Multiple sequence alignment - TraesCS5B01G384800

Loading Multiple Alignment...

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 TraesCS5B01G384800 chr5B 100.000 3782 0 0 1 3782 563462518 563466299 0.000000e+00 6985
1 TraesCS5B01G384800 chr5B 94.030 1474 61 10 1626 3095 563544300 563542850 0.000000e+00 2209
2 TraesCS5B01G384800 chr5B 90.326 951 49 23 670 1591 563545312 563544376 0.000000e+00 1206
3 TraesCS5B01G384800 chr5B 93.464 459 21 6 3117 3568 563542663 563542207 0.000000e+00 673
4 TraesCS5B01G384800 chr5B 92.177 294 19 2 35 327 563545799 563545509 2.720000e-111 412
5 TraesCS5B01G384800 chr5A 94.145 1281 47 14 1626 2891 578836870 578838137 0.000000e+00 1925
6 TraesCS5B01G384800 chr5A 89.568 1227 63 24 452 1629 578835620 578836830 0.000000e+00 1496
7 TraesCS5B01G384800 chr5A 88.251 366 23 12 3344 3691 578842253 578842616 1.620000e-113 420
8 TraesCS5B01G384800 chr5A 93.868 212 9 2 3117 3328 578841893 578842100 2.190000e-82 316
9 TraesCS5B01G384800 chr5A 89.212 241 20 2 2882 3118 578838187 578838425 2.860000e-76 296
10 TraesCS5B01G384800 chr5A 86.765 136 10 7 126 255 578834460 578834593 1.090000e-30 145
11 TraesCS5B01G384800 chr5A 94.030 67 3 1 367 433 578835563 578835628 2.400000e-17 100
12 TraesCS5B01G384800 chr5D 95.634 1168 37 6 1636 2800 459315073 459316229 0.000000e+00 1862
13 TraesCS5B01G384800 chr5D 91.468 797 30 20 751 1528 459314255 459315032 0.000000e+00 1061
14 TraesCS5B01G384800 chr5D 93.590 156 10 0 3538 3693 459327625 459327780 2.270000e-57 233
15 TraesCS5B01G384800 chr5D 94.964 139 5 2 453 590 459310904 459311041 2.290000e-52 217
16 TraesCS5B01G384800 chr5D 89.344 122 4 2 650 767 459312607 459312723 1.090000e-30 145
17 TraesCS5B01G384800 chr5D 80.460 174 12 9 2882 3037 459316371 459316540 3.090000e-21 113
18 TraesCS5B01G384800 chr3B 91.142 1095 94 1 1709 2803 60366537 60365446 0.000000e+00 1482
19 TraesCS5B01G384800 chr3B 89.579 499 47 4 967 1462 60368097 60367601 2.480000e-176 628
20 TraesCS5B01G384800 chr3D 91.201 1091 93 1 1709 2799 37969939 37968852 0.000000e+00 1480
21 TraesCS5B01G384800 chr3D 91.278 493 36 5 975 1462 37970930 37970440 0.000000e+00 665
22 TraesCS5B01G384800 chr7A 85.963 1090 152 1 1712 2800 4515760 4516849 0.000000e+00 1164
23 TraesCS5B01G384800 chr7A 85.793 1091 152 3 1712 2800 4556977 4555888 0.000000e+00 1153
24 TraesCS5B01G384800 chr7A 88.121 463 55 0 1000 1462 4559792 4559330 5.520000e-153 551
25 TraesCS5B01G384800 chr7A 87.619 420 49 2 1046 1462 4511363 4511782 5.680000e-133 484
26 TraesCS5B01G384800 chr3A 92.941 595 42 0 2209 2803 48663772 48663178 0.000000e+00 867
27 TraesCS5B01G384800 chr3A 89.940 497 49 1 967 1462 48665188 48664692 1.150000e-179 640
28 TraesCS5B01G384800 chr3A 89.212 482 49 1 1709 2190 48664334 48663856 1.940000e-167 599
29 TraesCS5B01G384800 chr4A 84.697 758 111 5 1712 2466 738980734 738979979 0.000000e+00 752
30 TraesCS5B01G384800 chr4A 87.342 474 59 1 990 1462 738983804 738983331 3.320000e-150 542
31 TraesCS5B01G384800 chr2B 84.977 213 32 0 2557 2769 439916536 439916324 2.290000e-52 217
32 TraesCS5B01G384800 chr6A 80.982 163 27 2 3342 3501 153507956 153508117 3.970000e-25 126
33 TraesCS5B01G384800 chr1D 93.151 73 2 1 3713 3782 460198210 460198138 1.860000e-18 104


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 TraesCS5B01G384800 chr5B 563462518 563466299 3781 False 6985.000000 6985 100.000000 1 3782 1 chr5B.!!$F1 3781
1 TraesCS5B01G384800 chr5B 563542207 563545799 3592 True 1125.000000 2209 92.499250 35 3568 4 chr5B.!!$R1 3533
2 TraesCS5B01G384800 chr5A 578834460 578842616 8156 False 671.142857 1925 90.834143 126 3691 7 chr5A.!!$F1 3565
3 TraesCS5B01G384800 chr5D 459310904 459316540 5636 False 679.600000 1862 90.374000 453 3037 5 chr5D.!!$F2 2584
4 TraesCS5B01G384800 chr3B 60365446 60368097 2651 True 1055.000000 1482 90.360500 967 2803 2 chr3B.!!$R1 1836
5 TraesCS5B01G384800 chr3D 37968852 37970930 2078 True 1072.500000 1480 91.239500 975 2799 2 chr3D.!!$R1 1824
6 TraesCS5B01G384800 chr7A 4555888 4559792 3904 True 852.000000 1153 86.957000 1000 2800 2 chr7A.!!$R1 1800
7 TraesCS5B01G384800 chr7A 4511363 4516849 5486 False 824.000000 1164 86.791000 1046 2800 2 chr7A.!!$F1 1754
8 TraesCS5B01G384800 chr3A 48663178 48665188 2010 True 702.000000 867 90.697667 967 2803 3 chr3A.!!$R1 1836
9 TraesCS5B01G384800 chr4A 738979979 738983804 3825 True 647.000000 752 86.019500 990 2466 2 chr4A.!!$R1 1476

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
916 4917 0.179004 TCACCACCAATCACCACCAC 60.179 55.0 0.0 0.0 0.00 4.16 F
1726 12659 0.758123 TATGCAGGTGATGATGCGGA 59.242 50.0 0.0 0.0 45.54 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 12995 0.388263 GGTTCTCGTCCACGTTCTCC 60.388 60.0 0.0 0.0 40.8 3.71 R
3693 18443 0.105453 TGATCTGTAGCCTCTCCCCC 60.105 60.0 0.0 0.0 0.0 5.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.836125 GTTGCCACTTGGGACATATATG 57.164 45.455 11.29 11.29 39.30 1.78
22 23 4.460263 GTTGCCACTTGGGACATATATGA 58.540 43.478 19.63 0.00 39.30 2.15
23 24 4.999469 TGCCACTTGGGACATATATGAT 57.001 40.909 19.63 3.75 39.30 2.45
24 25 5.323382 TGCCACTTGGGACATATATGATT 57.677 39.130 19.63 0.00 39.30 2.57
25 26 5.316167 TGCCACTTGGGACATATATGATTC 58.684 41.667 19.63 7.21 39.30 2.52
26 27 5.163109 TGCCACTTGGGACATATATGATTCA 60.163 40.000 19.63 10.34 39.30 2.57
27 28 5.948162 GCCACTTGGGACATATATGATTCAT 59.052 40.000 19.63 4.28 39.30 2.57
28 29 6.127814 GCCACTTGGGACATATATGATTCATG 60.128 42.308 19.63 15.27 39.30 3.07
29 30 6.944290 CCACTTGGGACATATATGATTCATGT 59.056 38.462 19.63 15.78 39.30 3.21
30 31 8.102676 CCACTTGGGACATATATGATTCATGTA 58.897 37.037 19.63 7.45 39.30 2.29
31 32 8.939929 CACTTGGGACATATATGATTCATGTAC 58.060 37.037 19.63 0.84 39.30 2.90
32 33 8.884323 ACTTGGGACATATATGATTCATGTACT 58.116 33.333 19.63 0.00 39.30 2.73
33 34 9.376075 CTTGGGACATATATGATTCATGTACTC 57.624 37.037 19.63 5.65 39.30 2.59
37 38 6.036470 ACATATATGATTCATGTACTCGCCG 58.964 40.000 19.63 0.00 31.26 6.46
41 42 2.100749 TGATTCATGTACTCGCCGACAT 59.899 45.455 0.00 0.00 36.73 3.06
53 54 3.651206 TCGCCGACATTAAACAGTTACA 58.349 40.909 0.00 0.00 0.00 2.41
54 55 4.247258 TCGCCGACATTAAACAGTTACAT 58.753 39.130 0.00 0.00 0.00 2.29
55 56 5.409211 TCGCCGACATTAAACAGTTACATA 58.591 37.500 0.00 0.00 0.00 2.29
124 126 8.217131 TCACTGGATGATTTGTTGATAATCTG 57.783 34.615 0.00 0.00 34.00 2.90
159 164 5.231568 GCAAGCAAGCATGTTTCATCTTATC 59.768 40.000 0.00 0.00 0.00 1.75
280 1177 7.130681 ACAGGGAAACATTAGAATCCTCTAG 57.869 40.000 0.00 0.00 35.55 2.43
283 1180 8.145122 CAGGGAAACATTAGAATCCTCTAGTAC 58.855 40.741 0.00 0.00 35.55 2.73
295 1192 4.922206 TCCTCTAGTACCGGAGTTTTACA 58.078 43.478 9.46 0.00 0.00 2.41
320 1217 7.062722 CAGTTTACTATACATCATCGGCTCATG 59.937 40.741 0.00 0.00 0.00 3.07
327 1224 5.474578 ACATCATCGGCTCATGTATAACT 57.525 39.130 0.00 0.00 0.00 2.24
328 1225 5.233225 ACATCATCGGCTCATGTATAACTG 58.767 41.667 0.00 0.00 0.00 3.16
330 1227 3.006859 TCATCGGCTCATGTATAACTGGG 59.993 47.826 0.00 0.00 0.00 4.45
331 1228 2.673258 TCGGCTCATGTATAACTGGGA 58.327 47.619 0.00 0.00 0.00 4.37
332 1229 3.035363 TCGGCTCATGTATAACTGGGAA 58.965 45.455 0.00 0.00 0.00 3.97
333 1230 3.452990 TCGGCTCATGTATAACTGGGAAA 59.547 43.478 0.00 0.00 0.00 3.13
334 1231 3.560068 CGGCTCATGTATAACTGGGAAAC 59.440 47.826 0.00 0.00 0.00 2.78
335 1232 4.523083 GGCTCATGTATAACTGGGAAACA 58.477 43.478 0.00 0.00 0.00 2.83
336 1233 5.133221 GGCTCATGTATAACTGGGAAACAT 58.867 41.667 0.00 0.00 0.00 2.71
337 1234 5.594317 GGCTCATGTATAACTGGGAAACATT 59.406 40.000 0.00 0.00 0.00 2.71
338 1235 6.770785 GGCTCATGTATAACTGGGAAACATTA 59.229 38.462 0.00 0.00 0.00 1.90
339 1236 7.041098 GGCTCATGTATAACTGGGAAACATTAG 60.041 40.741 0.00 0.00 0.00 1.73
340 1237 7.715249 GCTCATGTATAACTGGGAAACATTAGA 59.285 37.037 0.00 0.00 27.94 2.10
341 1238 9.613428 CTCATGTATAACTGGGAAACATTAGAA 57.387 33.333 0.00 0.00 27.94 2.10
344 1241 8.974060 TGTATAACTGGGAAACATTAGAATCC 57.026 34.615 0.00 0.00 0.00 3.01
345 1242 8.778059 TGTATAACTGGGAAACATTAGAATCCT 58.222 33.333 0.00 0.00 32.41 3.24
346 1243 9.274206 GTATAACTGGGAAACATTAGAATCCTC 57.726 37.037 0.00 0.00 32.41 3.71
347 1244 6.394345 AACTGGGAAACATTAGAATCCTCT 57.606 37.500 0.00 0.00 35.52 3.69
348 1245 7.510675 AACTGGGAAACATTAGAATCCTCTA 57.489 36.000 0.00 0.00 32.70 2.43
349 1246 7.510675 ACTGGGAAACATTAGAATCCTCTAA 57.489 36.000 0.00 0.00 45.93 2.10
350 1247 7.928873 ACTGGGAAACATTAGAATCCTCTAAA 58.071 34.615 0.00 0.00 45.20 1.85
351 1248 8.390921 ACTGGGAAACATTAGAATCCTCTAAAA 58.609 33.333 0.00 0.00 45.20 1.52
352 1249 9.243105 CTGGGAAACATTAGAATCCTCTAAAAA 57.757 33.333 0.00 0.00 45.20 1.94
353 1250 9.020731 TGGGAAACATTAGAATCCTCTAAAAAC 57.979 33.333 0.00 0.00 45.20 2.43
354 1251 9.020731 GGGAAACATTAGAATCCTCTAAAAACA 57.979 33.333 0.00 0.00 45.20 2.83
357 1254 8.581253 AACATTAGAATCCTCTAAAAACAGGG 57.419 34.615 0.00 0.00 45.20 4.45
358 1255 7.928873 ACATTAGAATCCTCTAAAAACAGGGA 58.071 34.615 0.00 0.00 45.20 4.20
359 1256 7.829706 ACATTAGAATCCTCTAAAAACAGGGAC 59.170 37.037 0.00 0.00 45.20 4.46
383 1280 8.757164 ACTTTATGATGCATGCATGATTATTG 57.243 30.769 36.73 22.51 36.70 1.90
420 1317 9.585099 GAATGATGGAAATTGTTTATGTTGCTA 57.415 29.630 0.00 0.00 0.00 3.49
424 1321 8.761575 ATGGAAATTGTTTATGTTGCTACTTG 57.238 30.769 0.00 0.00 0.00 3.16
425 1322 7.721402 TGGAAATTGTTTATGTTGCTACTTGT 58.279 30.769 0.00 0.00 0.00 3.16
426 1323 8.200792 TGGAAATTGTTTATGTTGCTACTTGTT 58.799 29.630 0.00 0.00 0.00 2.83
427 1324 8.487176 GGAAATTGTTTATGTTGCTACTTGTTG 58.513 33.333 0.00 0.00 0.00 3.33
428 1325 8.940768 AAATTGTTTATGTTGCTACTTGTTGT 57.059 26.923 0.00 0.00 0.00 3.32
433 1330 9.496873 TGTTTATGTTGCTACTTGTTGTATAGT 57.503 29.630 0.00 0.00 0.00 2.12
495 1392 3.890756 CCCATGCACTTCCAATATGCTTA 59.109 43.478 0.00 0.00 40.13 3.09
496 1393 4.261741 CCCATGCACTTCCAATATGCTTAC 60.262 45.833 0.00 0.00 40.13 2.34
497 1394 4.338964 CCATGCACTTCCAATATGCTTACA 59.661 41.667 0.00 0.00 40.13 2.41
498 1395 4.963276 TGCACTTCCAATATGCTTACAC 57.037 40.909 0.00 0.00 40.13 2.90
499 1396 4.331108 TGCACTTCCAATATGCTTACACA 58.669 39.130 0.00 0.00 40.13 3.72
510 1407 6.851222 ATATGCTTACACAATTCTTCCGAG 57.149 37.500 0.00 0.00 0.00 4.63
562 1459 3.508845 ACCTTTCCACTTGCAGTATGT 57.491 42.857 0.00 0.00 39.31 2.29
637 1534 0.686769 GGTAGGACCATCGGACCACT 60.687 60.000 4.38 0.00 39.89 4.00
640 1537 1.079127 GGACCATCGGACCACTGTG 60.079 63.158 0.00 0.00 37.47 3.66
642 1539 2.436646 CCATCGGACCACTGTGGC 60.437 66.667 26.20 17.90 42.67 5.01
719 3142 2.604046 AGAGAAGACAACGTTGCACT 57.396 45.000 27.61 22.42 0.00 4.40
720 3143 3.728076 AGAGAAGACAACGTTGCACTA 57.272 42.857 27.61 0.00 0.00 2.74
721 3144 4.054780 AGAGAAGACAACGTTGCACTAA 57.945 40.909 27.61 0.00 0.00 2.24
722 3145 4.632153 AGAGAAGACAACGTTGCACTAAT 58.368 39.130 27.61 17.21 0.00 1.73
723 3146 5.779922 AGAGAAGACAACGTTGCACTAATA 58.220 37.500 27.61 0.00 0.00 0.98
916 4917 0.179004 TCACCACCAATCACCACCAC 60.179 55.000 0.00 0.00 0.00 4.16
933 4934 4.028131 CACCACCACTACCTCTACCATTA 58.972 47.826 0.00 0.00 0.00 1.90
937 4940 2.035576 CCACTACCTCTACCATTACGCC 59.964 54.545 0.00 0.00 0.00 5.68
945 4948 5.047235 ACCTCTACCATTACGCCTATCATTC 60.047 44.000 0.00 0.00 0.00 2.67
1071 5090 2.331132 GCTGCAGGTGCTCAAGGTC 61.331 63.158 17.12 0.00 42.66 3.85
1458 5480 1.899437 GCCACATCAGGGAGGACGAA 61.899 60.000 0.00 0.00 0.00 3.85
1541 9043 8.585189 AACTTACAAGTAGTTAAGTACTGTGC 57.415 34.615 21.05 0.00 38.57 4.57
1582 9086 1.265905 AGCACGGCCGAAAAGTTAAAG 59.734 47.619 35.90 8.66 0.00 1.85
1583 9087 1.002142 GCACGGCCGAAAAGTTAAAGT 60.002 47.619 35.90 0.00 0.00 2.66
1602 9109 3.881795 AGTACGTAACACAGAACAGTCG 58.118 45.455 0.00 0.00 0.00 4.18
1629 9261 2.279935 AAAATACCGGCACCACAAGA 57.720 45.000 0.00 0.00 0.00 3.02
1630 9262 2.507407 AAATACCGGCACCACAAGAT 57.493 45.000 0.00 0.00 0.00 2.40
1657 9615 9.208022 TGAGACTTATGAATGAACAGTGTTTAG 57.792 33.333 10.45 0.00 0.00 1.85
1664 9622 5.813157 TGAATGAACAGTGTTTAGTTCGTCA 59.187 36.000 10.45 0.99 45.34 4.35
1726 12659 0.758123 TATGCAGGTGATGATGCGGA 59.242 50.000 0.00 0.00 45.54 5.54
2103 13043 1.068250 GCTCATCGGCCTACAGGAC 59.932 63.158 0.00 0.00 40.84 3.85
2243 13248 3.853330 CAACCCGCGCGTGATGAG 61.853 66.667 29.95 12.01 0.00 2.90
2547 13552 4.681978 GGCGCCGTGGACTTCACT 62.682 66.667 12.58 0.00 43.94 3.41
2849 13888 2.105328 TGTGTGTGTCCGTCGGTG 59.895 61.111 11.88 0.00 0.00 4.94
2865 13904 1.339097 GGTGCGTCCCCATCTACTAT 58.661 55.000 0.00 0.00 0.00 2.12
2866 13905 1.272769 GGTGCGTCCCCATCTACTATC 59.727 57.143 0.00 0.00 0.00 2.08
2867 13906 2.240279 GTGCGTCCCCATCTACTATCT 58.760 52.381 0.00 0.00 0.00 1.98
2868 13907 3.418995 GTGCGTCCCCATCTACTATCTA 58.581 50.000 0.00 0.00 0.00 1.98
2869 13908 3.440872 GTGCGTCCCCATCTACTATCTAG 59.559 52.174 0.00 0.00 0.00 2.43
2874 13913 5.508567 GTCCCCATCTACTATCTAGTACCC 58.491 50.000 0.00 0.00 37.73 3.69
2875 13914 5.014966 GTCCCCATCTACTATCTAGTACCCA 59.985 48.000 0.00 0.00 37.73 4.51
2877 13916 5.222275 CCCCATCTACTATCTAGTACCCACA 60.222 48.000 0.00 0.00 37.73 4.17
2878 13917 5.711036 CCCATCTACTATCTAGTACCCACAC 59.289 48.000 0.00 0.00 37.73 3.82
2879 13918 6.304624 CCATCTACTATCTAGTACCCACACA 58.695 44.000 0.00 0.00 37.73 3.72
2975 14077 3.393278 TGTAACCATGGAGGCCCTAATAC 59.607 47.826 21.47 7.44 43.14 1.89
3037 14156 4.006989 TGATTGGATTGTTGTTACTCCCG 58.993 43.478 0.00 0.00 0.00 5.14
3040 14159 3.929094 TGGATTGTTGTTACTCCCGTAC 58.071 45.455 0.00 0.00 0.00 3.67
3058 14181 2.177950 CGGGAGTACGTACTGCTGT 58.822 57.895 35.11 14.74 43.47 4.40
3066 14189 4.435425 AGTACGTACTGCTGTTGTTTGAA 58.565 39.130 26.87 0.00 34.72 2.69
3075 14198 9.672086 GTACTGCTGTTGTTTGAAACATTATTA 57.328 29.630 11.97 0.00 41.79 0.98
3096 14219 1.403679 TGTTCTTTGTTTGTCCTGCCG 59.596 47.619 0.00 0.00 0.00 5.69
3100 14223 2.285889 TTTGTTTGTCCTGCCGGGGA 62.286 55.000 2.18 0.00 35.33 4.81
3296 17890 3.398406 TCAAACAGCAAAGCATCTACGA 58.602 40.909 0.00 0.00 0.00 3.43
3299 17893 2.076863 ACAGCAAAGCATCTACGAACC 58.923 47.619 0.00 0.00 0.00 3.62
3313 17908 1.269166 CGAACCGACACTGACATAGC 58.731 55.000 0.00 0.00 0.00 2.97
3314 17909 1.135373 CGAACCGACACTGACATAGCT 60.135 52.381 0.00 0.00 0.00 3.32
3315 17910 2.096980 CGAACCGACACTGACATAGCTA 59.903 50.000 0.00 0.00 0.00 3.32
3316 17911 3.696898 GAACCGACACTGACATAGCTAG 58.303 50.000 0.00 0.00 0.00 3.42
3329 17924 2.125753 GCTAGACGCTGCACTGCT 60.126 61.111 1.98 0.00 35.14 4.24
3478 18213 6.222038 AGACTTTGAAATCTAGTATGCGGA 57.778 37.500 0.00 0.00 0.00 5.54
3495 18230 3.118920 TGCGGAGTAAAAATGATCGGAGA 60.119 43.478 0.00 0.00 45.75 3.71
3598 18339 5.389642 AGTACGATGCAAAACATACGATG 57.610 39.130 0.00 0.00 39.84 3.84
3606 18347 1.365699 AAACATACGATGGACCGTGC 58.634 50.000 0.00 0.00 43.27 5.34
3625 18366 2.099427 TGCGTAATCAACATGCATGCAT 59.901 40.909 27.46 27.46 33.08 3.96
3635 18384 1.727511 ATGCATGCATACGTGGGCAC 61.728 55.000 31.35 7.35 43.75 5.01
3693 18443 4.666105 GCCCAGGGCCTCTAAAAG 57.334 61.111 21.62 0.00 44.06 2.27
3695 18445 1.615262 CCCAGGGCCTCTAAAAGGG 59.385 63.158 0.95 6.51 46.32 3.95
3696 18446 1.615262 CCAGGGCCTCTAAAAGGGG 59.385 63.158 0.95 0.00 46.32 4.79
3697 18447 1.615262 CAGGGCCTCTAAAAGGGGG 59.385 63.158 0.95 0.00 46.32 5.40
3698 18448 0.919289 CAGGGCCTCTAAAAGGGGGA 60.919 60.000 0.95 0.00 46.32 4.81
3699 18449 0.624795 AGGGCCTCTAAAAGGGGGAG 60.625 60.000 0.00 0.00 46.32 4.30
3700 18450 0.623617 GGGCCTCTAAAAGGGGGAGA 60.624 60.000 0.84 0.00 46.32 3.71
3701 18451 0.840617 GGCCTCTAAAAGGGGGAGAG 59.159 60.000 0.00 0.00 46.32 3.20
3704 18454 1.886422 CTCTAAAAGGGGGAGAGGCT 58.114 55.000 0.00 0.00 34.31 4.58
3705 18455 3.047695 CTCTAAAAGGGGGAGAGGCTA 57.952 52.381 0.00 0.00 34.31 3.93
3706 18456 2.701423 CTCTAAAAGGGGGAGAGGCTAC 59.299 54.545 0.00 0.00 34.31 3.58
3707 18457 2.045326 TCTAAAAGGGGGAGAGGCTACA 59.955 50.000 0.00 0.00 0.00 2.74
3708 18458 1.290134 AAAAGGGGGAGAGGCTACAG 58.710 55.000 0.00 0.00 0.00 2.74
3709 18459 0.417841 AAAGGGGGAGAGGCTACAGA 59.582 55.000 0.00 0.00 0.00 3.41
3710 18460 0.644937 AAGGGGGAGAGGCTACAGAT 59.355 55.000 0.00 0.00 0.00 2.90
3711 18461 0.189822 AGGGGGAGAGGCTACAGATC 59.810 60.000 0.00 0.00 0.00 2.75
3712 18462 0.105453 GGGGGAGAGGCTACAGATCA 60.105 60.000 0.00 0.00 0.00 2.92
3713 18463 1.337118 GGGGAGAGGCTACAGATCAG 58.663 60.000 0.00 0.00 0.00 2.90
3714 18464 1.412361 GGGGAGAGGCTACAGATCAGT 60.412 57.143 0.00 0.00 0.00 3.41
3715 18465 1.960689 GGGAGAGGCTACAGATCAGTC 59.039 57.143 0.00 0.00 0.00 3.51
3716 18466 1.606668 GGAGAGGCTACAGATCAGTCG 59.393 57.143 0.00 0.00 0.00 4.18
3717 18467 2.566913 GAGAGGCTACAGATCAGTCGA 58.433 52.381 0.00 0.00 0.00 4.20
3718 18468 2.289547 GAGAGGCTACAGATCAGTCGAC 59.710 54.545 7.70 7.70 0.00 4.20
3719 18469 2.092646 AGAGGCTACAGATCAGTCGACT 60.093 50.000 13.58 13.58 0.00 4.18
3720 18470 2.020720 AGGCTACAGATCAGTCGACTG 58.979 52.381 34.76 34.76 45.08 3.51
3743 18493 6.943981 TGAATTTTTCAGTTAGTGTCAGTCG 58.056 36.000 0.00 0.00 34.08 4.18
3744 18494 4.789095 TTTTTCAGTTAGTGTCAGTCGC 57.211 40.909 0.00 0.00 0.00 5.19
3745 18495 2.046283 TTCAGTTAGTGTCAGTCGCG 57.954 50.000 0.00 0.00 0.00 5.87
3746 18496 0.949397 TCAGTTAGTGTCAGTCGCGT 59.051 50.000 5.77 0.00 0.00 6.01
3747 18497 1.053048 CAGTTAGTGTCAGTCGCGTG 58.947 55.000 5.77 0.00 0.00 5.34
3748 18498 0.039437 AGTTAGTGTCAGTCGCGTGG 60.039 55.000 5.77 0.00 0.00 4.94
3749 18499 0.039798 GTTAGTGTCAGTCGCGTGGA 60.040 55.000 5.77 0.00 0.00 4.02
3750 18500 0.039798 TTAGTGTCAGTCGCGTGGAC 60.040 55.000 5.77 12.89 46.45 4.02
3760 18510 4.124351 GCGTGGACCGTCGGATGA 62.124 66.667 20.51 0.00 39.32 2.92
3761 18511 2.569657 CGTGGACCGTCGGATGAA 59.430 61.111 20.51 0.00 0.00 2.57
3762 18512 1.080366 CGTGGACCGTCGGATGAAA 60.080 57.895 20.51 0.00 0.00 2.69
3763 18513 0.668096 CGTGGACCGTCGGATGAAAA 60.668 55.000 20.51 0.00 0.00 2.29
3764 18514 1.734163 GTGGACCGTCGGATGAAAAT 58.266 50.000 20.51 0.00 0.00 1.82
3765 18515 1.664151 GTGGACCGTCGGATGAAAATC 59.336 52.381 20.51 2.42 0.00 2.17
3766 18516 0.928229 GGACCGTCGGATGAAAATCG 59.072 55.000 20.51 0.00 0.00 3.34
3767 18517 1.636988 GACCGTCGGATGAAAATCGT 58.363 50.000 20.51 0.00 0.00 3.73
3768 18518 1.323534 GACCGTCGGATGAAAATCGTG 59.676 52.381 20.51 0.00 0.00 4.35
3769 18519 1.337447 ACCGTCGGATGAAAATCGTGT 60.337 47.619 20.51 0.00 0.00 4.49
3770 18520 1.060553 CCGTCGGATGAAAATCGTGTG 59.939 52.381 4.91 0.00 0.00 3.82
3771 18521 1.060553 CGTCGGATGAAAATCGTGTGG 59.939 52.381 0.00 0.00 0.00 4.17
3772 18522 1.083489 TCGGATGAAAATCGTGTGGC 58.917 50.000 0.00 0.00 0.00 5.01
3773 18523 0.801872 CGGATGAAAATCGTGTGGCA 59.198 50.000 0.00 0.00 0.00 4.92
3774 18524 1.202065 CGGATGAAAATCGTGTGGCAG 60.202 52.381 0.00 0.00 0.00 4.85
3775 18525 1.468054 GGATGAAAATCGTGTGGCAGC 60.468 52.381 0.00 0.00 0.00 5.25
3776 18526 1.470098 GATGAAAATCGTGTGGCAGCT 59.530 47.619 0.00 0.00 0.00 4.24
3777 18527 2.177394 TGAAAATCGTGTGGCAGCTA 57.823 45.000 0.00 0.00 0.00 3.32
3778 18528 2.076100 TGAAAATCGTGTGGCAGCTAG 58.924 47.619 0.00 0.00 0.00 3.42
3779 18529 2.289382 TGAAAATCGTGTGGCAGCTAGA 60.289 45.455 0.00 0.00 0.00 2.43
3780 18530 2.698855 AAATCGTGTGGCAGCTAGAT 57.301 45.000 0.00 0.00 0.00 1.98
3781 18531 2.231215 AATCGTGTGGCAGCTAGATC 57.769 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.460263 TCATATATGTCCCAAGTGGCAAC 58.540 43.478 12.42 0.00 0.00 4.17
1 2 4.787135 TCATATATGTCCCAAGTGGCAA 57.213 40.909 12.42 0.00 0.00 4.52
2 3 4.999469 ATCATATATGTCCCAAGTGGCA 57.001 40.909 12.42 0.00 0.00 4.92
3 4 5.316167 TGAATCATATATGTCCCAAGTGGC 58.684 41.667 12.42 0.00 0.00 5.01
5 6 7.991084 ACATGAATCATATATGTCCCAAGTG 57.009 36.000 12.42 7.04 29.55 3.16
6 7 8.884323 AGTACATGAATCATATATGTCCCAAGT 58.116 33.333 12.42 12.47 36.52 3.16
7 8 9.376075 GAGTACATGAATCATATATGTCCCAAG 57.624 37.037 12.42 8.14 36.52 3.61
8 9 8.034804 CGAGTACATGAATCATATATGTCCCAA 58.965 37.037 12.42 0.00 36.52 4.12
9 10 7.547227 CGAGTACATGAATCATATATGTCCCA 58.453 38.462 12.42 8.83 36.52 4.37
10 11 6.477033 GCGAGTACATGAATCATATATGTCCC 59.523 42.308 12.42 3.88 36.52 4.46
11 12 6.477033 GGCGAGTACATGAATCATATATGTCC 59.523 42.308 12.42 4.19 36.52 4.02
12 13 6.197282 CGGCGAGTACATGAATCATATATGTC 59.803 42.308 12.42 4.69 36.52 3.06
13 14 6.036470 CGGCGAGTACATGAATCATATATGT 58.964 40.000 12.42 0.00 38.48 2.29
14 15 6.197282 GTCGGCGAGTACATGAATCATATATG 59.803 42.308 11.20 6.36 0.00 1.78
15 16 6.127730 TGTCGGCGAGTACATGAATCATATAT 60.128 38.462 11.20 0.00 0.00 0.86
16 17 5.182380 TGTCGGCGAGTACATGAATCATATA 59.818 40.000 11.20 0.00 0.00 0.86
17 18 4.022329 TGTCGGCGAGTACATGAATCATAT 60.022 41.667 11.20 0.00 0.00 1.78
18 19 3.316868 TGTCGGCGAGTACATGAATCATA 59.683 43.478 11.20 0.00 0.00 2.15
19 20 2.100749 TGTCGGCGAGTACATGAATCAT 59.899 45.455 11.20 0.00 0.00 2.45
20 21 1.474879 TGTCGGCGAGTACATGAATCA 59.525 47.619 11.20 0.00 0.00 2.57
21 22 2.203800 TGTCGGCGAGTACATGAATC 57.796 50.000 11.20 0.00 0.00 2.52
22 23 2.890808 ATGTCGGCGAGTACATGAAT 57.109 45.000 11.20 0.00 35.06 2.57
23 24 2.665649 AATGTCGGCGAGTACATGAA 57.334 45.000 11.20 0.00 36.47 2.57
24 25 3.786516 TTAATGTCGGCGAGTACATGA 57.213 42.857 11.20 0.72 36.47 3.07
25 26 3.615056 TGTTTAATGTCGGCGAGTACATG 59.385 43.478 11.20 0.00 36.47 3.21
26 27 3.852286 TGTTTAATGTCGGCGAGTACAT 58.148 40.909 11.20 8.56 37.94 2.29
27 28 3.247442 CTGTTTAATGTCGGCGAGTACA 58.753 45.455 11.20 6.01 0.00 2.90
28 29 3.248266 ACTGTTTAATGTCGGCGAGTAC 58.752 45.455 11.20 0.00 0.00 2.73
29 30 3.581024 ACTGTTTAATGTCGGCGAGTA 57.419 42.857 11.20 2.31 0.00 2.59
30 31 2.450609 ACTGTTTAATGTCGGCGAGT 57.549 45.000 11.20 0.00 0.00 4.18
31 32 3.676172 TGTAACTGTTTAATGTCGGCGAG 59.324 43.478 11.20 0.00 0.00 5.03
32 33 3.651206 TGTAACTGTTTAATGTCGGCGA 58.349 40.909 4.99 4.99 0.00 5.54
33 34 4.593597 ATGTAACTGTTTAATGTCGGCG 57.406 40.909 0.00 0.00 0.00 6.46
67 68 5.475273 TTCATCGATCAAATGCAGAAGAC 57.525 39.130 0.00 0.00 0.00 3.01
75 76 3.680642 ACGCCTTTCATCGATCAAATG 57.319 42.857 0.00 0.00 0.00 2.32
102 104 7.812690 TCCAGATTATCAACAAATCATCCAG 57.187 36.000 0.00 0.00 36.09 3.86
122 124 3.314553 CTTGCTTGCAACAGAAATCCAG 58.685 45.455 3.70 0.00 0.00 3.86
124 126 2.064014 GCTTGCTTGCAACAGAAATCC 58.936 47.619 3.70 0.00 0.00 3.01
280 1177 9.290483 GTATAGTAAACTGTAAAACTCCGGTAC 57.710 37.037 0.00 0.00 0.00 3.34
283 1180 8.937634 ATGTATAGTAAACTGTAAAACTCCGG 57.062 34.615 0.00 0.00 0.00 5.14
295 1192 6.650427 TGAGCCGATGATGTATAGTAAACT 57.350 37.500 0.00 0.00 0.00 2.66
320 1217 9.274206 GAGGATTCTAATGTTTCCCAGTTATAC 57.726 37.037 0.00 0.00 0.00 1.47
327 1224 9.020731 GTTTTTAGAGGATTCTAATGTTTCCCA 57.979 33.333 0.00 0.00 43.53 4.37
328 1225 9.020731 TGTTTTTAGAGGATTCTAATGTTTCCC 57.979 33.333 0.00 0.00 43.53 3.97
331 1228 9.025041 CCCTGTTTTTAGAGGATTCTAATGTTT 57.975 33.333 0.00 0.00 43.53 2.83
332 1229 8.390921 TCCCTGTTTTTAGAGGATTCTAATGTT 58.609 33.333 0.00 0.00 43.53 2.71
333 1230 7.829706 GTCCCTGTTTTTAGAGGATTCTAATGT 59.170 37.037 0.00 0.00 43.53 2.71
334 1231 8.049721 AGTCCCTGTTTTTAGAGGATTCTAATG 58.950 37.037 0.00 0.00 43.53 1.90
335 1232 8.164057 AGTCCCTGTTTTTAGAGGATTCTAAT 57.836 34.615 0.00 0.00 43.53 1.73
336 1233 7.569599 AGTCCCTGTTTTTAGAGGATTCTAA 57.430 36.000 0.00 0.00 42.66 2.10
337 1234 7.569599 AAGTCCCTGTTTTTAGAGGATTCTA 57.430 36.000 0.00 0.00 34.79 2.10
338 1235 6.455690 AAGTCCCTGTTTTTAGAGGATTCT 57.544 37.500 0.00 0.00 37.46 2.40
339 1236 8.678199 CATAAAGTCCCTGTTTTTAGAGGATTC 58.322 37.037 0.00 0.00 0.00 2.52
340 1237 8.390921 TCATAAAGTCCCTGTTTTTAGAGGATT 58.609 33.333 0.00 0.00 0.00 3.01
341 1238 7.928873 TCATAAAGTCCCTGTTTTTAGAGGAT 58.071 34.615 0.00 0.00 0.00 3.24
342 1239 7.324388 TCATAAAGTCCCTGTTTTTAGAGGA 57.676 36.000 0.00 0.00 0.00 3.71
343 1240 7.415653 GCATCATAAAGTCCCTGTTTTTAGAGG 60.416 40.741 0.00 0.00 0.00 3.69
344 1241 7.121168 TGCATCATAAAGTCCCTGTTTTTAGAG 59.879 37.037 0.00 0.00 0.00 2.43
345 1242 6.945435 TGCATCATAAAGTCCCTGTTTTTAGA 59.055 34.615 0.00 0.00 0.00 2.10
346 1243 7.156876 TGCATCATAAAGTCCCTGTTTTTAG 57.843 36.000 0.00 0.00 0.00 1.85
347 1244 7.546358 CATGCATCATAAAGTCCCTGTTTTTA 58.454 34.615 0.00 0.00 0.00 1.52
348 1245 6.400568 CATGCATCATAAAGTCCCTGTTTTT 58.599 36.000 0.00 0.00 0.00 1.94
349 1246 5.625197 GCATGCATCATAAAGTCCCTGTTTT 60.625 40.000 14.21 0.00 0.00 2.43
350 1247 4.142093 GCATGCATCATAAAGTCCCTGTTT 60.142 41.667 14.21 0.00 0.00 2.83
351 1248 3.382546 GCATGCATCATAAAGTCCCTGTT 59.617 43.478 14.21 0.00 0.00 3.16
352 1249 2.954318 GCATGCATCATAAAGTCCCTGT 59.046 45.455 14.21 0.00 0.00 4.00
353 1250 2.953648 TGCATGCATCATAAAGTCCCTG 59.046 45.455 18.46 0.00 0.00 4.45
354 1251 3.301794 TGCATGCATCATAAAGTCCCT 57.698 42.857 18.46 0.00 0.00 4.20
355 1252 3.570975 TCATGCATGCATCATAAAGTCCC 59.429 43.478 30.07 0.00 33.90 4.46
356 1253 4.841443 TCATGCATGCATCATAAAGTCC 57.159 40.909 30.07 0.00 33.90 3.85
357 1254 8.860128 CAATAATCATGCATGCATCATAAAGTC 58.140 33.333 30.07 0.00 33.90 3.01
358 1255 8.364894 ACAATAATCATGCATGCATCATAAAGT 58.635 29.630 30.07 18.92 33.90 2.66
359 1256 8.647226 CACAATAATCATGCATGCATCATAAAG 58.353 33.333 30.07 17.59 33.90 1.85
383 1280 8.299570 ACAATTTCCATCATTCTTGACTTACAC 58.700 33.333 0.00 0.00 33.85 2.90
441 1338 8.355169 CGTACCAGCTATACAAGGTTTTATCTA 58.645 37.037 7.80 0.00 35.62 1.98
442 1339 7.147776 ACGTACCAGCTATACAAGGTTTTATCT 60.148 37.037 7.80 0.00 35.62 1.98
443 1340 6.982724 ACGTACCAGCTATACAAGGTTTTATC 59.017 38.462 7.80 0.00 35.62 1.75
444 1341 6.881570 ACGTACCAGCTATACAAGGTTTTAT 58.118 36.000 7.80 0.00 35.62 1.40
445 1342 6.284891 ACGTACCAGCTATACAAGGTTTTA 57.715 37.500 7.80 0.00 35.62 1.52
446 1343 5.156608 ACGTACCAGCTATACAAGGTTTT 57.843 39.130 7.80 0.00 35.62 2.43
447 1344 4.813750 ACGTACCAGCTATACAAGGTTT 57.186 40.909 7.80 0.00 35.62 3.27
448 1345 4.813750 AACGTACCAGCTATACAAGGTT 57.186 40.909 7.80 2.27 35.62 3.50
449 1346 4.020839 ACAAACGTACCAGCTATACAAGGT 60.021 41.667 7.80 2.77 38.14 3.50
450 1347 4.501071 ACAAACGTACCAGCTATACAAGG 58.499 43.478 7.80 0.00 0.00 3.61
495 1392 2.749621 GCATTCCTCGGAAGAATTGTGT 59.250 45.455 4.53 0.00 41.32 3.72
496 1393 2.749076 TGCATTCCTCGGAAGAATTGTG 59.251 45.455 4.53 0.00 41.32 3.33
497 1394 3.071874 TGCATTCCTCGGAAGAATTGT 57.928 42.857 4.53 0.00 41.32 2.71
498 1395 4.082571 ACTTTGCATTCCTCGGAAGAATTG 60.083 41.667 4.53 0.00 41.32 2.32
499 1396 4.082125 ACTTTGCATTCCTCGGAAGAATT 58.918 39.130 4.53 0.00 41.32 2.17
600 1497 8.517896 GGTCCTACCCCAACCTACTATATATAT 58.482 40.741 0.00 0.00 30.04 0.86
601 1498 7.468502 TGGTCCTACCCCAACCTACTATATATA 59.531 40.741 0.00 0.00 37.50 0.86
621 1518 1.229209 ACAGTGGTCCGATGGTCCT 60.229 57.895 0.00 0.00 32.23 3.85
637 1534 2.330440 TATAGACTACCGTCGCCACA 57.670 50.000 0.00 0.00 44.93 4.17
640 1537 3.137533 AGACTTATAGACTACCGTCGCC 58.862 50.000 0.00 0.00 44.93 5.54
642 1539 6.584184 TCGAATAGACTTATAGACTACCGTCG 59.416 42.308 0.00 0.00 44.93 5.12
719 3142 6.317642 GGCAACACTGTGTGATGGTTATATTA 59.682 38.462 15.11 0.00 36.93 0.98
720 3143 5.125417 GGCAACACTGTGTGATGGTTATATT 59.875 40.000 15.11 0.00 36.93 1.28
721 3144 4.640201 GGCAACACTGTGTGATGGTTATAT 59.360 41.667 15.11 0.00 36.93 0.86
722 3145 4.006989 GGCAACACTGTGTGATGGTTATA 58.993 43.478 15.11 0.00 36.93 0.98
723 3146 2.819608 GGCAACACTGTGTGATGGTTAT 59.180 45.455 15.11 0.00 36.93 1.89
886 4887 1.598130 GGTGGTGACTGGTGTGAGC 60.598 63.158 0.00 0.00 0.00 4.26
916 4917 2.035576 GGCGTAATGGTAGAGGTAGTGG 59.964 54.545 0.00 0.00 0.00 4.00
937 4940 5.105752 GCTAGGGCTTATCACGAATGATAG 58.894 45.833 0.00 0.00 46.23 2.08
1065 5084 3.262420 CATCGGTTTCAGGTAGACCTTG 58.738 50.000 0.00 0.00 46.09 3.61
1071 5090 0.810031 CCCGCATCGGTTTCAGGTAG 60.810 60.000 4.47 0.00 46.80 3.18
1201 5223 1.093496 CCGAGCTGCAGCATCATGAA 61.093 55.000 38.24 0.00 45.16 2.57
1557 9059 1.573829 CTTTTCGGCCGTGCTGCTAA 61.574 55.000 27.15 7.12 34.49 3.09
1582 9086 2.403037 GCGACTGTTCTGTGTTACGTAC 59.597 50.000 0.00 0.00 0.00 3.67
1583 9087 2.653890 GCGACTGTTCTGTGTTACGTA 58.346 47.619 0.00 0.00 0.00 3.57
1617 9124 0.798776 GTCTCAATCTTGTGGTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
1628 9260 8.261492 ACACTGTTCATTCATAAGTCTCAATC 57.739 34.615 0.00 0.00 0.00 2.67
1629 9261 8.627208 AACACTGTTCATTCATAAGTCTCAAT 57.373 30.769 0.00 0.00 0.00 2.57
1630 9262 8.450578 AAACACTGTTCATTCATAAGTCTCAA 57.549 30.769 0.00 0.00 0.00 3.02
1657 9615 0.635731 CACGAATCGAGCTGACGAAC 59.364 55.000 10.55 0.00 45.16 3.95
1726 12659 2.733301 CTCGCGGATCTGCTCCAT 59.267 61.111 23.71 0.00 45.24 3.41
1812 12746 4.302509 TTCTTCCCGAACGCCGCA 62.303 61.111 0.00 0.00 36.84 5.69
1884 12818 1.678970 GGGGATGTTGAAGCCGCTT 60.679 57.895 4.98 4.98 0.00 4.68
2054 12994 0.728466 GTTCTCGTCCACGTTCTCCG 60.728 60.000 0.00 0.00 44.03 4.63
2055 12995 0.388263 GGTTCTCGTCCACGTTCTCC 60.388 60.000 0.00 0.00 40.80 3.71
2235 13240 1.088340 CCTGCAGCTTCCTCATCACG 61.088 60.000 8.66 0.00 0.00 4.35
2243 13248 3.355957 ATCTGGGCCTGCAGCTTCC 62.356 63.158 8.66 9.62 43.05 3.46
2547 13552 1.079819 GAACTCGTAGCTGCTGCCA 60.080 57.895 13.43 0.00 40.80 4.92
2586 13591 3.645268 GAAGCCGGGGCACATCCTT 62.645 63.158 12.97 0.00 44.88 3.36
2849 13888 3.688235 ACTAGATAGTAGATGGGGACGC 58.312 50.000 0.00 0.00 34.13 5.19
2865 13904 1.878070 CGCGTGTGTGGGTACTAGA 59.122 57.895 0.00 0.00 0.00 2.43
2866 13905 1.804326 GCGCGTGTGTGGGTACTAG 60.804 63.158 8.43 0.00 0.00 2.57
2867 13906 2.259204 GCGCGTGTGTGGGTACTA 59.741 61.111 8.43 0.00 0.00 1.82
2975 14077 0.319383 CCAGATCGATCGGCCTCAAG 60.319 60.000 19.33 1.64 0.00 3.02
3040 14159 0.524862 AACAGCAGTACGTACTCCCG 59.475 55.000 25.10 17.16 33.46 5.14
3075 14198 2.034558 CGGCAGGACAAACAAAGAACAT 59.965 45.455 0.00 0.00 0.00 2.71
3092 14215 2.515979 ATGCGATATGTCCCCGGCA 61.516 57.895 0.00 0.00 0.00 5.69
3096 14219 3.262420 GTGATACATGCGATATGTCCCC 58.738 50.000 8.72 2.26 33.76 4.81
3100 14223 2.288763 TGCCGTGATACATGCGATATGT 60.289 45.455 10.06 10.06 36.13 2.29
3296 17890 3.128938 GTCTAGCTATGTCAGTGTCGGTT 59.871 47.826 0.00 0.00 0.00 4.44
3299 17893 2.851386 GCGTCTAGCTATGTCAGTGTCG 60.851 54.545 0.00 0.00 44.04 4.35
3313 17908 0.453793 ACTAGCAGTGCAGCGTCTAG 59.546 55.000 19.20 11.29 40.15 2.43
3314 17909 0.888619 AACTAGCAGTGCAGCGTCTA 59.111 50.000 19.20 0.00 40.15 2.59
3315 17910 0.389166 GAACTAGCAGTGCAGCGTCT 60.389 55.000 19.20 0.00 40.15 4.18
3316 17911 0.667487 TGAACTAGCAGTGCAGCGTC 60.667 55.000 19.20 13.06 40.15 5.19
3328 17923 6.976349 TGGTATACTAAATGCACGTGAACTAG 59.024 38.462 22.23 15.61 0.00 2.57
3329 17924 6.865411 TGGTATACTAAATGCACGTGAACTA 58.135 36.000 22.23 3.17 0.00 2.24
3417 18152 9.679596 CCGTGTTTATACAAGAAACTATTAACG 57.320 33.333 1.10 0.00 37.62 3.18
3441 18176 5.229921 TCAAAGTCTTTGAAGTTTGACCG 57.770 39.130 22.87 0.00 45.94 4.79
3478 18213 8.294954 TCTTACTCTCTCCGATCATTTTTACT 57.705 34.615 0.00 0.00 0.00 2.24
3495 18230 6.767902 TGCAGACATGAACTTTTTCTTACTCT 59.232 34.615 0.00 0.00 32.36 3.24
3598 18339 1.062002 CATGTTGATTACGCACGGTCC 59.938 52.381 0.00 0.00 0.00 4.46
3606 18347 3.901877 CGTATGCATGCATGTTGATTACG 59.098 43.478 37.43 31.23 37.82 3.18
3635 18384 0.179134 GGTAGCTGTACCTCTGCACG 60.179 60.000 0.00 0.00 45.01 5.34
3636 18385 3.742983 GGTAGCTGTACCTCTGCAC 57.257 57.895 0.00 0.00 45.01 4.57
3691 18441 0.644937 ATCTGTAGCCTCTCCCCCTT 59.355 55.000 0.00 0.00 0.00 3.95
3692 18442 0.189822 GATCTGTAGCCTCTCCCCCT 59.810 60.000 0.00 0.00 0.00 4.79
3693 18443 0.105453 TGATCTGTAGCCTCTCCCCC 60.105 60.000 0.00 0.00 0.00 5.40
3694 18444 1.337118 CTGATCTGTAGCCTCTCCCC 58.663 60.000 0.00 0.00 0.00 4.81
3695 18445 1.960689 GACTGATCTGTAGCCTCTCCC 59.039 57.143 5.09 0.00 0.00 4.30
3696 18446 1.606668 CGACTGATCTGTAGCCTCTCC 59.393 57.143 5.09 0.00 0.00 3.71
3697 18447 2.289547 GTCGACTGATCTGTAGCCTCTC 59.710 54.545 8.70 0.00 0.00 3.20
3698 18448 2.092646 AGTCGACTGATCTGTAGCCTCT 60.093 50.000 19.30 3.08 0.00 3.69
3699 18449 2.032799 CAGTCGACTGATCTGTAGCCTC 59.967 54.545 36.73 0.00 46.59 4.70
3700 18450 2.020720 CAGTCGACTGATCTGTAGCCT 58.979 52.381 36.73 0.00 46.59 4.58
3701 18451 2.483583 CAGTCGACTGATCTGTAGCC 57.516 55.000 36.73 0.00 46.59 3.93
3719 18469 6.511121 GCGACTGACACTAACTGAAAAATTCA 60.511 38.462 0.00 0.00 38.17 2.57
3720 18470 5.846473 GCGACTGACACTAACTGAAAAATTC 59.154 40.000 0.00 0.00 0.00 2.17
3721 18471 5.558273 CGCGACTGACACTAACTGAAAAATT 60.558 40.000 0.00 0.00 0.00 1.82
3722 18472 4.084537 CGCGACTGACACTAACTGAAAAAT 60.085 41.667 0.00 0.00 0.00 1.82
3723 18473 3.244345 CGCGACTGACACTAACTGAAAAA 59.756 43.478 0.00 0.00 0.00 1.94
3724 18474 2.792674 CGCGACTGACACTAACTGAAAA 59.207 45.455 0.00 0.00 0.00 2.29
3725 18475 2.223641 ACGCGACTGACACTAACTGAAA 60.224 45.455 15.93 0.00 0.00 2.69
3726 18476 1.335810 ACGCGACTGACACTAACTGAA 59.664 47.619 15.93 0.00 0.00 3.02
3727 18477 0.949397 ACGCGACTGACACTAACTGA 59.051 50.000 15.93 0.00 0.00 3.41
3728 18478 1.053048 CACGCGACTGACACTAACTG 58.947 55.000 15.93 0.00 0.00 3.16
3729 18479 0.039437 CCACGCGACTGACACTAACT 60.039 55.000 15.93 0.00 0.00 2.24
3730 18480 0.039798 TCCACGCGACTGACACTAAC 60.040 55.000 15.93 0.00 0.00 2.34
3731 18481 0.039798 GTCCACGCGACTGACACTAA 60.040 55.000 15.93 0.00 38.57 2.24
3732 18482 1.577922 GTCCACGCGACTGACACTA 59.422 57.895 15.93 0.00 38.57 2.74
3733 18483 2.335369 GTCCACGCGACTGACACT 59.665 61.111 15.93 0.00 38.57 3.55
3734 18484 2.733593 GGTCCACGCGACTGACAC 60.734 66.667 15.93 6.63 41.64 3.67
3745 18495 1.664151 GATTTTCATCCGACGGTCCAC 59.336 52.381 14.79 0.00 0.00 4.02
3746 18496 1.737696 CGATTTTCATCCGACGGTCCA 60.738 52.381 14.79 0.00 0.00 4.02
3747 18497 0.928229 CGATTTTCATCCGACGGTCC 59.072 55.000 14.79 0.00 0.00 4.46
3748 18498 1.323534 CACGATTTTCATCCGACGGTC 59.676 52.381 14.79 0.75 0.00 4.79
3749 18499 1.337447 ACACGATTTTCATCCGACGGT 60.337 47.619 14.79 0.00 0.00 4.83
3750 18500 1.060553 CACACGATTTTCATCCGACGG 59.939 52.381 7.84 7.84 0.00 4.79
3751 18501 1.060553 CCACACGATTTTCATCCGACG 59.939 52.381 0.00 0.00 0.00 5.12
3752 18502 1.202031 GCCACACGATTTTCATCCGAC 60.202 52.381 0.00 0.00 0.00 4.79
3753 18503 1.083489 GCCACACGATTTTCATCCGA 58.917 50.000 0.00 0.00 0.00 4.55
3754 18504 0.801872 TGCCACACGATTTTCATCCG 59.198 50.000 0.00 0.00 0.00 4.18
3755 18505 1.468054 GCTGCCACACGATTTTCATCC 60.468 52.381 0.00 0.00 0.00 3.51
3756 18506 1.470098 AGCTGCCACACGATTTTCATC 59.530 47.619 0.00 0.00 0.00 2.92
3757 18507 1.538047 AGCTGCCACACGATTTTCAT 58.462 45.000 0.00 0.00 0.00 2.57
3758 18508 2.076100 CTAGCTGCCACACGATTTTCA 58.924 47.619 0.00 0.00 0.00 2.69
3759 18509 2.346803 TCTAGCTGCCACACGATTTTC 58.653 47.619 0.00 0.00 0.00 2.29
3760 18510 2.472695 TCTAGCTGCCACACGATTTT 57.527 45.000 0.00 0.00 0.00 1.82
3761 18511 2.555199 GATCTAGCTGCCACACGATTT 58.445 47.619 0.00 0.00 0.00 2.17
3762 18512 2.231215 GATCTAGCTGCCACACGATT 57.769 50.000 0.00 0.00 0.00 3.34
3763 18513 3.976339 GATCTAGCTGCCACACGAT 57.024 52.632 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.