 3.71
3948 7241 2.755103 GGGACTGCTGGAAAATTCGAAT 59.245 45.455 4.39 4.39 0.00 3.34
3949 7242 3.181496 GGGACTGCTGGAAAATTCGAATC 60.181 47.826 11.83 0.00 0.00 2.52
3950 7243 3.691609 GGACTGCTGGAAAATTCGAATCT 59.308 43.478 11.83 1.43 0.00 2.40
3951 7244 4.437930 GGACTGCTGGAAAATTCGAATCTG 60.438 45.833 11.83 4.27 0.00 2.90
3952 7245 4.326826 ACTGCTGGAAAATTCGAATCTGA 58.673 39.130 11.83 0.00 0.00 3.27
3953 7246 4.761739 ACTGCTGGAAAATTCGAATCTGAA 59.238 37.500 11.83 0.00 0.00 3.02
3954 7247 5.046910 TGCTGGAAAATTCGAATCTGAAC 57.953 39.130 11.83 2.30 0.00 3.18
3955 7248 4.082787 TGCTGGAAAATTCGAATCTGAACC 60.083 41.667 11.83 11.05 0.00 3.62
3956 7249 4.675408 GCTGGAAAATTCGAATCTGAACCC 60.675 45.833 11.83 7.84 0.00 4.11
3957 7250 3.438781 TGGAAAATTCGAATCTGAACCCG 59.561 43.478 11.83 0.00 0.00 5.28
3958 7251 3.687698 GGAAAATTCGAATCTGAACCCGA 59.312 43.478 11.83 0.00 0.00 5.14
3959 7252 4.201822 GGAAAATTCGAATCTGAACCCGAG 60.202 45.833 11.83 0.00 32.41 4.63
3960 7253 1.941325 ATTCGAATCTGAACCCGAGC 58.059 50.000 4.39 0.00 32.41 5.03
3961 7254 0.895530 TTCGAATCTGAACCCGAGCT 59.104 50.000 0.00 0.00 32.41 4.09
3962 7255 0.895530 TCGAATCTGAACCCGAGCTT 59.104 50.000 0.00 0.00 0.00 3.74
3963 7256 2.097036 TCGAATCTGAACCCGAGCTTA 58.903 47.619 0.00 0.00 0.00 3.09
3964 7257 2.693591 TCGAATCTGAACCCGAGCTTAT 59.306 45.455 0.00 0.00 0.00 1.73
3965 7258 3.053455 CGAATCTGAACCCGAGCTTATC 58.947 50.000 0.00 0.00 0.00 1.75
3966 7259 3.243569 CGAATCTGAACCCGAGCTTATCT 60.244 47.826 0.00 0.00 0.00 1.98
3967 7260 3.742433 ATCTGAACCCGAGCTTATCTG 57.258 47.619 0.00 0.00 0.00 2.90
3968 7261 1.137086 TCTGAACCCGAGCTTATCTGC 59.863 52.381 0.00 0.00 0.00 4.26
3969 7262 0.901827 TGAACCCGAGCTTATCTGCA 59.098 50.000 0.00 0.00 34.99 4.41
3970 7263 1.291132 GAACCCGAGCTTATCTGCAC 58.709 55.000 0.00 0.00 34.99 4.57
3971 7264 0.107654 AACCCGAGCTTATCTGCACC 60.108 55.000 0.00 0.00 34.99 5.01
3972 7265 0.978146 ACCCGAGCTTATCTGCACCT 60.978 55.000 0.00 0.00 34.99 4.00
3973 7266 0.531532 CCCGAGCTTATCTGCACCTG 60.532 60.000 0.00 0.00 34.99 4.00
3974 7267 1.156645 CCGAGCTTATCTGCACCTGC 61.157 60.000 0.00 0.00 42.50 4.85
3975 7268 1.485838 CGAGCTTATCTGCACCTGCG 61.486 60.000 0.00 0.00 45.83 5.18
3976 7269 1.770085 GAGCTTATCTGCACCTGCGC 61.770 60.000 0.00 0.00 45.83 6.09
3977 7270 1.817099 GCTTATCTGCACCTGCGCT 60.817 57.895 9.73 0.00 45.83 5.92
3978 7271 1.770085 GCTTATCTGCACCTGCGCTC 61.770 60.000 9.73 0.00 45.83 5.03
3979 7272 0.460811 CTTATCTGCACCTGCGCTCA 60.461 55.000 9.73 0.00 45.83 4.26
3980 7273 0.740868 TTATCTGCACCTGCGCTCAC 60.741 55.000 9.73 0.00 45.83 3.51
3981 7274 2.889154 TATCTGCACCTGCGCTCACG 62.889 60.000 9.73 0.00 45.83 4.35
3983 7276 4.600576 TGCACCTGCGCTCACGAA 62.601 61.111 9.73 0.00 45.83 3.85
3984 7277 3.345808 GCACCTGCGCTCACGAAA 61.346 61.111 9.73 0.00 43.93 3.46
3985 7278 2.892334 GCACCTGCGCTCACGAAAA 61.892 57.895 9.73 0.00 43.93 2.29
3986 7279 1.646540 CACCTGCGCTCACGAAAAA 59.353 52.632 9.73 0.00 43.93 1.94
4050 7343 6.676237 AAAATTTGTGTGGTGGACAATTTC 57.324 33.333 0.00 0.00 35.91 2.17
4051 7344 5.350504 AATTTGTGTGGTGGACAATTTCA 57.649 34.783 0.00 0.00 35.91 2.69
4052 7345 5.549742 ATTTGTGTGGTGGACAATTTCAT 57.450 34.783 0.00 0.00 35.91 2.57
4053 7346 4.319139 TTGTGTGGTGGACAATTTCATG 57.681 40.909 0.00 0.00 35.91 3.07
4054 7347 2.035704 TGTGTGGTGGACAATTTCATGC 59.964 45.455 0.00 0.00 35.91 4.06
4055 7348 1.269174 TGTGGTGGACAATTTCATGCG 59.731 47.619 0.00 0.00 0.00 4.73
4056 7349 1.269448 GTGGTGGACAATTTCATGCGT 59.731 47.619 0.00 0.00 0.00 5.24
4057 7350 1.269174 TGGTGGACAATTTCATGCGTG 59.731 47.619 0.00 0.00 0.00 5.34
4058 7351 1.539388 GGTGGACAATTTCATGCGTGA 59.461 47.619 3.97 3.97 0.00 4.35
4059 7352 2.414559 GGTGGACAATTTCATGCGTGAG 60.415 50.000 8.93 0.00 35.39 3.51
4060 7353 1.811965 TGGACAATTTCATGCGTGAGG 59.188 47.619 8.93 3.39 35.39 3.86
4061 7354 1.812571 GGACAATTTCATGCGTGAGGT 59.187 47.619 8.93 6.52 35.39 3.85
4062 7355 3.006940 GGACAATTTCATGCGTGAGGTA 58.993 45.455 8.93 0.00 35.39 3.08
4063 7356 3.181510 GGACAATTTCATGCGTGAGGTAC 60.182 47.826 8.93 3.94 35.39 3.34
4072 7365 3.436001 CGTGAGGTACGCTCCAATT 57.564 52.632 8.36 0.00 46.92 2.32
4073 7366 1.722011 CGTGAGGTACGCTCCAATTT 58.278 50.000 8.36 0.00 46.92 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 101 9.049523 GCGGCCTTTATTAATACTAGTAGTTTT 57.950 33.333 8.34 9.55 0.00 2.43
99 102 7.658982 GGCGGCCTTTATTAATACTAGTAGTTT 59.341 37.037 12.87 1.11 0.00 2.66
100 103 7.157347 GGCGGCCTTTATTAATACTAGTAGTT 58.843 38.462 12.87 5.65 0.00 2.24
101 104 6.295518 GGGCGGCCTTTATTAATACTAGTAGT 60.296 42.308 22.87 8.47 0.00 2.73
102 105 6.070938 AGGGCGGCCTTTATTAATACTAGTAG 60.071 42.308 27.45 0.00 0.00 2.57
103 106 5.781818 AGGGCGGCCTTTATTAATACTAGTA 59.218 40.000 27.45 4.77 0.00 1.82
104 107 4.596212 AGGGCGGCCTTTATTAATACTAGT 59.404 41.667 27.45 0.00 0.00 2.57
105 108 5.046520 AGAGGGCGGCCTTTATTAATACTAG 60.047 44.000 33.28 0.00 0.00 2.57
106 109 4.842380 AGAGGGCGGCCTTTATTAATACTA 59.158 41.667 33.28 0.00 0.00 1.82
107 110 3.651423 AGAGGGCGGCCTTTATTAATACT 59.349 43.478 33.28 17.77 0.00 2.12
111 114 1.749286 GCAGAGGGCGGCCTTTATTAA 60.749 52.381 33.28 0.00 0.00 1.40
127 130 1.123861 AGCTGACAAGGACAGGCAGA 61.124 55.000 0.00 0.00 36.09 4.26
128 131 0.610174 TAGCTGACAAGGACAGGCAG 59.390 55.000 0.00 0.00 36.09 4.85
129 132 0.321671 GTAGCTGACAAGGACAGGCA 59.678 55.000 0.00 0.00 36.09 4.75
130 133 0.610687 AGTAGCTGACAAGGACAGGC 59.389 55.000 0.00 0.00 36.09 4.85
131 134 1.895798 TCAGTAGCTGACAAGGACAGG 59.104 52.381 0.00 0.00 35.39 4.00
136 140 6.701145 TTCTACTATCAGTAGCTGACAAGG 57.299 41.667 8.23 0.00 45.93 3.61
192 196 1.807165 CACCGTGAGTGGATCGCAG 60.807 63.158 0.00 0.00 43.26 5.18
238 242 3.763360 TGTTTTCTAATCACATGGCAGGG 59.237 43.478 3.46 0.00 0.00 4.45
286 290 4.078516 AGTTCTACGCCGGCACCC 62.079 66.667 28.98 7.34 0.00 4.61
323 327 2.544072 TGCAGAGCAATGCTACACAGC 61.544 52.381 8.12 5.25 46.63 4.40
325 329 1.894881 TTGCAGAGCAATGCTACACA 58.105 45.000 8.12 3.38 43.99 3.72
350 354 3.006967 TGAACAAGTCCAAGACCTCTAGC 59.993 47.826 0.00 0.00 32.18 3.42
392 400 2.221169 CAGCAGACTACAACAGGCAAA 58.779 47.619 0.00 0.00 32.94 3.68
475 484 4.111577 TCTTCCCCTTATGTTCCATCACT 58.888 43.478 0.00 0.00 0.00 3.41
480 489 2.580322 TGCATCTTCCCCTTATGTTCCA 59.420 45.455 0.00 0.00 0.00 3.53
485 494 3.565764 TGAGTGCATCTTCCCCTTATG 57.434 47.619 0.00 0.00 0.00 1.90
503 512 1.001520 TCTGTCGCCGAAAAAGGATGA 59.998 47.619 0.00 0.00 0.00 2.92
559 573 0.770499 TGGACCCATCTGAACAAGCA 59.230 50.000 0.00 0.00 0.00 3.91
560 574 1.909700 TTGGACCCATCTGAACAAGC 58.090 50.000 0.00 0.00 0.00 4.01
561 575 5.256474 AGTATTTGGACCCATCTGAACAAG 58.744 41.667 0.00 0.00 0.00 3.16
562 576 5.255397 AGTATTTGGACCCATCTGAACAA 57.745 39.130 0.00 0.00 0.00 2.83
563 577 4.927267 AGTATTTGGACCCATCTGAACA 57.073 40.909 0.00 0.00 0.00 3.18
564 578 5.010282 ACAAGTATTTGGACCCATCTGAAC 58.990 41.667 2.81 0.00 38.66 3.18
565 579 5.009631 CACAAGTATTTGGACCCATCTGAA 58.990 41.667 2.81 0.00 38.66 3.02
566 580 4.567537 CCACAAGTATTTGGACCCATCTGA 60.568 45.833 2.81 0.00 38.66 3.27
567 581 3.696051 CCACAAGTATTTGGACCCATCTG 59.304 47.826 2.81 0.00 38.66 2.90
568 582 3.333680 ACCACAAGTATTTGGACCCATCT 59.666 43.478 2.81 0.00 38.66 2.90
569 583 3.694566 GACCACAAGTATTTGGACCCATC 59.305 47.826 2.81 0.00 38.66 3.51
582 596 4.910195 TGAATGAAGCATAGACCACAAGT 58.090 39.130 0.00 0.00 0.00 3.16
686 700 8.215926 TCTAGTCTTCTACTACAGAATCTTGC 57.784 38.462 0.00 0.00 42.44 4.01
743 761 8.575589 TGCAGATAACACTACAAAATGACAATT 58.424 29.630 0.00 0.00 0.00 2.32
769 822 6.876257 TGTTTTCTGCCAAATTACAACAGTTT 59.124 30.769 0.00 0.00 0.00 2.66
809 862 6.265196 AGGTCAGAGATCATGTAGTGAGATTC 59.735 42.308 0.00 0.00 40.92 2.52
837 890 5.675684 AAGTGGTTTCAAATCAAGTTGGT 57.324 34.783 2.34 0.00 0.00 3.67
838 891 6.340522 AGAAAGTGGTTTCAAATCAAGTTGG 58.659 36.000 2.34 0.00 44.08 3.77
840 893 7.122650 TGAGAGAAAGTGGTTTCAAATCAAGTT 59.877 33.333 0.00 0.00 44.08 2.66
842 895 7.012704 TCTGAGAGAAAGTGGTTTCAAATCAAG 59.987 37.037 0.00 0.00 44.08 3.02
843 896 6.828273 TCTGAGAGAAAGTGGTTTCAAATCAA 59.172 34.615 0.00 0.00 44.08 2.57
860 919 4.462508 AATTCATCGTGCTTCTGAGAGA 57.537 40.909 0.00 0.00 0.00 3.10
867 926 8.452989 ACTTCAAAATAAATTCATCGTGCTTC 57.547 30.769 0.00 0.00 0.00 3.86
871 930 9.611284 TCTGAACTTCAAAATAAATTCATCGTG 57.389 29.630 0.00 0.00 0.00 4.35
938 1003 8.523464 GCGAAATGATGATAAATTAACACACAC 58.477 33.333 0.00 0.00 0.00 3.82
955 1020 5.389859 TCAACCTTCAAATGCGAAATGAT 57.610 34.783 0.00 0.00 0.00 2.45
963 1030 1.340889 TGTGGCTCAACCTTCAAATGC 59.659 47.619 0.00 0.00 40.22 3.56
981 1048 6.428159 GGAACATGATGTCTTCAACTTACTGT 59.572 38.462 0.00 0.00 38.03 3.55
1005 1072 3.782042 GAAGCGTGCTTCCTACGG 58.218 61.111 21.13 0.00 44.76 4.02
1069 1136 6.661805 AGAGTAACCAAAACCTGACTTTCAAA 59.338 34.615 0.00 0.00 0.00 2.69
1182 1256 9.273016 AGTATTACTGGTGCATATGTTATCAAC 57.727 33.333 4.29 0.00 0.00 3.18
1253 1327 9.927668 TCCCATGTTAATCTCATTTTCTTTTTC 57.072 29.630 0.00 0.00 0.00 2.29
1257 1331 8.534496 CCTTTCCCATGTTAATCTCATTTTCTT 58.466 33.333 0.00 0.00 0.00 2.52
1273 1347 9.825109 TTTAAGTTTTTCTTTACCTTTCCCATG 57.175 29.630 0.00 0.00 37.56 3.66
1298 1373 5.619981 GCTGAAGTTGTCACACTGAAACTTT 60.620 40.000 1.60 0.00 37.58 2.66
1329 1404 3.483421 TGCATATGAGATGGAAGCTTGG 58.517 45.455 2.10 0.00 22.26 3.61
1371 1479 4.527509 TGTTCAGGTTCAAAGTTTTGCA 57.472 36.364 0.00 0.00 38.05 4.08
1391 1499 5.157940 ACCATTCAGGCTACTATGCTATG 57.842 43.478 0.00 0.00 43.14 2.23
1440 1558 6.826668 TGGGTGATTACTTACATGTATCTGG 58.173 40.000 6.36 0.80 0.00 3.86
1480 1671 5.940192 ATGTCAAACTATTTGTCTCGCAA 57.060 34.783 1.50 0.00 41.36 4.85
1537 1728 9.933723 CATATTGTCACAGTATCATTCCTATCA 57.066 33.333 0.00 0.00 0.00 2.15
1541 1732 8.928448 AGTACATATTGTCACAGTATCATTCCT 58.072 33.333 0.00 0.00 0.00 3.36
1593 1784 7.251281 TCAGTAGTCAATGTAAGATCTGAACG 58.749 38.462 0.00 0.00 0.00 3.95
1609 1800 9.677567 GCAAAACTAAATTTCATTCAGTAGTCA 57.322 29.630 0.00 0.00 0.00 3.41
1623 1814 5.189180 TGGGCTTTTGTGCAAAACTAAATT 58.811 33.333 6.04 0.00 35.57 1.82
1627 1818 5.537300 TTATGGGCTTTTGTGCAAAACTA 57.463 34.783 6.04 0.00 35.57 2.24
1628 1819 4.414337 TTATGGGCTTTTGTGCAAAACT 57.586 36.364 6.04 0.00 35.57 2.66
1651 1842 8.177119 ACATTTCACACTCCTAAAAATGCTAA 57.823 30.769 6.14 0.00 39.68 3.09
1663 1854 4.686554 GTGTAGTCAGACATTTCACACTCC 59.313 45.833 2.66 0.00 33.69 3.85
1676 1874 6.156748 TGTAGAAAAGCTTGTGTAGTCAGA 57.843 37.500 0.00 0.00 0.00 3.27
1677 1875 6.425114 ACATGTAGAAAAGCTTGTGTAGTCAG 59.575 38.462 0.00 0.00 0.00 3.51
1678 1876 6.202762 CACATGTAGAAAAGCTTGTGTAGTCA 59.797 38.462 0.00 0.00 36.58 3.41
1679 1877 6.593978 CACATGTAGAAAAGCTTGTGTAGTC 58.406 40.000 0.00 0.00 36.58 2.59
1680 1878 5.049405 GCACATGTAGAAAAGCTTGTGTAGT 60.049 40.000 0.00 0.00 40.57 2.73
1681 1879 5.180117 AGCACATGTAGAAAAGCTTGTGTAG 59.820 40.000 0.00 0.00 40.57 2.74
1734 1936 1.270678 GGGGGCTATGTTGTATCGGAC 60.271 57.143 0.00 0.00 0.00 4.79
1735 1937 1.053424 GGGGGCTATGTTGTATCGGA 58.947 55.000 0.00 0.00 0.00 4.55
1736 1938 1.056660 AGGGGGCTATGTTGTATCGG 58.943 55.000 0.00 0.00 0.00 4.18
1737 1939 2.550208 GGAAGGGGGCTATGTTGTATCG 60.550 54.545 0.00 0.00 0.00 2.92
1738 1940 2.550208 CGGAAGGGGGCTATGTTGTATC 60.550 54.545 0.00 0.00 0.00 2.24
1739 1941 1.420138 CGGAAGGGGGCTATGTTGTAT 59.580 52.381 0.00 0.00 0.00 2.29
1740 1942 0.834612 CGGAAGGGGGCTATGTTGTA 59.165 55.000 0.00 0.00 0.00 2.41
1741 1943 1.205460 ACGGAAGGGGGCTATGTTGT 61.205 55.000 0.00 0.00 0.00 3.32
1762 1964 2.703007 AGAAAGCTCCTGTAGGCTATGG 59.297 50.000 0.00 3.82 37.87 2.74
1764 1966 5.841237 TCATAAGAAAGCTCCTGTAGGCTAT 59.159 40.000 0.00 0.00 37.87 2.97
1765 1967 5.208890 TCATAAGAAAGCTCCTGTAGGCTA 58.791 41.667 0.00 0.00 37.87 3.93
1771 1973 9.171877 CTAAAGAATTCATAAGAAAGCTCCTGT 57.828 33.333 8.44 0.00 37.29 4.00
1791 1993 7.741785 TCCACTTAACTGGAAACATCTAAAGA 58.258 34.615 1.68 0.00 41.51 2.52
1810 2012 0.109723 TTGCTTACGGGCTTCCACTT 59.890 50.000 0.00 0.00 0.00 3.16
1834 2036 4.080526 ACAAGAACTACGGGCTTCCATATT 60.081 41.667 0.00 0.00 0.00 1.28
1837 2039 1.628846 ACAAGAACTACGGGCTTCCAT 59.371 47.619 0.00 0.00 0.00 3.41
1838 2040 1.001633 GACAAGAACTACGGGCTTCCA 59.998 52.381 0.00 0.00 0.00 3.53
1839 2041 1.001633 TGACAAGAACTACGGGCTTCC 59.998 52.381 0.00 0.00 0.00 3.46
1840 2042 2.450609 TGACAAGAACTACGGGCTTC 57.549 50.000 0.00 0.00 0.00 3.86
1842 2044 2.367567 TCTTTGACAAGAACTACGGGCT 59.632 45.455 0.00 0.00 35.99 5.19
1843 2045 2.479275 GTCTTTGACAAGAACTACGGGC 59.521 50.000 0.00 0.00 40.90 6.13
1844 2046 3.724374 TGTCTTTGACAAGAACTACGGG 58.276 45.455 0.00 0.00 40.90 5.28
1874 2076 5.551760 AACGAAAGATGCAGATACCAAAG 57.448 39.130 0.00 0.00 0.00 2.77
1875 2077 7.041030 TGTTTAACGAAAGATGCAGATACCAAA 60.041 33.333 0.00 0.00 0.00 3.28
1893 2095 9.165014 ACGCAAAAATAGCATATATGTTTAACG 57.835 29.630 14.14 13.80 0.00 3.18
1916 2121 4.678509 TTGTTACATGAGAAATGGACGC 57.321 40.909 0.00 0.00 0.00 5.19
2041 2247 4.072131 ACTTGTCAATATTCCAGTTGCGT 58.928 39.130 0.00 0.00 0.00 5.24
2054 2260 7.004086 TCCAACATTTTCCTAGACTTGTCAAT 58.996 34.615 3.49 0.00 0.00 2.57
2139 2350 2.991866 GAGCATTGCAAGGAAGAAAAGC 59.008 45.455 16.56 2.76 0.00 3.51
2174 2392 5.941058 TGTTTGGTTACTTGACTGTCTTTGA 59.059 36.000 9.51 0.00 0.00 2.69
2179 2397 6.619801 AGAATGTTTGGTTACTTGACTGTC 57.380 37.500 0.00 0.00 0.00 3.51
2182 2400 8.062065 TCAAAAGAATGTTTGGTTACTTGACT 57.938 30.769 0.00 0.00 38.72 3.41
2183 2401 8.871686 ATCAAAAGAATGTTTGGTTACTTGAC 57.128 30.769 0.00 0.00 38.72 3.18
2555 2815 2.113860 TATTTGCACTGTCTCTGGCC 57.886 50.000 0.00 0.00 0.00 5.36
2639 3559 1.468914 GGCACCTTAAAGAAAGCCTCG 59.531 52.381 0.00 0.00 39.02 4.63
2658 3578 0.103026 TGATCGATGTTCAGAGGCGG 59.897 55.000 0.54 0.00 0.00 6.13
2673 3597 7.659390 CAGAACCAGAGTAATAAAGGGATGATC 59.341 40.741 0.00 0.00 0.00 2.92
2713 3663 6.579292 CAGAATATAGTCGTAGCTCTTTTCGG 59.421 42.308 0.00 0.00 0.00 4.30
2723 3679 9.175060 CATCAGAAACACAGAATATAGTCGTAG 57.825 37.037 0.00 0.00 0.00 3.51
2724 3680 8.683615 ACATCAGAAACACAGAATATAGTCGTA 58.316 33.333 0.00 0.00 0.00 3.43
2725 3681 7.548097 ACATCAGAAACACAGAATATAGTCGT 58.452 34.615 0.00 0.00 0.00 4.34
2726 3682 7.993821 ACATCAGAAACACAGAATATAGTCG 57.006 36.000 0.00 0.00 0.00 4.18
2727 3683 8.821894 GGAACATCAGAAACACAGAATATAGTC 58.178 37.037 0.00 0.00 0.00 2.59
2728 3684 8.321353 TGGAACATCAGAAACACAGAATATAGT 58.679 33.333 0.00 0.00 0.00 2.12
2783 3850 3.469739 TCGGGTCAAGGAACACTTTTAC 58.530 45.455 0.00 0.00 37.29 2.01
3083 4151 1.226802 CAGGTGAGATGGCTCGTCG 60.227 63.158 0.00 0.00 44.33 5.12
3084 4152 1.520342 GCAGGTGAGATGGCTCGTC 60.520 63.158 0.00 0.00 44.33 4.20
3085 4153 0.684479 TAGCAGGTGAGATGGCTCGT 60.684 55.000 0.00 0.00 44.33 4.18
3214 4298 7.609760 TTGTAACATCACAAGCGAGATATTT 57.390 32.000 0.00 0.00 33.55 1.40
3273 4357 4.636206 GGGAATATGGAACTGTTGTGAGAC 59.364 45.833 0.00 0.00 0.00 3.36
3362 4451 9.613428 AGCTGCATATTACAGATTTAAGTGTAA 57.387 29.630 1.02 8.67 41.98 2.41
3374 4463 4.037089 TGAAATGGCAGCTGCATATTACAG 59.963 41.667 37.63 0.00 44.36 2.74
3502 4593 2.814805 ATGGACATGAGGTTTCCCTG 57.185 50.000 0.00 0.00 42.86 4.45
3505 4596 8.697507 AAATAGATAATGGACATGAGGTTTCC 57.302 34.615 0.00 0.00 0.00 3.13
3544 6837 4.067896 CAACCAGAGAGAAAAGCAGCTAA 58.932 43.478 0.00 0.00 0.00 3.09
3547 6840 1.068679 GCAACCAGAGAGAAAAGCAGC 60.069 52.381 0.00 0.00 0.00 5.25
3574 6867 9.112725 TCACGAGATTGATTATGAATTGATTGT 57.887 29.630 0.00 0.00 0.00 2.71
3614 6907 4.373156 AACTTTGCCTCACAATCCTAGT 57.627 40.909 0.00 0.00 38.31 2.57
3615 6908 5.051891 CAAACTTTGCCTCACAATCCTAG 57.948 43.478 0.00 0.00 38.31 3.02
3703 6996 2.827921 ACCAATGAACATCCAAAGCCTC 59.172 45.455 0.00 0.00 0.00 4.70
3707 7000 4.082571 GGAGACACCAATGAACATCCAAAG 60.083 45.833 0.00 0.00 38.79 2.77
3736 7029 9.099454 AGCCGACAGATTAGACTTAAATTTTAG 57.901 33.333 0.00 0.00 0.00 1.85
3746 7039 2.691011 GAGGAAGCCGACAGATTAGACT 59.309 50.000 0.00 0.00 0.00 3.24
3788 7081 2.533266 AGCTCCAACTATGCGGTATG 57.467 50.000 0.00 0.00 0.00 2.39
3794 7087 4.467795 TCTCCCATATAGCTCCAACTATGC 59.532 45.833 0.00 0.00 34.66 3.14
3803 7096 1.552792 GCCAGGTCTCCCATATAGCTC 59.447 57.143 0.00 0.00 0.00 4.09
3821 7114 3.425162 AATAGGCTAACAGCTATGGCC 57.575 47.619 15.74 15.74 41.99 5.36
3829 7122 9.227777 ACAACCTTAACTTTAATAGGCTAACAG 57.772 33.333 0.00 0.00 0.00 3.16
3832 7125 7.612633 CCCACAACCTTAACTTTAATAGGCTAA 59.387 37.037 0.00 0.00 0.00 3.09
3833 7126 7.037442 TCCCACAACCTTAACTTTAATAGGCTA 60.037 37.037 0.00 0.00 0.00 3.93
3834 7127 5.949952 CCCACAACCTTAACTTTAATAGGCT 59.050 40.000 0.00 0.00 0.00 4.58
3835 7128 5.947566 TCCCACAACCTTAACTTTAATAGGC 59.052 40.000 0.00 0.00 0.00 3.93
3836 7129 7.336176 GTCTCCCACAACCTTAACTTTAATAGG 59.664 40.741 0.00 0.00 0.00 2.57
3837 7130 7.064253 CGTCTCCCACAACCTTAACTTTAATAG 59.936 40.741 0.00 0.00 0.00 1.73
3838 7131 6.875195 CGTCTCCCACAACCTTAACTTTAATA 59.125 38.462 0.00 0.00 0.00 0.98
3839 7132 5.704053 CGTCTCCCACAACCTTAACTTTAAT 59.296 40.000 0.00 0.00 0.00 1.40
3882 7175 4.323553 ACTAGTAAATCCGCTAGCCAAG 57.676 45.455 9.66 0.00 38.50 3.61
3883 7176 4.748277 AACTAGTAAATCCGCTAGCCAA 57.252 40.909 9.66 0.00 38.50 4.52
3884 7177 4.748277 AAACTAGTAAATCCGCTAGCCA 57.252 40.909 9.66 0.00 38.50 4.75
3923 7216 1.260544 ATTTTCCAGCAGTCCCTTGC 58.739 50.000 0.00 0.00 44.41 4.01
3924 7217 2.095059 CGAATTTTCCAGCAGTCCCTTG 60.095 50.000 0.00 0.00 0.00 3.61
3925 7218 2.162681 CGAATTTTCCAGCAGTCCCTT 58.837 47.619 0.00 0.00 0.00 3.95
3926 7219 1.351017 TCGAATTTTCCAGCAGTCCCT 59.649 47.619 0.00 0.00 0.00 4.20
3927 7220 1.821216 TCGAATTTTCCAGCAGTCCC 58.179 50.000 0.00 0.00 0.00 4.46
3928 7221 3.691609 AGATTCGAATTTTCCAGCAGTCC 59.308 43.478 12.81 0.00 0.00 3.85
3929 7222 4.393062 TCAGATTCGAATTTTCCAGCAGTC 59.607 41.667 12.81 0.00 0.00 3.51
3930 7223 4.326826 TCAGATTCGAATTTTCCAGCAGT 58.673 39.130 12.81 0.00 0.00 4.40
3931 7224 4.952262 TCAGATTCGAATTTTCCAGCAG 57.048 40.909 12.81 0.00 0.00 4.24
3932 7225 4.082787 GGTTCAGATTCGAATTTTCCAGCA 60.083 41.667 12.81 0.00 0.00 4.41
3933 7226 4.415735 GGTTCAGATTCGAATTTTCCAGC 58.584 43.478 12.81 2.36 0.00 4.85
3934 7227 4.437390 CGGGTTCAGATTCGAATTTTCCAG 60.437 45.833 12.81 7.99 0.00 3.86
3935 7228 3.438781 CGGGTTCAGATTCGAATTTTCCA 59.561 43.478 12.81 0.00 0.00 3.53
3936 7229 3.687698 TCGGGTTCAGATTCGAATTTTCC 59.312 43.478 12.81 10.36 0.00 3.13
3937 7230 4.728021 GCTCGGGTTCAGATTCGAATTTTC 60.728 45.833 12.81 0.03 0.00 2.29
3938 7231 3.127030 GCTCGGGTTCAGATTCGAATTTT 59.873 43.478 12.81 1.04 0.00 1.82
3939 7232 2.678336 GCTCGGGTTCAGATTCGAATTT 59.322 45.455 12.81 3.29 0.00 1.82
3940 7233 2.093447 AGCTCGGGTTCAGATTCGAATT 60.093 45.455 12.81 0.00 0.00 2.17
3941 7234 1.482593 AGCTCGGGTTCAGATTCGAAT 59.517 47.619 11.20 11.20 0.00 3.34
3942 7235 0.895530 AGCTCGGGTTCAGATTCGAA 59.104 50.000 0.00 0.00 0.00 3.71
3943 7236 0.895530 AAGCTCGGGTTCAGATTCGA 59.104 50.000 0.00 0.00 0.00 3.71
3944 7237 2.579207 TAAGCTCGGGTTCAGATTCG 57.421 50.000 0.00 0.00 0.00 3.34
3945 7238 4.054671 CAGATAAGCTCGGGTTCAGATTC 58.945 47.826 0.00 0.00 0.00 2.52
3946 7239 3.742640 GCAGATAAGCTCGGGTTCAGATT 60.743 47.826 0.00 0.00 0.00 2.40
3947 7240 2.224161 GCAGATAAGCTCGGGTTCAGAT 60.224 50.000 0.00 0.00 0.00 2.90
3948 7241 1.137086 GCAGATAAGCTCGGGTTCAGA 59.863 52.381 0.00 0.00 0.00 3.27
3949 7242 1.134699 TGCAGATAAGCTCGGGTTCAG 60.135 52.381 0.00 0.00 34.99 3.02
3950 7243 0.901827 TGCAGATAAGCTCGGGTTCA 59.098 50.000 0.00 0.00 34.99 3.18
3951 7244 1.291132 GTGCAGATAAGCTCGGGTTC 58.709 55.000 0.00 0.00 34.99 3.62
3952 7245 0.107654 GGTGCAGATAAGCTCGGGTT 60.108 55.000 0.00 0.00 34.99 4.11
3953 7246 0.978146 AGGTGCAGATAAGCTCGGGT 60.978 55.000 0.00 0.00 34.99 5.28
3954 7247 0.531532 CAGGTGCAGATAAGCTCGGG 60.532 60.000 0.00 0.00 34.99 5.14
3955 7248 1.156645 GCAGGTGCAGATAAGCTCGG 61.157 60.000 0.00 0.00 41.59 4.63
3956 7249 1.485838 CGCAGGTGCAGATAAGCTCG 61.486 60.000 2.33 0.00 42.21 5.03
3957 7250 1.770085 GCGCAGGTGCAGATAAGCTC 61.770 60.000 0.30 0.00 42.21 4.09
3958 7251 1.817099 GCGCAGGTGCAGATAAGCT 60.817 57.895 0.30 0.00 42.21 3.74
3959 7252 1.770085 GAGCGCAGGTGCAGATAAGC 61.770 60.000 11.47 0.00 39.88 3.09
3960 7253 0.460811 TGAGCGCAGGTGCAGATAAG 60.461 55.000 11.47 0.00 39.88 1.73
3961 7254 0.740868 GTGAGCGCAGGTGCAGATAA 60.741 55.000 11.47 0.00 39.88 1.75
3962 7255 1.153568 GTGAGCGCAGGTGCAGATA 60.154 57.895 11.47 0.00 39.88 1.98
3963 7256 2.435586 GTGAGCGCAGGTGCAGAT 60.436 61.111 11.47 0.00 39.88 2.90
3966 7259 4.600576 TTCGTGAGCGCAGGTGCA 62.601 61.111 11.47 0.00 39.88 4.57
3967 7260 2.387125 TTTTTCGTGAGCGCAGGTGC 62.387 55.000 11.47 0.00 39.88 5.01
3968 7261 1.646540 TTTTTCGTGAGCGCAGGTG 59.353 52.632 11.47 0.00 39.88 4.00
3969 7262 4.134623 TTTTTCGTGAGCGCAGGT 57.865 50.000 11.47 0.00 46.54 4.00
4026 7319 6.656693 TGAAATTGTCCACCACACAAATTTTT 59.343 30.769 0.00 0.00 37.30 1.94
4027 7320 6.176183 TGAAATTGTCCACCACACAAATTTT 58.824 32.000 0.00 0.00 37.30 1.82
4028 7321 5.738909 TGAAATTGTCCACCACACAAATTT 58.261 33.333 0.00 0.00 37.30 1.82
4029 7322 5.350504 TGAAATTGTCCACCACACAAATT 57.649 34.783 0.00 0.00 37.30 1.82
4030 7323 5.299148 CATGAAATTGTCCACCACACAAAT 58.701 37.500 0.00 0.00 37.30 2.32
4031 7324 4.691175 CATGAAATTGTCCACCACACAAA 58.309 39.130 0.00 0.00 37.30 2.83
4032 7325 3.492309 GCATGAAATTGTCCACCACACAA 60.492 43.478 0.00 0.00 38.12 3.33
4033 7326 2.035704 GCATGAAATTGTCCACCACACA 59.964 45.455 0.00 0.00 33.41 3.72
4034 7327 2.676076 GCATGAAATTGTCCACCACAC 58.324 47.619 0.00 0.00 33.41 3.82
4035 7328 1.269174 CGCATGAAATTGTCCACCACA 59.731 47.619 0.00 0.00 0.00 4.17
4036 7329 1.269448 ACGCATGAAATTGTCCACCAC 59.731 47.619 0.00 0.00 0.00 4.16
4037 7330 1.269174 CACGCATGAAATTGTCCACCA 59.731 47.619 0.00 0.00 0.00 4.17
4038 7331 1.539388 TCACGCATGAAATTGTCCACC 59.461 47.619 0.00 0.00 0.00 4.61
4039 7332 2.414559 CCTCACGCATGAAATTGTCCAC 60.415 50.000 0.00 0.00 33.30 4.02
4040 7333 1.811965 CCTCACGCATGAAATTGTCCA 59.188 47.619 0.00 0.00 33.30 4.02
4041 7334 1.812571 ACCTCACGCATGAAATTGTCC 59.187 47.619 0.00 0.00 33.30 4.02
4042 7335 3.483574 CGTACCTCACGCATGAAATTGTC 60.484 47.826 0.00 0.00 45.03 3.18
4043 7336 2.415168 CGTACCTCACGCATGAAATTGT 59.585 45.455 0.00 0.00 45.03 2.71
4044 7337 3.038352 CGTACCTCACGCATGAAATTG 57.962 47.619 0.00 0.00 45.03 2.32


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

AutoCloner maintained by Alex Coulton.