Multiple sequence alignment - TraesCS2A01G495200

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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 TraesCS2A01G495200 chr2A 100.000 6267 0 0 1 6267 726760872 726767138 0.000000e+00 11574.0
1 TraesCS2A01G495200 chr2A 83.293 413 56 7 2716 3115 728076861 728076449 9.930000e-98 368.0
2 TraesCS2A01G495200 chr2A 87.379 309 30 5 2372 2676 728077177 728076874 4.650000e-91 346.0
3 TraesCS2A01G495200 chr2A 84.110 365 36 14 3308 3669 728076140 728075795 3.620000e-87 333.0
4 TraesCS2A01G495200 chr2A 76.257 716 108 29 3755 4417 728075751 728075045 2.180000e-84 324.0
5 TraesCS2A01G495200 chr2A 87.402 254 30 2 1831 2084 728078035 728077784 2.210000e-74 291.0
6 TraesCS2A01G495200 chr2A 80.982 326 49 8 4554 4878 728074896 728074583 4.850000e-61 246.0
7 TraesCS2A01G495200 chr2A 90.625 128 12 0 1670 1797 728078254 728078127 3.000000e-38 171.0
8 TraesCS2A01G495200 chr2D 94.328 3332 145 21 2463 5763 592283982 592287300 0.000000e+00 5066.0
9 TraesCS2A01G495200 chr2D 90.355 394 35 2 917 1310 592283390 592283780 1.200000e-141 514.0
10 TraesCS2A01G495200 chr2D 91.644 371 31 0 5897 6267 592287495 592287865 1.200000e-141 514.0
11 TraesCS2A01G495200 chr2D 87.004 277 18 11 26 300 592282632 592282892 4.750000e-76 296.0
12 TraesCS2A01G495200 chr2D 96.970 132 3 1 2334 2464 592283799 592283930 2.940000e-53 220.0
13 TraesCS2A01G495200 chr2D 92.958 142 9 1 5759 5899 592287327 592287468 8.240000e-49 206.0
14 TraesCS2A01G495200 chr2D 80.303 264 26 14 364 603 592282914 592283175 6.460000e-40 176.0
15 TraesCS2A01G495200 chr2B 88.622 4078 277 93 6 4044 717913976 717917905 0.000000e+00 4787.0
16 TraesCS2A01G495200 chr2B 96.196 736 27 1 4273 5008 717923999 717924733 0.000000e+00 1203.0
17 TraesCS2A01G495200 chr2B 88.204 941 45 23 5003 5899 717927178 717928096 0.000000e+00 1062.0
18 TraesCS2A01G495200 chr2B 92.837 363 26 0 5897 6259 717928123 717928485 1.550000e-145 527.0
19 TraesCS2A01G495200 chr2B 84.988 413 49 5 2716 3115 719529099 719528687 2.100000e-109 407.0
20 TraesCS2A01G495200 chr2B 95.708 233 10 0 4038 4270 717923684 717923916 5.930000e-100 375.0
21 TraesCS2A01G495200 chr2B 76.257 716 113 32 3753 4417 719527876 719527167 1.680000e-85 327.0
22 TraesCS2A01G495200 chr2B 86.567 268 34 1 1817 2084 719530455 719530190 1.710000e-75 294.0
23 TraesCS2A01G495200 chr2B 79.819 332 53 10 4550 4878 719527022 719526702 4.890000e-56 230.0
24 TraesCS2A01G495200 chr2B 88.824 170 19 0 2479 2648 719529307 719529138 6.370000e-50 209.0
25 TraesCS2A01G495200 chr2B 90.370 135 13 0 1663 1797 719530782 719530648 1.800000e-40 178.0
26 TraesCS2A01G495200 chr2B 92.553 94 3 3 2372 2464 719529566 719529476 1.420000e-26 132.0
27 TraesCS2A01G495200 chr7B 81.654 387 64 6 2729 3111 371038842 371038459 1.310000e-81 315.0
28 TraesCS2A01G495200 chr7B 85.106 235 32 3 1852 2084 371039903 371039670 2.920000e-58 237.0
29 TraesCS2A01G495200 chr7B 80.233 258 42 8 2372 2625 371039163 371038911 1.070000e-42 185.0
30 TraesCS2A01G495200 chr7D 81.000 400 71 4 2716 3111 376092004 376091606 4.720000e-81 313.0
31 TraesCS2A01G495200 chr7D 83.404 235 39 0 1842 2076 376093101 376092867 1.060000e-52 219.0
32 TraesCS2A01G495200 chr7D 97.872 47 1 0 5488 5534 336507590 336507544 1.450000e-11 82.4
33 TraesCS2A01G495200 chr7D 97.872 47 1 0 5488 5534 336508064 336508018 1.450000e-11 82.4
34 TraesCS2A01G495200 chr7A 80.750 400 72 4 2716 3111 422831552 422831154 2.190000e-79 307.0
35 TraesCS2A01G495200 chr7A 83.051 236 38 2 1842 2076 422832638 422832404 4.920000e-51 213.0
36 TraesCS2A01G495200 chr7A 80.916 262 41 8 2372 2629 422831860 422831604 1.380000e-46 198.0
37 TraesCS2A01G495200 chr4D 97.872 47 1 0 5488 5534 19915988 19916034 1.450000e-11 82.4
38 TraesCS2A01G495200 chr3D 97.872 47 1 0 5488 5534 21904116 21904162 1.450000e-11 82.4
39 TraesCS2A01G495200 chr1D 97.872 47 1 0 5488 5534 19957524 19957570 1.450000e-11 82.4
40 TraesCS2A01G495200 chr1D 97.872 47 1 0 5488 5534 254497488 254497534 1.450000e-11 82.4
41 TraesCS2A01G495200 chr1A 97.872 47 1 0 5488 5534 112776542 112776496 1.450000e-11 82.4


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 TraesCS2A01G495200 chr2A 726760872 726767138 6266 False 11574.000000 11574 100.000000 1 6267 1 chr2A.!!$F1 6266
1 TraesCS2A01G495200 chr2A 728074583 728078254 3671 True 297.000000 368 84.292571 1670 4878 7 chr2A.!!$R1 3208
2 TraesCS2A01G495200 chr2D 592282632 592287865 5233 False 998.857143 5066 90.508857 26 6267 7 chr2D.!!$F1 6241
3 TraesCS2A01G495200 chr2B 717913976 717917905 3929 False 4787.000000 4787 88.622000 6 4044 1 chr2B.!!$F1 4038
4 TraesCS2A01G495200 chr2B 717923684 717928485 4801 False 791.750000 1203 93.236250 4038 6259 4 chr2B.!!$F2 2221
5 TraesCS2A01G495200 chr2B 719526702 719530782 4080 True 253.857143 407 85.625429 1663 4878 7 chr2B.!!$R1 3215
6 TraesCS2A01G495200 chr7B 371038459 371039903 1444 True 245.666667 315 82.331000 1852 3111 3 chr7B.!!$R1 1259
7 TraesCS2A01G495200 chr7D 376091606 376093101 1495 True 266.000000 313 82.202000 1842 3111 2 chr7D.!!$R2 1269
8 TraesCS2A01G495200 chr7A 422831154 422832638 1484 True 239.333333 307 81.572333 1842 3111 3 chr7A.!!$R1 1269

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
20 21 0.179234 AGAGAGAGATCGAGGTCGCA 59.821 55.000 0.00 0.00 39.60 5.10 F
99 106 0.535797 GCTTAAGTACCGGAGCCTGT 59.464 55.000 9.46 0.00 0.00 4.00 F
1433 1527 0.590195 GCGAGATTGGCCATTAGCAG 59.410 55.000 6.09 0.00 46.50 4.24 F
1614 1708 0.034670 GGTGGCCTTCAGATGCTTCT 60.035 55.000 3.32 0.00 0.00 2.85 F
1755 1849 0.466189 AGATGCTTTACCATGGGCGG 60.466 55.000 18.09 4.33 0.00 6.13 F
1791 1885 1.209019 CCAGAACAGGAGGAGGTGATG 59.791 57.143 0.00 0.00 0.00 3.07 F
2991 3944 1.512926 GCCGTGGCAGGATTACATAG 58.487 55.000 9.09 0.00 41.49 2.23 F
4023 5240 1.687123 AGCCTCTGTCGTACTGTTTGT 59.313 47.619 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1689 0.034670 AGAAGCATCTGAAGGCCACC 60.035 55.000 5.01 0.0 33.59 4.61 R
1608 1702 0.238553 CACTCGACGAGTCAGAAGCA 59.761 55.000 27.03 0.0 41.37 3.91 R
2772 3712 2.108250 AGAGGCCAACCATGTAACAGTT 59.892 45.455 5.01 0.0 39.06 3.16 R
2975 3928 2.158755 ACTGCCTATGTAATCCTGCCAC 60.159 50.000 0.00 0.0 0.00 5.01 R
2991 3944 2.685897 TGTAATTTGCCCGAATACTGCC 59.314 45.455 0.00 0.0 0.00 4.85 R
3634 4832 3.966665 GGATGGGAAAATAGCATTGGGAA 59.033 43.478 0.00 0.0 0.00 3.97 R
4258 5486 1.220529 TGCAAGAGTGAGTGAAAGCG 58.779 50.000 0.00 0.0 0.00 4.68 R
5835 9692 0.107066 TCATCACGCATTGCATCCCT 60.107 50.000 9.69 0.0 0.00 4.20 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
20 21 0.179234 AGAGAGAGATCGAGGTCGCA 59.821 55.000 0.00 0.00 39.60 5.10
76 78 3.195002 CGTACTCGCCGGTCGGTA 61.195 66.667 16.35 13.89 39.05 4.02
77 79 2.537560 CGTACTCGCCGGTCGGTAT 61.538 63.158 16.35 6.73 39.05 2.73
86 93 2.334838 GCCGGTCGGTATATGCTTAAG 58.665 52.381 11.25 0.00 37.65 1.85
99 106 0.535797 GCTTAAGTACCGGAGCCTGT 59.464 55.000 9.46 0.00 0.00 4.00
100 107 1.066358 GCTTAAGTACCGGAGCCTGTT 60.066 52.381 9.46 0.00 0.00 3.16
101 108 2.614734 GCTTAAGTACCGGAGCCTGTTT 60.615 50.000 9.46 0.00 0.00 2.83
102 109 3.671716 CTTAAGTACCGGAGCCTGTTTT 58.328 45.455 9.46 0.00 0.00 2.43
103 110 2.651382 AAGTACCGGAGCCTGTTTTT 57.349 45.000 9.46 0.00 0.00 1.94
142 149 5.126396 AGCTTTGCTTGTCTATTGGAAAC 57.874 39.130 0.00 0.00 33.89 2.78
190 198 4.506654 GCGGCGTGGAACTATATATATTGG 59.493 45.833 9.37 0.00 31.75 3.16
253 262 4.060205 GCTTCAAATCAGGTTTGTGCAAT 58.940 39.130 16.45 0.00 45.87 3.56
297 306 3.918220 GCGCGCACAATCGAGGAG 61.918 66.667 29.10 0.00 0.00 3.69
298 307 3.918220 CGCGCACAATCGAGGAGC 61.918 66.667 8.75 0.00 0.00 4.70
299 308 3.567797 GCGCACAATCGAGGAGCC 61.568 66.667 0.30 0.00 0.00 4.70
300 309 3.257561 CGCACAATCGAGGAGCCG 61.258 66.667 0.00 0.00 0.00 5.52
301 310 2.125512 GCACAATCGAGGAGCCGT 60.126 61.111 0.00 0.00 0.00 5.68
302 311 2.167861 GCACAATCGAGGAGCCGTC 61.168 63.158 0.00 0.00 0.00 4.79
303 312 1.519455 CACAATCGAGGAGCCGTCC 60.519 63.158 0.00 0.00 44.33 4.79
304 313 1.982395 ACAATCGAGGAGCCGTCCA 60.982 57.895 0.00 0.00 46.80 4.02
305 314 1.330655 ACAATCGAGGAGCCGTCCAT 61.331 55.000 0.00 0.00 46.80 3.41
306 315 0.877649 CAATCGAGGAGCCGTCCATG 60.878 60.000 0.00 0.00 46.80 3.66
307 316 2.650813 AATCGAGGAGCCGTCCATGC 62.651 60.000 0.00 0.00 46.80 4.06
340 352 7.859377 GCCTTAAACCTAATTAATTAACTCCGC 59.141 37.037 9.15 1.37 0.00 5.54
344 356 5.997843 ACCTAATTAATTAACTCCGCACCT 58.002 37.500 9.15 0.00 0.00 4.00
353 365 2.683933 TCCGCACCTCTCTTCCCC 60.684 66.667 0.00 0.00 0.00 4.81
355 367 4.148825 CGCACCTCTCTTCCCCGG 62.149 72.222 0.00 0.00 0.00 5.73
356 368 4.475135 GCACCTCTCTTCCCCGGC 62.475 72.222 0.00 0.00 0.00 6.13
357 369 4.148825 CACCTCTCTTCCCCGGCG 62.149 72.222 0.00 0.00 0.00 6.46
358 370 4.377760 ACCTCTCTTCCCCGGCGA 62.378 66.667 9.30 0.00 0.00 5.54
359 371 3.839432 CCTCTCTTCCCCGGCGAC 61.839 72.222 9.30 0.00 0.00 5.19
429 443 1.829096 GTAGCGTCTCTCCCTCCCC 60.829 68.421 0.00 0.00 0.00 4.81
482 505 3.558099 CTGCTATCGATCGCCGCCA 62.558 63.158 18.17 4.32 38.37 5.69
540 593 2.201732 GCGAAACGAGATTAGCCATCA 58.798 47.619 0.00 0.00 33.75 3.07
544 597 5.041287 CGAAACGAGATTAGCCATCAGTTA 58.959 41.667 0.00 0.00 35.32 2.24
546 599 6.346120 CGAAACGAGATTAGCCATCAGTTATG 60.346 42.308 0.00 0.00 35.32 1.90
560 613 7.182361 CATCAGTTATGGCAACTGTATGTAG 57.818 40.000 16.61 1.91 45.75 2.74
574 627 5.108187 TGTATGTAGTTAGGTCGGACTCT 57.892 43.478 8.23 6.27 0.00 3.24
575 628 5.503927 TGTATGTAGTTAGGTCGGACTCTT 58.496 41.667 8.23 0.00 0.00 2.85
617 670 2.470257 CGGCTATTACACCGTCGAATTC 59.530 50.000 0.00 0.00 44.46 2.17
625 678 2.733026 ACACCGTCGAATTCTTTAACCG 59.267 45.455 3.52 0.00 0.00 4.44
672 725 7.469260 ACAAAACCTTTATGTATGTATGTCGC 58.531 34.615 0.00 0.00 0.00 5.19
676 729 4.621460 CCTTTATGTATGTATGTCGCCTCG 59.379 45.833 0.00 0.00 0.00 4.63
780 834 2.038387 AACTGCAAAGTCGTGGTTCT 57.962 45.000 0.00 0.00 0.00 3.01
781 835 2.902705 ACTGCAAAGTCGTGGTTCTA 57.097 45.000 0.00 0.00 0.00 2.10
786 840 5.067283 ACTGCAAAGTCGTGGTTCTAAAAAT 59.933 36.000 0.00 0.00 0.00 1.82
789 843 7.653647 TGCAAAGTCGTGGTTCTAAAAATAAT 58.346 30.769 0.00 0.00 0.00 1.28
819 907 9.243637 GCAAAGTGTAATTTTATTGTGTCAAGA 57.756 29.630 0.00 0.00 0.00 3.02
823 911 9.337396 AGTGTAATTTTATTGTGTCAAGAGTCA 57.663 29.630 0.00 0.00 0.00 3.41
824 912 9.944663 GTGTAATTTTATTGTGTCAAGAGTCAA 57.055 29.630 0.00 0.00 0.00 3.18
853 941 5.178809 GGTACAAAGTGAAATAAGCGACAGT 59.821 40.000 0.00 0.00 0.00 3.55
858 946 5.135508 AGTGAAATAAGCGACAGTGTACT 57.864 39.130 0.00 0.00 0.00 2.73
865 953 2.511659 AGCGACAGTGTACTAGGTGAA 58.488 47.619 0.00 0.00 0.00 3.18
866 954 2.889045 AGCGACAGTGTACTAGGTGAAA 59.111 45.455 0.00 0.00 0.00 2.69
867 955 3.057456 AGCGACAGTGTACTAGGTGAAAG 60.057 47.826 0.00 0.00 0.00 2.62
868 956 3.305199 GCGACAGTGTACTAGGTGAAAGT 60.305 47.826 0.00 0.00 0.00 2.66
869 957 4.083110 GCGACAGTGTACTAGGTGAAAGTA 60.083 45.833 0.00 0.00 0.00 2.24
870 958 5.388944 CGACAGTGTACTAGGTGAAAGTAC 58.611 45.833 0.00 6.47 46.23 2.73
907 995 6.926272 TGTGTTGTTTTGGAACTAATAATGGC 59.074 34.615 0.00 0.00 36.70 4.40
959 1053 0.953727 TGTGCTAGCTTTGCAGGTTG 59.046 50.000 17.23 0.00 41.41 3.77
971 1065 1.430632 CAGGTTGCATTGGCTAGCG 59.569 57.895 9.00 0.00 45.71 4.26
997 1091 3.216290 GCATCGCGACGAAGCTAG 58.784 61.111 12.93 0.00 45.16 3.42
998 1092 1.586564 GCATCGCGACGAAGCTAGT 60.587 57.895 12.93 0.00 45.16 2.57
1039 1133 3.940303 GATGAAATCGACGGTCCAATTG 58.060 45.455 1.91 0.00 31.13 2.32
1083 1177 2.957402 TGAAGAAGAACATGCCCACT 57.043 45.000 0.00 0.00 0.00 4.00
1090 1184 3.224007 AACATGCCCACTCCCACCC 62.224 63.158 0.00 0.00 0.00 4.61
1103 1197 1.450312 CCACCCGCTCATCAGGAAC 60.450 63.158 0.00 0.00 0.00 3.62
1209 1303 4.271696 TGATTCAGACGATGACAAACCT 57.728 40.909 0.00 0.00 37.77 3.50
1216 1310 3.935203 AGACGATGACAAACCTATTGCAG 59.065 43.478 0.00 0.00 0.00 4.41
1250 1344 4.827284 GGTTTGTGAGAGGAAATCAAAGGA 59.173 41.667 0.00 0.00 0.00 3.36
1255 1349 6.306199 TGTGAGAGGAAATCAAAGGAAATCA 58.694 36.000 0.00 0.00 0.00 2.57
1310 1404 2.036992 AGGATGAGAGACCGATTGCATC 59.963 50.000 0.00 0.00 33.29 3.91
1337 1431 6.265422 AGGAAAAATGTTCGTGAGAGGAAATT 59.735 34.615 0.00 0.00 43.69 1.82
1340 1434 5.613358 AATGTTCGTGAGAGGAAATTGAC 57.387 39.130 0.00 0.00 43.69 3.18
1343 1437 2.942710 TCGTGAGAGGAAATTGACGAC 58.057 47.619 0.00 0.00 31.34 4.34
1344 1438 2.295070 TCGTGAGAGGAAATTGACGACA 59.705 45.455 0.00 0.00 31.34 4.35
1351 1445 6.128200 TGAGAGGAAATTGACGACAATCAATG 60.128 38.462 13.32 0.00 46.35 2.82
1379 1473 1.442526 GCCAAGGCAGATGGTGATCG 61.443 60.000 6.14 0.00 40.23 3.69
1387 1481 2.698803 CAGATGGTGATCGTGACCAAA 58.301 47.619 7.43 0.00 46.57 3.28
1408 1502 4.889832 AATTCAGATGATGAGAAACCGC 57.110 40.909 0.00 0.00 39.68 5.68
1430 1524 1.845809 GCCGCGAGATTGGCCATTAG 61.846 60.000 6.09 0.00 45.73 1.73
1431 1525 1.571460 CGCGAGATTGGCCATTAGC 59.429 57.895 6.09 9.08 42.60 3.09
1433 1527 0.590195 GCGAGATTGGCCATTAGCAG 59.410 55.000 6.09 0.00 46.50 4.24
1434 1528 0.590195 CGAGATTGGCCATTAGCAGC 59.410 55.000 6.09 0.00 46.50 5.25
1448 1542 4.233408 CAGCGCTGCTCCAAAAAC 57.767 55.556 26.68 0.00 36.40 2.43
1449 1543 1.372128 CAGCGCTGCTCCAAAAACC 60.372 57.895 26.68 0.00 36.40 3.27
1486 1580 5.601313 TCTGATGATGATTCAGAGGATGACA 59.399 40.000 0.00 0.00 43.49 3.58
1503 1597 3.560251 AAGCCACTGACTGCCCGT 61.560 61.111 0.00 0.00 0.00 5.28
1504 1598 3.120086 AAGCCACTGACTGCCCGTT 62.120 57.895 0.00 0.00 0.00 4.44
1507 1601 0.887387 GCCACTGACTGCCCGTTTTA 60.887 55.000 0.00 0.00 0.00 1.52
1508 1602 1.600023 CCACTGACTGCCCGTTTTAA 58.400 50.000 0.00 0.00 0.00 1.52
1511 1605 3.074412 CACTGACTGCCCGTTTTAATCT 58.926 45.455 0.00 0.00 0.00 2.40
1514 1608 3.482436 TGACTGCCCGTTTTAATCTTGT 58.518 40.909 0.00 0.00 0.00 3.16
1532 1626 2.675242 TTACCGGGGGTGCATCCAG 61.675 63.158 20.00 11.17 36.19 3.86
1536 1630 2.046285 CGGGGGTGCATCCAGAAAC 61.046 63.158 20.00 0.00 38.11 2.78
1543 1637 1.728971 GTGCATCCAGAAACTCAGTCG 59.271 52.381 0.00 0.00 0.00 4.18
1550 1644 3.005897 TCCAGAAACTCAGTCGAAAGGAG 59.994 47.826 7.48 7.48 34.85 3.69
1566 1660 1.285373 AGGAGAGGTGGTCGTAGTGAT 59.715 52.381 0.00 0.00 0.00 3.06
1575 1669 3.673809 GTGGTCGTAGTGATCAAACAGTC 59.326 47.826 0.00 0.00 40.07 3.51
1578 1672 4.167268 GTCGTAGTGATCAAACAGTCTCC 58.833 47.826 0.00 0.00 0.00 3.71
1592 1686 4.279145 ACAGTCTCCGCTCTTAATAAGGA 58.721 43.478 0.00 0.00 0.00 3.36
1593 1687 4.098196 ACAGTCTCCGCTCTTAATAAGGAC 59.902 45.833 0.00 0.00 0.00 3.85
1595 1689 4.339814 AGTCTCCGCTCTTAATAAGGACAG 59.660 45.833 0.00 0.00 0.00 3.51
1596 1690 3.637229 TCTCCGCTCTTAATAAGGACAGG 59.363 47.826 0.00 0.29 0.00 4.00
1597 1691 3.371965 TCCGCTCTTAATAAGGACAGGT 58.628 45.455 0.00 0.00 0.00 4.00
1608 1702 1.994463 GGACAGGTGGCCTTCAGAT 59.006 57.895 3.32 0.00 41.12 2.90
1614 1708 0.034670 GGTGGCCTTCAGATGCTTCT 60.035 55.000 3.32 0.00 0.00 2.85
1657 1751 1.452108 CCCAAGGATGAACCCGAGC 60.452 63.158 0.00 0.00 40.05 5.03
1659 1753 1.026718 CCAAGGATGAACCCGAGCAC 61.027 60.000 0.00 0.00 40.05 4.40
1666 1760 1.810030 GAACCCGAGCACGATGGTC 60.810 63.158 4.70 0.00 41.16 4.02
1747 1841 4.009675 TCATGGTGTCAAGATGCTTTACC 58.990 43.478 0.00 0.00 0.00 2.85
1754 1848 1.066002 CAAGATGCTTTACCATGGGCG 59.934 52.381 18.09 2.00 0.00 6.13
1755 1849 0.466189 AGATGCTTTACCATGGGCGG 60.466 55.000 18.09 4.33 0.00 6.13
1791 1885 1.209019 CCAGAACAGGAGGAGGTGATG 59.791 57.143 0.00 0.00 0.00 3.07
1797 1891 4.265856 ACAGGAGGAGGTGATGTACATA 57.734 45.455 8.71 0.00 0.00 2.29
1798 1892 4.219115 ACAGGAGGAGGTGATGTACATAG 58.781 47.826 8.71 0.00 0.00 2.23
1839 2106 5.551760 ATTAAGAACATGCTTCCGTCTTG 57.448 39.130 0.00 0.00 0.00 3.02
1933 2200 5.036737 CGCATCCAAGGAAACATTTATCAC 58.963 41.667 0.00 0.00 0.00 3.06
1986 2253 8.267620 TCTTGGTAAAACACATATCATCACAG 57.732 34.615 0.00 0.00 0.00 3.66
2028 2295 3.817084 CACACCGATCTATGAATGGCATT 59.183 43.478 13.54 13.54 38.44 3.56
2050 2317 4.792521 TCCGAGAGAAGGAGAAGAAAAG 57.207 45.455 0.00 0.00 33.19 2.27
2054 2321 4.000325 GAGAGAAGGAGAAGAAAAGCCAC 59.000 47.826 0.00 0.00 0.00 5.01
2070 2337 2.169352 AGCCACATGACATCAGAGGTAC 59.831 50.000 0.00 0.00 0.00 3.34
2127 2493 4.385754 GCTGGACAAGGGAGATTTATCCTT 60.386 45.833 0.00 0.00 41.15 3.36
2131 2497 5.607171 GGACAAGGGAGATTTATCCTTCCTA 59.393 44.000 0.00 0.00 38.70 2.94
2201 2587 4.214332 GCAGGAAGAGAAATCGAAACAAGT 59.786 41.667 0.00 0.00 0.00 3.16
2202 2588 5.408604 GCAGGAAGAGAAATCGAAACAAGTA 59.591 40.000 0.00 0.00 0.00 2.24
2329 2824 3.572642 AGGTTACTGTTTTCCTTTGGGG 58.427 45.455 0.00 0.00 0.00 4.96
2446 3227 3.019564 AGCATCCAAAGGTACAGATTGC 58.980 45.455 0.00 0.00 0.00 3.56
2465 3401 8.964150 CAGATTGCAAACATGTAATCACATATG 58.036 33.333 17.29 0.00 43.73 1.78
2566 3502 3.428870 GCATCCGACCAAGTGATATTACG 59.571 47.826 0.00 0.00 0.00 3.18
2607 3543 2.264794 CGTCCCAGTGTGCCCTAC 59.735 66.667 0.00 0.00 0.00 3.18
2760 3700 1.888215 TCTGCAGCTGGAAAGAAGTG 58.112 50.000 17.12 0.00 0.00 3.16
2769 3709 5.048224 CAGCTGGAAAGAAGTGAAACATGAT 60.048 40.000 5.57 0.00 41.43 2.45
2772 3712 7.231317 AGCTGGAAAGAAGTGAAACATGATAAA 59.769 33.333 0.00 0.00 41.43 1.40
2792 3732 2.200373 ACTGTTACATGGTTGGCCTC 57.800 50.000 3.32 0.00 35.27 4.70
2820 3760 6.522165 GGAACGATCCAATAAACGAAAAAGAC 59.478 38.462 6.88 0.00 45.79 3.01
2829 3769 9.113876 CCAATAAACGAAAAAGACATCAAGTAC 57.886 33.333 0.00 0.00 0.00 2.73
2920 3860 5.819825 ACTGAAGGTGAGAAAGTTTGTTC 57.180 39.130 0.00 0.00 0.00 3.18
2922 3862 6.650120 ACTGAAGGTGAGAAAGTTTGTTCTA 58.350 36.000 0.00 0.00 37.98 2.10
2975 3928 4.320494 GCAATAATTGTCCTTCTATGGCCG 60.320 45.833 0.00 0.00 0.00 6.13
2991 3944 1.512926 GCCGTGGCAGGATTACATAG 58.487 55.000 9.09 0.00 41.49 2.23
3026 3979 4.627035 GCAAATTACACCAAGGATTTCAGC 59.373 41.667 0.00 0.00 0.00 4.26
3153 4215 6.524101 TCCCCTTTTATTCTACAATGTTGC 57.476 37.500 0.00 0.00 0.00 4.17
3175 4237 4.760683 CGACACAATTTTTGTTGGCAATC 58.239 39.130 1.92 0.00 43.23 2.67
3398 4593 6.260050 CAGATACTGTTGGTTGTTGTACACTT 59.740 38.462 0.00 0.00 0.00 3.16
3502 4697 9.512435 TGCTCACTACGAGTAATTAATTTCTAC 57.488 33.333 5.91 0.00 44.33 2.59
3503 4698 9.733219 GCTCACTACGAGTAATTAATTTCTACT 57.267 33.333 5.91 3.91 44.33 2.57
3610 4808 3.552875 TGAACTAGCTGTATACGAGGCT 58.447 45.455 17.49 17.49 38.62 4.58
3634 4832 7.229506 GCTATTAAGGAATTCTGTGCAGGTATT 59.770 37.037 5.23 0.71 0.00 1.89
3778 4976 7.396906 TTTCTAGGTAAAAAGAAGGGAGGAA 57.603 36.000 0.00 0.00 33.49 3.36
3826 5024 8.939929 CAACTAAACTAAATGCTCATCTCAAGA 58.060 33.333 0.00 0.00 0.00 3.02
3892 5090 2.815589 GCTTCCATCACTTTGGACACCT 60.816 50.000 0.00 0.00 45.42 4.00
3965 5182 4.705507 AGTACTGTTTAGGCTCGATGAAGA 59.294 41.667 0.00 0.00 0.00 2.87
4022 5239 2.329379 GAGCCTCTGTCGTACTGTTTG 58.671 52.381 0.00 0.00 0.00 2.93
4023 5240 1.687123 AGCCTCTGTCGTACTGTTTGT 59.313 47.619 0.00 0.00 0.00 2.83
4027 5244 4.201881 GCCTCTGTCGTACTGTTTGTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
4028 5245 5.263185 CCTCTGTCGTACTGTTTGTTTTTG 58.737 41.667 0.00 0.00 0.00 2.44
4029 5246 5.163794 CCTCTGTCGTACTGTTTGTTTTTGT 60.164 40.000 0.00 0.00 0.00 2.83
4030 5247 6.036300 CCTCTGTCGTACTGTTTGTTTTTGTA 59.964 38.462 0.00 0.00 0.00 2.41
4222 5450 4.216257 ACAGATGGAACCGTTGATGAAAAG 59.784 41.667 0.00 0.00 0.00 2.27
4246 5474 5.294552 GGCTAAAGTCTATCAACGAGCAAAT 59.705 40.000 0.00 0.00 0.00 2.32
4258 5486 6.894828 TCAACGAGCAAATAAAGAGGTAAAC 58.105 36.000 0.00 0.00 0.00 2.01
4282 5590 4.082895 GCTTTCACTCACTCTTGCATCATT 60.083 41.667 0.00 0.00 0.00 2.57
4476 5830 2.403259 CCCCGCAAACTTTTTGTCATC 58.597 47.619 0.91 0.00 0.00 2.92
4544 5899 8.822652 AGAATTGGAGAAAGCAAATAAACTTG 57.177 30.769 0.00 0.00 0.00 3.16
4558 5913 7.647715 GCAAATAAACTTGTGTCTAAAAGAGCA 59.352 33.333 0.00 0.00 0.00 4.26
4668 6023 5.705609 TCATTTTCTTTCTGTACTTGCCC 57.294 39.130 0.00 0.00 0.00 5.36
4731 6086 3.181516 GCAGGTTGCAGAAGAAGTTATCG 60.182 47.826 0.00 0.00 44.26 2.92
4935 6290 8.962884 TTCTTGCTTCTATTATGAGTTATGCA 57.037 30.769 0.00 0.00 0.00 3.96
5147 8952 9.925268 AAACGACTACTTGTTTAATTGTTACTG 57.075 29.630 0.00 0.00 36.59 2.74
5269 9074 5.163405 CGACCCAGATTTCAGATTCTAAGGA 60.163 44.000 0.00 0.00 0.00 3.36
5311 9116 2.225068 GGTACGTCCAGGATCATGTG 57.775 55.000 6.62 0.00 35.97 3.21
5318 9126 4.695455 ACGTCCAGGATCATGTGTTTTTAG 59.305 41.667 6.62 0.00 0.00 1.85
5319 9127 4.935205 CGTCCAGGATCATGTGTTTTTAGA 59.065 41.667 6.62 0.00 0.00 2.10
5416 9224 7.670559 ACCAGTAGAGTAGATTGTTAGTGTTCT 59.329 37.037 0.00 0.00 0.00 3.01
5429 9237 7.627298 TGTTAGTGTTCTATCCAGTAGAGAC 57.373 40.000 0.00 0.00 40.42 3.36
5534 9360 0.380378 TTGTGTTTCTTGGCAGCGAC 59.620 50.000 0.00 0.00 0.00 5.19
5565 9391 1.964223 ACAACTTCTCTCTCGAAGCCA 59.036 47.619 0.00 0.00 43.22 4.75
5571 9397 1.620819 TCTCTCTCGAAGCCAGCTTTT 59.379 47.619 6.31 0.00 36.26 2.27
5613 9439 4.345257 AGCCATAAGGTCGATTGATACAGT 59.655 41.667 0.00 0.00 37.19 3.55
5615 9441 5.739070 GCCATAAGGTCGATTGATACAGTGA 60.739 44.000 0.00 0.00 37.19 3.41
5659 9485 7.603784 ACAAAGCCATTCAAATAAAAAGCTAGG 59.396 33.333 0.00 0.00 0.00 3.02
5694 9520 4.235939 ACAACGCATAAGAAATGCACAA 57.764 36.364 10.30 0.00 44.75 3.33
5718 9544 1.000731 GCCACCAAGCAAAAGCACATA 59.999 47.619 0.00 0.00 0.00 2.29
5738 9564 3.314541 AAGTAGCGGAACCACAACTAG 57.685 47.619 0.00 0.00 0.00 2.57
5756 9582 6.982724 ACAACTAGTAACAACAACTGAGGTAC 59.017 38.462 0.00 0.00 0.00 3.34
5760 9617 5.045872 AGTAACAACAACTGAGGTACGAAC 58.954 41.667 0.00 0.00 0.00 3.95
5835 9692 0.320946 GCCACCAAACGCTAGTACCA 60.321 55.000 0.00 0.00 0.00 3.25
5852 9709 4.993307 AGGGATGCAATGCGTGAT 57.007 50.000 3.99 0.00 34.31 3.06
5877 9735 1.068055 CAAGCTTGCTCGAAAATGCCT 60.068 47.619 14.65 0.00 0.00 4.75
5910 9797 2.293856 ACCAGAGGGAGGGTAATGACAT 60.294 50.000 0.00 0.00 35.09 3.06
5944 9831 1.000843 CACATCCGTCAGAACAGACCA 59.999 52.381 0.00 0.00 35.07 4.02
6025 9912 0.106619 CTAGGAGGGACGCTACACCT 60.107 60.000 4.32 4.16 37.31 4.00
6091 9978 2.167693 GGTATTCCATCACACCTCGTCA 59.832 50.000 0.00 0.00 0.00 4.35
6119 10006 3.702048 GCTACCGAGCCCACCACA 61.702 66.667 0.00 0.00 43.49 4.17
6149 10036 3.839490 CCCAGCCTCTAGATCAAGATCAT 59.161 47.826 12.21 1.14 40.22 2.45
6184 10071 2.859538 CAAGTGTTGACAACATTGCCAC 59.140 45.455 23.14 9.87 44.35 5.01
6248 10135 2.923035 CACCACCCTGTCCCGACT 60.923 66.667 0.00 0.00 0.00 4.18
6259 10146 3.071892 CCTGTCCCGACTAGATCTAGACT 59.928 52.174 31.91 13.98 36.97 3.24
6260 10147 4.283978 CCTGTCCCGACTAGATCTAGACTA 59.716 50.000 31.91 13.67 36.97 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.586319 GCGACCTCGATCTCTCTCTG 59.414 60.000 0.00 0.00 43.02 3.35
1 2 0.179234 TGCGACCTCGATCTCTCTCT 59.821 55.000 0.00 0.00 43.02 3.10
2 3 0.586319 CTGCGACCTCGATCTCTCTC 59.414 60.000 0.00 0.00 43.02 3.20
3 4 1.444119 GCTGCGACCTCGATCTCTCT 61.444 60.000 0.00 0.00 43.02 3.10
4 5 1.008995 GCTGCGACCTCGATCTCTC 60.009 63.158 0.00 0.00 43.02 3.20
5 6 2.829206 CGCTGCGACCTCGATCTCT 61.829 63.158 18.66 0.00 43.02 3.10
6 7 2.352915 CGCTGCGACCTCGATCTC 60.353 66.667 18.66 0.00 43.02 2.75
8 9 4.933064 CCCGCTGCGACCTCGATC 62.933 72.222 25.45 0.00 43.02 3.69
29 30 3.431725 CCGTTGCCTTCCTTCCGC 61.432 66.667 0.00 0.00 0.00 5.54
56 57 2.575262 CGACCGGCGAGTACGAAC 60.575 66.667 9.30 0.00 44.57 3.95
57 58 3.803082 CCGACCGGCGAGTACGAA 61.803 66.667 17.96 0.00 44.57 3.85
76 78 3.006967 CAGGCTCCGGTACTTAAGCATAT 59.993 47.826 12.13 0.00 36.47 1.78
77 79 2.364324 CAGGCTCCGGTACTTAAGCATA 59.636 50.000 12.13 0.00 36.47 3.14
118 125 3.002791 TCCAATAGACAAGCAAAGCTCG 58.997 45.455 0.00 0.00 38.25 5.03
142 149 3.115554 CCAAACAAGAAAGACGCCTTTG 58.884 45.455 0.00 0.00 42.30 2.77
171 179 9.367444 GGAAGAACCAATATATATAGTTCCACG 57.633 37.037 22.80 0.00 38.03 4.94
232 241 9.563345 CAAGCATTGCACAAACCTGATTTGAAG 62.563 40.741 11.91 0.00 44.54 3.02
303 312 2.695759 TTTAAGGCCGCACCGCATG 61.696 57.895 0.00 0.00 46.52 4.06
304 313 2.360600 TTTAAGGCCGCACCGCAT 60.361 55.556 0.00 0.00 46.52 4.73
305 314 3.358707 GTTTAAGGCCGCACCGCA 61.359 61.111 0.00 0.00 46.52 5.69
306 315 4.111016 GGTTTAAGGCCGCACCGC 62.111 66.667 0.00 0.00 46.52 5.68
307 316 0.674269 TTAGGTTTAAGGCCGCACCG 60.674 55.000 0.00 0.00 46.52 4.94
308 317 1.758936 ATTAGGTTTAAGGCCGCACC 58.241 50.000 0.00 1.93 39.61 5.01
309 318 4.968812 TTAATTAGGTTTAAGGCCGCAC 57.031 40.909 0.00 0.00 0.00 5.34
310 319 7.339976 AGTTAATTAATTAGGTTTAAGGCCGCA 59.660 33.333 7.91 0.00 0.00 5.69
311 320 7.709947 AGTTAATTAATTAGGTTTAAGGCCGC 58.290 34.615 7.91 0.00 0.00 6.53
312 321 8.347771 GGAGTTAATTAATTAGGTTTAAGGCCG 58.652 37.037 7.91 0.00 0.00 6.13
313 322 8.347771 CGGAGTTAATTAATTAGGTTTAAGGCC 58.652 37.037 7.91 0.00 0.00 5.19
340 352 4.148825 CGCCGGGGAAGAGAGGTG 62.149 72.222 14.46 0.00 0.00 4.00
359 371 4.109675 ATCCCGGCCTTCCCAACG 62.110 66.667 0.00 0.00 0.00 4.10
361 373 2.612430 TGATCCCGGCCTTCCCAA 60.612 61.111 0.00 0.00 0.00 4.12
362 374 3.089874 CTGATCCCGGCCTTCCCA 61.090 66.667 0.00 0.00 0.00 4.37
468 483 4.337060 CCGTGGCGGCGATCGATA 62.337 66.667 21.57 0.00 41.17 2.92
501 524 4.666397 TAAGCAACACGGCCGCGA 62.666 61.111 28.58 0.00 0.00 5.87
502 525 4.147322 CTAAGCAACACGGCCGCG 62.147 66.667 28.58 20.53 0.00 6.46
503 526 3.799755 CCTAAGCAACACGGCCGC 61.800 66.667 28.58 8.56 0.00 6.53
504 527 3.799755 GCCTAAGCAACACGGCCG 61.800 66.667 26.86 26.86 39.53 6.13
505 528 3.799755 CGCCTAAGCAACACGGCC 61.800 66.667 0.00 0.00 39.34 6.13
506 529 1.847890 TTTCGCCTAAGCAACACGGC 61.848 55.000 0.00 0.00 39.83 5.68
507 530 0.110373 GTTTCGCCTAAGCAACACGG 60.110 55.000 0.00 0.00 39.83 4.94
521 544 3.448686 ACTGATGGCTAATCTCGTTTCG 58.551 45.455 2.37 0.00 36.15 3.46
522 545 6.882072 CATAACTGATGGCTAATCTCGTTTC 58.118 40.000 10.64 0.00 36.15 2.78
540 593 7.093024 ACCTAACTACATACAGTTGCCATAACT 60.093 37.037 0.00 0.00 39.12 2.24
544 597 5.671493 GACCTAACTACATACAGTTGCCAT 58.329 41.667 0.00 0.00 39.12 4.40
546 599 4.110482 CGACCTAACTACATACAGTTGCC 58.890 47.826 0.00 0.00 39.12 4.52
549 602 5.259632 AGTCCGACCTAACTACATACAGTT 58.740 41.667 0.00 0.00 41.56 3.16
560 613 7.548427 AGCTAATTAAAAAGAGTCCGACCTAAC 59.452 37.037 0.00 0.00 0.00 2.34
574 627 6.583912 CGTCATCTCGGAGCTAATTAAAAA 57.416 37.500 0.00 0.00 0.00 1.94
657 710 2.554893 TGCGAGGCGACATACATACATA 59.445 45.455 0.00 0.00 0.00 2.29
664 717 2.983402 TATACTGCGAGGCGACATAC 57.017 50.000 0.00 0.00 0.00 2.39
666 719 1.670087 GCATATACTGCGAGGCGACAT 60.670 52.381 0.00 0.00 41.97 3.06
805 859 6.483307 CCAGTCTTGACTCTTGACACAATAAA 59.517 38.462 0.00 0.00 33.56 1.40
819 907 5.353394 TTCACTTTGTACCAGTCTTGACT 57.647 39.130 0.00 0.00 0.00 3.41
820 908 6.619801 ATTTCACTTTGTACCAGTCTTGAC 57.380 37.500 0.00 0.00 0.00 3.18
821 909 7.041372 GCTTATTTCACTTTGTACCAGTCTTGA 60.041 37.037 0.00 0.00 0.00 3.02
822 910 7.078228 GCTTATTTCACTTTGTACCAGTCTTG 58.922 38.462 0.00 0.00 0.00 3.02
823 911 6.073222 CGCTTATTTCACTTTGTACCAGTCTT 60.073 38.462 0.00 0.00 0.00 3.01
824 912 5.408604 CGCTTATTTCACTTTGTACCAGTCT 59.591 40.000 0.00 0.00 0.00 3.24
825 913 5.407387 TCGCTTATTTCACTTTGTACCAGTC 59.593 40.000 0.00 0.00 0.00 3.51
826 914 5.178809 GTCGCTTATTTCACTTTGTACCAGT 59.821 40.000 0.00 0.00 0.00 4.00
858 946 6.598457 CACTAGTAGCTCTGTACTTTCACCTA 59.402 42.308 0.00 0.00 34.91 3.08
865 953 5.535406 ACAACACACTAGTAGCTCTGTACTT 59.465 40.000 0.00 0.00 34.91 2.24
866 954 5.071370 ACAACACACTAGTAGCTCTGTACT 58.929 41.667 0.00 0.00 37.09 2.73
867 955 5.373981 ACAACACACTAGTAGCTCTGTAC 57.626 43.478 0.00 0.00 0.00 2.90
868 956 6.401047 AAACAACACACTAGTAGCTCTGTA 57.599 37.500 0.00 0.00 0.00 2.74
869 957 4.939052 AACAACACACTAGTAGCTCTGT 57.061 40.909 0.00 0.00 0.00 3.41
870 958 5.050091 CCAAAACAACACACTAGTAGCTCTG 60.050 44.000 0.00 0.00 0.00 3.35
875 963 6.920569 AGTTCCAAAACAACACACTAGTAG 57.079 37.500 0.00 0.00 37.88 2.57
959 1053 1.348594 GAACGACGCTAGCCAATGC 59.651 57.895 9.66 0.00 37.95 3.56
961 1055 0.460284 CAGGAACGACGCTAGCCAAT 60.460 55.000 9.66 0.00 0.00 3.16
968 1062 2.507102 CGATGCAGGAACGACGCT 60.507 61.111 0.00 0.00 0.00 5.07
971 1065 2.506217 TCGCGATGCAGGAACGAC 60.506 61.111 3.71 0.00 0.00 4.34
994 1088 2.287069 CGTGGAGAGACGGCATTACTAG 60.287 54.545 0.00 0.00 35.65 2.57
995 1089 1.674441 CGTGGAGAGACGGCATTACTA 59.326 52.381 0.00 0.00 35.65 1.82
996 1090 0.456221 CGTGGAGAGACGGCATTACT 59.544 55.000 0.00 0.00 35.65 2.24
997 1091 2.959275 CGTGGAGAGACGGCATTAC 58.041 57.895 0.00 0.00 35.65 1.89
1039 1133 4.781280 AGGCACTTGACCTCTTGAAGGC 62.781 54.545 0.00 0.00 43.84 4.35
1083 1177 3.083349 CCTGATGAGCGGGTGGGA 61.083 66.667 0.00 0.00 38.31 4.37
1090 1184 2.164422 TCACTACAGTTCCTGATGAGCG 59.836 50.000 0.00 0.00 35.18 5.03
1103 1197 3.733337 AGACTGTTTGGCTTCACTACAG 58.267 45.455 0.00 0.00 38.36 2.74
1106 1200 3.135712 TCCAAGACTGTTTGGCTTCACTA 59.864 43.478 13.49 0.00 43.41 2.74
1134 1228 6.761714 GTCTTTTCAGGTTACTCTTCTGACAA 59.238 38.462 0.00 0.00 37.28 3.18
1149 1243 3.380479 TCCACACGTAGTCTTTTCAGG 57.620 47.619 0.00 0.00 41.61 3.86
1209 1303 6.150976 CACAAACCTTCATCCTTACTGCAATA 59.849 38.462 0.00 0.00 0.00 1.90
1216 1310 4.938226 CCTCTCACAAACCTTCATCCTTAC 59.062 45.833 0.00 0.00 0.00 2.34
1250 1344 5.422145 GCATGGCACCTTTTCTAATGATTT 58.578 37.500 0.00 0.00 0.00 2.17
1255 1349 2.762327 CTGGCATGGCACCTTTTCTAAT 59.238 45.455 19.43 0.00 0.00 1.73
1310 1404 4.515191 TCCTCTCACGAACATTTTTCCTTG 59.485 41.667 0.00 0.00 0.00 3.61
1337 1431 2.349590 CTCCTGCATTGATTGTCGTCA 58.650 47.619 0.00 0.00 0.00 4.35
1340 1434 1.399440 CACCTCCTGCATTGATTGTCG 59.601 52.381 0.00 0.00 0.00 4.35
1351 1445 4.666253 TGCCTTGGCACCTCCTGC 62.666 66.667 10.65 0.00 46.31 4.85
1376 1470 5.882000 TCATCATCTGAATTTTGGTCACGAT 59.118 36.000 0.00 0.00 0.00 3.73
1379 1473 6.748333 TCTCATCATCTGAATTTTGGTCAC 57.252 37.500 0.00 0.00 32.14 3.67
1387 1481 4.334759 CAGCGGTTTCTCATCATCTGAATT 59.665 41.667 0.00 0.00 32.14 2.17
1415 1509 0.590195 GCTGCTAATGGCCAATCTCG 59.410 55.000 10.96 0.00 40.92 4.04
1417 1511 1.450531 GCGCTGCTAATGGCCAATCT 61.451 55.000 10.96 0.00 40.92 2.40
1419 1513 1.454479 AGCGCTGCTAATGGCCAAT 60.454 52.632 10.96 2.97 36.99 3.16
1431 1525 1.372128 GGTTTTTGGAGCAGCGCTG 60.372 57.895 32.83 32.83 39.88 5.18
1433 1527 2.429069 CGGTTTTTGGAGCAGCGC 60.429 61.111 0.00 0.00 0.00 5.92
1434 1528 2.187599 CTCCGGTTTTTGGAGCAGCG 62.188 60.000 0.00 0.00 45.99 5.18
1448 1542 0.467384 ATCAGAGACATTGCCTCCGG 59.533 55.000 0.00 0.00 0.00 5.14
1449 1543 1.137675 TCATCAGAGACATTGCCTCCG 59.862 52.381 0.00 0.00 0.00 4.63
1503 1597 4.080687 CACCCCCGGTAACAAGATTAAAA 58.919 43.478 0.00 0.00 32.11 1.52
1504 1598 3.688235 CACCCCCGGTAACAAGATTAAA 58.312 45.455 0.00 0.00 32.11 1.52
1507 1601 0.323087 GCACCCCCGGTAACAAGATT 60.323 55.000 0.00 0.00 32.11 2.40
1508 1602 1.301954 GCACCCCCGGTAACAAGAT 59.698 57.895 0.00 0.00 32.11 2.40
1511 1605 1.001887 GATGCACCCCCGGTAACAA 60.002 57.895 0.00 0.00 32.11 2.83
1514 1608 2.611172 TGGATGCACCCCCGGTAA 60.611 61.111 0.00 0.00 38.00 2.85
1532 1626 3.006003 ACCTCTCCTTTCGACTGAGTTTC 59.994 47.826 0.00 0.00 0.00 2.78
1536 1630 1.203523 CCACCTCTCCTTTCGACTGAG 59.796 57.143 0.00 0.00 0.00 3.35
1543 1637 2.094649 CACTACGACCACCTCTCCTTTC 60.095 54.545 0.00 0.00 0.00 2.62
1550 1644 3.251571 GTTTGATCACTACGACCACCTC 58.748 50.000 0.00 0.00 0.00 3.85
1566 1660 4.537135 ATTAAGAGCGGAGACTGTTTGA 57.463 40.909 0.00 0.00 0.00 2.69
1575 1669 3.385111 ACCTGTCCTTATTAAGAGCGGAG 59.615 47.826 4.96 1.10 0.00 4.63
1578 1672 3.458189 CCACCTGTCCTTATTAAGAGCG 58.542 50.000 4.96 0.00 0.00 5.03
1592 1686 1.001641 GCATCTGAAGGCCACCTGT 60.002 57.895 5.01 0.00 32.13 4.00
1593 1687 0.323178 AAGCATCTGAAGGCCACCTG 60.323 55.000 5.01 0.00 32.13 4.00
1595 1689 0.034670 AGAAGCATCTGAAGGCCACC 60.035 55.000 5.01 0.00 33.59 4.61
1596 1690 3.566130 AGAAGCATCTGAAGGCCAC 57.434 52.632 5.01 0.00 33.59 5.01
1608 1702 0.238553 CACTCGACGAGTCAGAAGCA 59.761 55.000 27.03 0.00 41.37 3.91
1614 1708 4.348857 TCGACACTCGACGAGTCA 57.651 55.556 27.03 9.20 44.82 3.41
1657 1751 2.742053 ACCATTTCTTTCGACCATCGTG 59.258 45.455 0.00 0.00 41.35 4.35
1659 1753 3.262420 AGACCATTTCTTTCGACCATCG 58.738 45.455 0.00 0.00 42.10 3.84
1666 1760 5.689819 CACCAAAGTAGACCATTTCTTTCG 58.310 41.667 0.00 0.00 35.55 3.46
1747 1841 2.440796 ATCAACAGGCCGCCCATG 60.441 61.111 5.55 0.79 0.00 3.66
1754 1848 1.077429 GGGGTCAGATCAACAGGCC 60.077 63.158 0.00 0.00 0.00 5.19
1755 1849 0.393537 CTGGGGTCAGATCAACAGGC 60.394 60.000 0.00 0.00 43.49 4.85
1811 2078 7.552687 AGACGGAAGCATGTTCTTAATAATCAA 59.447 33.333 0.00 0.00 0.00 2.57
1815 2082 6.653320 ACAAGACGGAAGCATGTTCTTAATAA 59.347 34.615 0.00 0.00 0.00 1.40
1986 2253 4.458708 GTGAAATCACAAAGCTCGAACTC 58.541 43.478 8.63 0.00 45.75 3.01
2028 2295 4.561734 GCTTTTCTTCTCCTTCTCTCGGAA 60.562 45.833 0.00 0.00 0.00 4.30
2050 2317 2.093500 TGTACCTCTGATGTCATGTGGC 60.093 50.000 0.00 0.00 0.00 5.01
2054 2321 9.112725 TCATAAAAATGTACCTCTGATGTCATG 57.887 33.333 0.00 0.00 0.00 3.07
2084 2382 8.903820 GTCCAGCCTACTAAATTTTGTCATTAT 58.096 33.333 8.57 0.00 0.00 1.28
2085 2383 7.885922 TGTCCAGCCTACTAAATTTTGTCATTA 59.114 33.333 8.57 0.00 0.00 1.90
2086 2384 6.719370 TGTCCAGCCTACTAAATTTTGTCATT 59.281 34.615 8.57 0.00 0.00 2.57
2087 2385 6.245408 TGTCCAGCCTACTAAATTTTGTCAT 58.755 36.000 8.57 0.00 0.00 3.06
2095 2461 3.456277 CTCCCTTGTCCAGCCTACTAAAT 59.544 47.826 0.00 0.00 0.00 1.40
2105 2471 5.372373 GAAGGATAAATCTCCCTTGTCCAG 58.628 45.833 0.00 0.00 40.14 3.86
2156 2532 5.477984 TGCAATGCTTTCTTCTCCTGTAAAT 59.522 36.000 6.82 0.00 0.00 1.40
2201 2587 6.303839 ACAAAAGCCCACATAAACTTCTCTA 58.696 36.000 0.00 0.00 0.00 2.43
2202 2588 5.140454 ACAAAAGCCCACATAAACTTCTCT 58.860 37.500 0.00 0.00 0.00 3.10
2316 2811 5.163290 TGTGTAAAATCCCCCAAAGGAAAAC 60.163 40.000 0.00 0.00 40.04 2.43
2321 2816 6.183360 GGAATATGTGTAAAATCCCCCAAAGG 60.183 42.308 0.00 0.00 0.00 3.11
2465 3401 6.647895 TCCCGTACTTGAAACAGAATAAAGAC 59.352 38.462 0.00 0.00 0.00 3.01
2486 3422 3.610911 AGAGCCTTAAATTGAAGTCCCG 58.389 45.455 1.77 0.00 0.00 5.14
2566 3502 4.303282 GAGCCTCTTCTCCGATGTTTATC 58.697 47.826 0.00 0.00 0.00 1.75
2760 3700 9.691362 AACCATGTAACAGTTTTATCATGTTTC 57.309 29.630 13.92 0.00 38.14 2.78
2769 3709 4.475345 AGGCCAACCATGTAACAGTTTTA 58.525 39.130 5.01 0.00 39.06 1.52
2772 3712 2.108250 AGAGGCCAACCATGTAACAGTT 59.892 45.455 5.01 0.00 39.06 3.16
2805 3745 8.553696 ACGTACTTGATGTCTTTTTCGTTTATT 58.446 29.630 0.00 0.00 0.00 1.40
2820 3760 3.479006 CGCAAGGAAAACGTACTTGATG 58.521 45.455 19.74 10.97 43.13 3.07
2920 3860 7.041508 GGGTCACAAAAGCTCTATGAATCATAG 60.042 40.741 21.07 21.07 43.52 2.23
2922 3862 5.591877 GGGTCACAAAAGCTCTATGAATCAT 59.408 40.000 0.00 0.00 0.00 2.45
2943 3883 2.765699 GGACAATTATTGCACATGGGGT 59.234 45.455 4.68 0.00 0.00 4.95
2975 3928 2.158755 ACTGCCTATGTAATCCTGCCAC 60.159 50.000 0.00 0.00 0.00 5.01
2991 3944 2.685897 TGTAATTTGCCCGAATACTGCC 59.314 45.455 0.00 0.00 0.00 4.85
3026 3979 4.698780 TGTTTCTTCCTCTGATCATTGCTG 59.301 41.667 0.00 0.00 0.00 4.41
3131 4193 5.124776 TCGCAACATTGTAGAATAAAAGGGG 59.875 40.000 0.00 0.00 0.00 4.79
3153 4215 4.507388 AGATTGCCAACAAAAATTGTGTCG 59.493 37.500 0.00 0.00 44.59 4.35
3175 4237 9.137459 AGCAGCTTATATATATGGGTACAGTAG 57.863 37.037 5.44 0.00 0.00 2.57
3332 4526 7.707624 AAAAGGATTGAAGTAGCATGATCAA 57.292 32.000 0.00 0.00 36.35 2.57
3334 4528 8.348507 CCTAAAAAGGATTGAAGTAGCATGATC 58.651 37.037 0.00 0.00 0.00 2.92
3398 4593 7.492994 GGCAAACAAGTAACATTTTCAACCTTA 59.507 33.333 0.00 0.00 0.00 2.69
3610 4808 9.120538 GAAATACCTGCACAGAATTCCTTAATA 57.879 33.333 0.65 0.00 0.00 0.98
3634 4832 3.966665 GGATGGGAAAATAGCATTGGGAA 59.033 43.478 0.00 0.00 0.00 3.97
3778 4976 6.882610 TGTATCAAGCTTGTCAAAGACATT 57.117 33.333 25.19 2.82 42.40 2.71
3826 5024 1.355720 AGTCAGGCCAGGCATTAAGTT 59.644 47.619 15.19 0.00 0.00 2.66
3892 5090 7.199766 AGTGAAATTTGCATTCAACTTACGAA 58.800 30.769 2.87 0.00 38.44 3.85
3965 5182 1.736032 GCGACGTACTTGAGGCAATCT 60.736 52.381 0.00 0.00 0.00 2.40
4222 5450 3.782046 TGCTCGTTGATAGACTTTAGCC 58.218 45.455 0.00 0.00 0.00 3.93
4246 5474 5.464389 GTGAGTGAAAGCGTTTACCTCTTTA 59.536 40.000 3.74 0.00 30.97 1.85
4258 5486 1.220529 TGCAAGAGTGAGTGAAAGCG 58.779 50.000 0.00 0.00 0.00 4.68
4303 5621 4.642429 AGCAACCTGAGTAAACGAGAAAT 58.358 39.130 0.00 0.00 0.00 2.17
4398 5716 4.747605 GCAACAACCAACCGTTAATTCATT 59.252 37.500 0.00 0.00 31.77 2.57
4476 5830 5.181245 TGAGCCTGGAGAAAGAAATAAAACG 59.819 40.000 0.00 0.00 0.00 3.60
4544 5899 6.044512 TCGTTTCTTTGCTCTTTTAGACAC 57.955 37.500 0.00 0.00 0.00 3.67
4558 5913 3.883489 AGCCTACAAGCTTTCGTTTCTTT 59.117 39.130 0.00 0.00 41.41 2.52
4668 6023 4.202441 AGATTGTCCCCATTCTTTGATCG 58.798 43.478 0.00 0.00 29.21 3.69
4731 6086 4.081087 TCCACTATCCTAGTTTCAACCTGC 60.081 45.833 0.00 0.00 36.76 4.85
4933 6288 4.617959 TCACGAGGTTAATAGCTATGTGC 58.382 43.478 7.09 0.25 37.83 4.57
4935 6290 5.736492 GCACTCACGAGGTTAATAGCTATGT 60.736 44.000 7.09 0.53 30.79 2.29
5008 6363 7.520614 GCTTAATTTCTATCAGACGAATTGGGG 60.521 40.741 0.00 0.00 0.00 4.96
5073 8878 5.375417 TGGCACACAACTAATTTGATGAG 57.625 39.130 4.30 0.00 38.73 2.90
5147 8952 5.048013 AGCTTGTTAAGGACTGTAAAATGCC 60.048 40.000 0.00 0.00 0.00 4.40
5269 9074 1.059098 TGACCAGACAGCCAGACAAT 58.941 50.000 0.00 0.00 0.00 2.71
5311 9116 6.104146 AGTTCCTGGACTCTCTCTAAAAAC 57.896 41.667 0.00 0.00 0.00 2.43
5318 9126 3.655615 TCCTAGTTCCTGGACTCTCTC 57.344 52.381 0.00 0.00 0.00 3.20
5319 9127 3.529734 TGATCCTAGTTCCTGGACTCTCT 59.470 47.826 0.00 0.00 34.90 3.10
5429 9237 3.560068 ACTGTTTGTACAAGAAAGAGCGG 59.440 43.478 8.56 0.00 32.92 5.52
5534 9360 6.031751 AGAGAGAAGTTGTACAAGGCTTAG 57.968 41.667 8.98 0.00 0.00 2.18
5565 9391 6.554334 TGTCTATAAAGCGAAACAAAAGCT 57.446 33.333 0.00 0.00 43.90 3.74
5613 9439 7.414098 GCTTTGTAAGAGTGTTTTCTCAACTCA 60.414 37.037 4.99 0.00 36.97 3.41
5615 9441 6.183360 GGCTTTGTAAGAGTGTTTTCTCAACT 60.183 38.462 0.00 0.00 36.97 3.16
5668 9494 4.933514 GCATTTCTTATGCGTTGTTGTTG 58.066 39.130 0.00 0.00 35.17 3.33
5694 9520 0.249996 GCTTTTGCTTGGTGGCATGT 60.250 50.000 0.00 0.00 42.09 3.21
5718 9544 2.631545 ACTAGTTGTGGTTCCGCTACTT 59.368 45.455 20.13 5.43 35.15 2.24
5738 9564 4.209911 GGTTCGTACCTCAGTTGTTGTTAC 59.790 45.833 3.61 0.00 41.53 2.50
5756 9582 2.096496 GGCAATGAAGTCTGATGGTTCG 59.904 50.000 0.00 0.00 0.00 3.95
5760 9617 0.379669 GCGGCAATGAAGTCTGATGG 59.620 55.000 0.00 0.00 0.00 3.51
5791 9648 4.761739 TGTTTTGCCTCCTCTCATTTACAG 59.238 41.667 0.00 0.00 0.00 2.74
5835 9692 0.107066 TCATCACGCATTGCATCCCT 60.107 50.000 9.69 0.00 0.00 4.20
5852 9709 2.183478 TTTCGAGCAAGCTTGGATCA 57.817 45.000 27.10 4.40 0.00 2.92
5877 9735 3.220999 CTCTGGTTGTCGTGCGGGA 62.221 63.158 0.00 0.00 0.00 5.14
5885 9743 1.652947 TTACCCTCCCTCTGGTTGTC 58.347 55.000 0.00 0.00 36.04 3.18
5910 9797 3.295304 ATGTGGCAGCGACGCACTA 62.295 57.895 23.70 8.80 32.28 2.74
5944 9831 1.202486 TCGTGCTCCGAGTGAAAACTT 60.202 47.619 0.00 0.00 41.60 2.66
5965 9852 1.545651 GGGTGTTCTCCCTCACTTTGG 60.546 57.143 3.04 0.00 43.85 3.28
6091 9978 0.613777 CTCGGTAGCCAGGTTCCTTT 59.386 55.000 0.00 0.00 0.00 3.11
6119 10006 3.066208 TCTAGAGGCTGGGATCCAATT 57.934 47.619 15.23 0.00 30.80 2.32
6129 10016 4.823157 CCATGATCTTGATCTAGAGGCTG 58.177 47.826 12.40 8.69 0.00 4.85
6161 10048 2.859538 GGCAATGTTGTCAACACTTGTG 59.140 45.455 20.41 15.74 45.50 3.33
6162 10049 2.495270 TGGCAATGTTGTCAACACTTGT 59.505 40.909 20.41 2.05 45.50 3.16
6167 10054 0.383590 CCGTGGCAATGTTGTCAACA 59.616 50.000 20.28 20.28 45.39 3.33
6206 10093 0.107456 CGGTGAGCTATGCCCTCAAT 59.893 55.000 0.00 0.00 40.69 2.57


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

AutoCloner maintained by Alex Coulton.