Multiple sequence alignment - TraesCS4D01G364400

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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 TraesCS4D01G364400 chr4D 100.000 3790 0 0 1 3790 509285203 509281414 0.000000e+00 6999.0
1 TraesCS4D01G364400 chr4D 85.444 1058 128 15 1748 2791 509339975 509338930 0.000000e+00 1077.0
2 TraesCS4D01G364400 chr4D 83.457 943 92 27 464 1373 509341495 509340584 0.000000e+00 819.0
3 TraesCS4D01G364400 chr4D 84.061 458 56 8 2975 3415 509338602 509338145 3.500000e-115 425.0
4 TraesCS4D01G364400 chr4D 88.492 252 20 6 456 704 509355863 509355618 2.860000e-76 296.0
5 TraesCS4D01G364400 chr4D 85.283 265 33 4 461 723 509326361 509326101 6.240000e-68 268.0
6 TraesCS4D01G364400 chr4D 90.551 127 11 1 3621 3747 509338046 509337921 2.340000e-37 167.0
7 TraesCS4D01G364400 chr4D 80.469 128 20 4 92 217 378271470 378271346 4.030000e-15 93.5
8 TraesCS4D01G364400 chr4D 91.803 61 2 1 1508 1565 509340233 509340173 8.730000e-12 82.4
9 TraesCS4D01G364400 chr4B 90.900 2099 143 24 1732 3790 657527388 657529478 0.000000e+00 2774.0
10 TraesCS4D01G364400 chr4B 89.071 1098 85 11 52 1143 657525561 657526629 0.000000e+00 1330.0
11 TraesCS4D01G364400 chr4B 85.795 1056 125 15 1748 2787 657516626 657517672 0.000000e+00 1096.0
12 TraesCS4D01G364400 chr4B 83.444 906 90 26 485 1373 657497910 657498772 0.000000e+00 787.0
13 TraesCS4D01G364400 chr4B 83.204 905 98 30 485 1373 657515095 657515961 0.000000e+00 780.0
14 TraesCS4D01G364400 chr4B 90.274 401 26 4 920 1307 657509718 657510118 2.610000e-141 512.0
15 TraesCS4D01G364400 chr4B 84.942 518 63 7 1748 2255 657499437 657499949 9.390000e-141 510.0
16 TraesCS4D01G364400 chr4B 83.878 459 55 8 2975 3415 657518005 657518462 1.630000e-113 420.0
17 TraesCS4D01G364400 chr4B 85.075 335 42 4 3462 3790 657518464 657518796 6.070000e-88 335.0
18 TraesCS4D01G364400 chr4B 87.805 123 11 4 1456 1576 657527163 657527283 1.420000e-29 141.0
19 TraesCS4D01G364400 chr4B 80.000 125 18 4 1447 1565 657498952 657499075 6.750000e-13 86.1
20 TraesCS4D01G364400 chr4B 80.000 125 18 4 1447 1565 657516141 657516264 6.750000e-13 86.1
21 TraesCS4D01G364400 chr4B 93.333 45 2 1 1644 1687 623420962 623421006 8.790000e-07 65.8
22 TraesCS4D01G364400 chr4B 87.500 56 6 1 108 162 334104357 334104302 3.160000e-06 63.9
23 TraesCS4D01G364400 chr5A 91.059 2002 141 20 1718 3686 698163138 698161142 0.000000e+00 2671.0
24 TraesCS4D01G364400 chr5A 87.528 1323 114 16 53 1365 698164809 698163528 0.000000e+00 1482.0
25 TraesCS4D01G364400 chr5A 85.033 1049 134 16 1748 2787 698179778 698178744 0.000000e+00 1046.0
26 TraesCS4D01G364400 chr5A 81.779 933 94 36 464 1373 698181135 698180256 0.000000e+00 712.0
27 TraesCS4D01G364400 chr5A 80.351 570 77 25 2249 2791 698144721 698144160 2.120000e-107 399.0
28 TraesCS4D01G364400 chr5A 80.714 420 55 19 2989 3383 698178400 698177982 1.710000e-78 303.0
29 TraesCS4D01G364400 chr5A 89.908 109 9 2 1453 1560 698163247 698163140 5.100000e-29 139.0
30 TraesCS4D01G364400 chr5A 89.720 107 8 1 3684 3790 698160936 698160833 2.380000e-27 134.0
31 TraesCS4D01G364400 chr5A 100.000 36 0 0 3380 3415 698177726 698177691 2.440000e-07 67.6
32 TraesCS4D01G364400 chrUn 88.828 1101 85 12 52 1143 402488964 402487893 0.000000e+00 1317.0
33 TraesCS4D01G364400 chrUn 86.592 537 62 6 2257 2787 343816555 343817087 5.460000e-163 584.0
34 TraesCS4D01G364400 chrUn 90.274 401 26 4 920 1307 324637550 324637150 2.610000e-141 512.0
35 TraesCS4D01G364400 chrUn 83.878 459 55 8 2975 3415 343817420 343817877 1.630000e-113 420.0
36 TraesCS4D01G364400 chrUn 84.478 335 44 4 3462 3790 343817879 343818211 1.310000e-84 324.0
37 TraesCS4D01G364400 chr1D 81.283 187 24 9 52 233 458476562 458476742 1.420000e-29 141.0
38 TraesCS4D01G364400 chr1D 97.368 38 1 0 1644 1681 394464397 394464360 8.790000e-07 65.8
39 TraesCS4D01G364400 chr2B 80.978 184 28 5 53 233 197213578 197213399 5.100000e-29 139.0
40 TraesCS4D01G364400 chr2B 93.182 44 2 1 1637 1679 25291733 25291690 3.160000e-06 63.9
41 TraesCS4D01G364400 chr3A 78.351 194 40 2 62 255 164778614 164778423 1.430000e-24 124.0
42 TraesCS4D01G364400 chr3A 97.619 42 1 0 1644 1685 575606796 575606837 5.250000e-09 73.1
43 TraesCS4D01G364400 chr7A 78.857 175 31 6 84 258 635016900 635017068 3.090000e-21 113.0
44 TraesCS4D01G364400 chr5D 84.906 106 11 3 129 233 329439799 329439900 6.700000e-18 102.0
45 TraesCS4D01G364400 chr5D 97.297 37 1 0 1644 1680 62177133 62177097 3.160000e-06 63.9
46 TraesCS4D01G364400 chr3B 80.315 127 24 1 134 259 669950114 669949988 1.120000e-15 95.3
47 TraesCS4D01G364400 chr3B 97.368 38 1 0 1644 1681 226086332 226086295 8.790000e-07 65.8
48 TraesCS4D01G364400 chr6B 93.333 45 2 1 1637 1680 173830960 173831004 8.790000e-07 65.8
49 TraesCS4D01G364400 chr6B 97.297 37 1 0 1644 1680 576435129 576435093 3.160000e-06 63.9
50 TraesCS4D01G364400 chr1B 92.857 42 2 1 1637 1677 429586165 429586124 4.090000e-05 60.2


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 TraesCS4D01G364400 chr4D 509281414 509285203 3789 True 6999.000000 6999 100.000000 1 3790 1 chr4D.!!$R2 3789
1 TraesCS4D01G364400 chr4D 509337921 509341495 3574 True 514.080000 1077 87.063200 464 3747 5 chr4D.!!$R5 3283
2 TraesCS4D01G364400 chr4B 657525561 657529478 3917 False 1415.000000 2774 89.258667 52 3790 3 chr4B.!!$F5 3738
3 TraesCS4D01G364400 chr4B 657515095 657518796 3701 False 543.420000 1096 83.590400 485 3790 5 chr4B.!!$F4 3305
4 TraesCS4D01G364400 chr4B 657497910 657499949 2039 False 461.033333 787 82.795333 485 2255 3 chr4B.!!$F3 1770
5 TraesCS4D01G364400 chr5A 698160833 698164809 3976 True 1106.500000 2671 89.553750 53 3790 4 chr5A.!!$R2 3737
6 TraesCS4D01G364400 chr5A 698177691 698181135 3444 True 532.150000 1046 86.881500 464 3415 4 chr5A.!!$R3 2951
7 TraesCS4D01G364400 chr5A 698144160 698144721 561 True 399.000000 399 80.351000 2249 2791 1 chr5A.!!$R1 542
8 TraesCS4D01G364400 chrUn 402487893 402488964 1071 True 1317.000000 1317 88.828000 52 1143 1 chrUn.!!$R2 1091
9 TraesCS4D01G364400 chrUn 343816555 343818211 1656 False 442.666667 584 84.982667 2257 3790 3 chrUn.!!$F1 1533

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
619 636 0.034574 TGGCCTTGCGTGGACATAAT 60.035 50.0 3.32 0.0 40.85 1.28 F
1386 1442 0.032515 TCGATGGGACCTCCTGCTAA 60.033 55.0 0.00 0.0 36.20 3.09 F
1662 2082 0.039165 GGCAACAGCTTTACCACTGC 60.039 55.0 0.00 0.0 37.42 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 2019 0.252197 AAAGTGGTCGGACCCTATGC 59.748 55.000 23.81 9.21 37.5 3.14 R
2463 3147 1.699083 TGGCACCTGAACATCAAGAGA 59.301 47.619 0.00 0.00 0.0 3.10 R
3571 4707 1.676967 CAGCTTGAGGTTGGAGGGC 60.677 63.158 0.00 0.00 0.0 5.19 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
17 18 2.776072 CAAATCACCGTCGCCGAC 59.224 61.111 7.29 7.29 35.63 4.79
26 27 2.504244 GTCGCCGACGTCTCTTGG 60.504 66.667 14.70 8.44 41.18 3.61
27 28 2.981909 TCGCCGACGTCTCTTGGT 60.982 61.111 14.70 0.00 41.18 3.67
28 29 2.504244 CGCCGACGTCTCTTGGTC 60.504 66.667 14.70 3.26 33.53 4.02
29 30 2.963371 GCCGACGTCTCTTGGTCT 59.037 61.111 14.70 0.00 0.00 3.85
30 31 1.444553 GCCGACGTCTCTTGGTCTG 60.445 63.158 14.70 0.00 0.00 3.51
31 32 1.444553 CCGACGTCTCTTGGTCTGC 60.445 63.158 14.70 0.00 0.00 4.26
32 33 1.285950 CGACGTCTCTTGGTCTGCA 59.714 57.895 14.70 0.00 0.00 4.41
33 34 0.109086 CGACGTCTCTTGGTCTGCAT 60.109 55.000 14.70 0.00 0.00 3.96
34 35 1.670087 CGACGTCTCTTGGTCTGCATT 60.670 52.381 14.70 0.00 0.00 3.56
35 36 1.728971 GACGTCTCTTGGTCTGCATTG 59.271 52.381 8.70 0.00 0.00 2.82
36 37 1.344438 ACGTCTCTTGGTCTGCATTGA 59.656 47.619 0.00 0.00 0.00 2.57
37 38 1.728971 CGTCTCTTGGTCTGCATTGAC 59.271 52.381 0.00 0.00 36.31 3.18
38 39 1.728971 GTCTCTTGGTCTGCATTGACG 59.271 52.381 0.49 0.00 37.81 4.35
39 40 1.618343 TCTCTTGGTCTGCATTGACGA 59.382 47.619 0.00 0.00 37.81 4.20
40 41 1.728971 CTCTTGGTCTGCATTGACGAC 59.271 52.381 0.00 0.00 37.81 4.34
41 42 1.344438 TCTTGGTCTGCATTGACGACT 59.656 47.619 3.40 0.00 37.81 4.18
42 43 2.146342 CTTGGTCTGCATTGACGACTT 58.854 47.619 3.40 0.00 37.81 3.01
43 44 1.795768 TGGTCTGCATTGACGACTTC 58.204 50.000 3.40 0.00 37.81 3.01
44 45 1.079503 GGTCTGCATTGACGACTTCC 58.920 55.000 3.40 0.00 37.81 3.46
45 46 1.079503 GTCTGCATTGACGACTTCCC 58.920 55.000 0.00 0.00 0.00 3.97
46 47 0.389817 TCTGCATTGACGACTTCCCG 60.390 55.000 0.00 0.00 0.00 5.14
47 48 1.970917 CTGCATTGACGACTTCCCGC 61.971 60.000 0.00 0.00 0.00 6.13
48 49 1.741770 GCATTGACGACTTCCCGCT 60.742 57.895 0.00 0.00 0.00 5.52
49 50 1.696832 GCATTGACGACTTCCCGCTC 61.697 60.000 0.00 0.00 0.00 5.03
50 51 1.153823 ATTGACGACTTCCCGCTCG 60.154 57.895 0.00 0.00 35.96 5.03
90 91 0.175760 GCTACGTCAAGATGGAGGCA 59.824 55.000 0.00 0.00 0.00 4.75
97 98 3.350833 GTCAAGATGGAGGCACAAAGAT 58.649 45.455 0.00 0.00 0.00 2.40
173 174 1.177401 GGCACCCCTAAAGCTTTGAG 58.823 55.000 22.02 12.08 0.00 3.02
184 185 7.384932 CCCCTAAAGCTTTGAGTGTAATTTTTG 59.615 37.037 22.02 0.00 0.00 2.44
213 214 3.876309 ATGGGTGTGTTTGTAAGGTCT 57.124 42.857 0.00 0.00 0.00 3.85
254 257 8.962884 ATGGTTTTAAGACTCTTTGCAAAAAT 57.037 26.923 13.84 1.11 0.00 1.82
264 268 8.755018 AGACTCTTTGCAAAAATAAAATTCACG 58.245 29.630 13.84 0.00 0.00 4.35
276 280 3.508744 AAATTCACGCCCATGACATTC 57.491 42.857 0.00 0.00 0.00 2.67
277 281 2.127271 ATTCACGCCCATGACATTCA 57.873 45.000 0.00 0.00 0.00 2.57
290 294 9.715121 GCCCATGACATTCATATTTTTATGATT 57.285 29.630 0.00 0.00 34.28 2.57
322 326 7.167801 TGTTTTTGTTACCTAAAAATGTAGCGC 59.832 33.333 0.00 0.00 38.71 5.92
337 341 2.319136 AGCGCCAAACGGATACATAA 57.681 45.000 2.29 0.00 43.93 1.90
347 351 6.483307 CCAAACGGATACATAACATGATGAGT 59.517 38.462 0.00 0.00 0.00 3.41
354 358 7.652105 GGATACATAACATGATGAGTAACACGT 59.348 37.037 0.00 0.00 0.00 4.49
397 401 4.133820 CAACCAATACCAACTGTCTGTCA 58.866 43.478 0.00 0.00 0.00 3.58
530 543 6.326375 GTTTCCATTGTGTTGTGTTTGTCTA 58.674 36.000 0.00 0.00 0.00 2.59
574 587 6.736794 GCATCTCCTTTTTGTTTGACAGTGAT 60.737 38.462 0.00 0.00 0.00 3.06
619 636 0.034574 TGGCCTTGCGTGGACATAAT 60.035 50.000 3.32 0.00 40.85 1.28
728 746 2.419324 GGATCGTATCTATTCCGACGCT 59.581 50.000 0.00 0.00 35.33 5.07
729 747 2.963498 TCGTATCTATTCCGACGCTG 57.037 50.000 0.00 0.00 35.33 5.18
815 834 0.689055 TTGTCTGGTCTGCAGCTCAT 59.311 50.000 9.47 0.00 0.00 2.90
868 889 2.309162 AGAGACACAGTACAGCCCTAGA 59.691 50.000 0.00 0.00 0.00 2.43
934 968 4.164413 TCTTCTTCCTCGACATCTCTCCTA 59.836 45.833 0.00 0.00 0.00 2.94
962 996 0.179056 ACCAGACCACACCAGAAACG 60.179 55.000 0.00 0.00 0.00 3.60
1052 1087 2.672651 CTGCCCGCACCACATGAA 60.673 61.111 0.00 0.00 0.00 2.57
1056 1091 1.302431 CCCGCACCACATGAACTCA 60.302 57.895 0.00 0.00 0.00 3.41
1077 1118 3.310774 CACCCGTTCTTCATCATCATCAC 59.689 47.826 0.00 0.00 0.00 3.06
1099 1140 1.338107 TCATCAGGAACACCGACTGT 58.662 50.000 0.00 0.00 34.02 3.55
1143 1184 2.115910 CAGCACCACCACCACCAT 59.884 61.111 0.00 0.00 0.00 3.55
1340 1396 3.568853 GCCACCATCGTGAGTAGTACTAT 59.431 47.826 5.75 0.00 43.14 2.12
1356 1412 9.953565 AGTAGTACTATTGCTTAATTGTTCCAA 57.046 29.630 5.75 0.00 0.00 3.53
1368 1424 1.808411 TGTTCCAACTCTTGCCGATC 58.192 50.000 0.00 0.00 0.00 3.69
1373 1429 0.933097 CAACTCTTGCCGATCGATGG 59.067 55.000 18.66 0.00 0.00 3.51
1375 1431 1.043116 ACTCTTGCCGATCGATGGGA 61.043 55.000 28.49 15.93 0.00 4.37
1378 1434 2.032860 CTTGCCGATCGATGGGACCT 62.033 60.000 28.49 0.00 0.00 3.85
1380 1436 3.052081 CCGATCGATGGGACCTCC 58.948 66.667 20.90 0.00 0.00 4.30
1381 1437 1.531840 CCGATCGATGGGACCTCCT 60.532 63.158 20.90 0.00 36.20 3.69
1382 1438 1.662608 CGATCGATGGGACCTCCTG 59.337 63.158 10.26 0.00 36.20 3.86
1383 1439 1.369321 GATCGATGGGACCTCCTGC 59.631 63.158 0.54 0.00 36.20 4.85
1385 1441 0.188587 ATCGATGGGACCTCCTGCTA 59.811 55.000 0.00 0.00 36.20 3.49
1386 1442 0.032515 TCGATGGGACCTCCTGCTAA 60.033 55.000 0.00 0.00 36.20 3.09
1387 1443 0.105039 CGATGGGACCTCCTGCTAAC 59.895 60.000 0.00 0.00 36.20 2.34
1392 1453 2.175931 TGGGACCTCCTGCTAACAAAAA 59.824 45.455 0.00 0.00 36.20 1.94
1393 1454 3.181423 TGGGACCTCCTGCTAACAAAAAT 60.181 43.478 0.00 0.00 36.20 1.82
1395 1456 4.079253 GGACCTCCTGCTAACAAAAATCA 58.921 43.478 0.00 0.00 0.00 2.57
1397 1458 3.502211 ACCTCCTGCTAACAAAAATCACG 59.498 43.478 0.00 0.00 0.00 4.35
1402 1463 4.403453 CTGCTAACAAAAATCACGCCTAC 58.597 43.478 0.00 0.00 0.00 3.18
1408 1469 7.753580 GCTAACAAAAATCACGCCTACTTAATT 59.246 33.333 0.00 0.00 0.00 1.40
1414 1475 8.514330 AAAATCACGCCTACTTAATTTCCATA 57.486 30.769 0.00 0.00 0.00 2.74
1418 1479 7.959175 TCACGCCTACTTAATTTCCATATACT 58.041 34.615 0.00 0.00 0.00 2.12
1422 1483 6.817140 GCCTACTTAATTTCCATATACTCCCG 59.183 42.308 0.00 0.00 0.00 5.14
1424 1485 5.557866 ACTTAATTTCCATATACTCCCGCC 58.442 41.667 0.00 0.00 0.00 6.13
1426 1487 4.657814 AATTTCCATATACTCCCGCCAT 57.342 40.909 0.00 0.00 0.00 4.40
1427 1488 3.695830 TTTCCATATACTCCCGCCATC 57.304 47.619 0.00 0.00 0.00 3.51
1428 1489 2.623418 TCCATATACTCCCGCCATCT 57.377 50.000 0.00 0.00 0.00 2.90
1429 1490 2.457598 TCCATATACTCCCGCCATCTC 58.542 52.381 0.00 0.00 0.00 2.75
1465 1763 4.340666 TGTTTATGCTGGCAGAAAGTTTGA 59.659 37.500 20.86 0.00 37.73 2.69
1470 1768 3.181487 TGCTGGCAGAAAGTTTGAGTTTC 60.181 43.478 20.86 0.00 37.70 2.78
1471 1769 3.067320 GCTGGCAGAAAGTTTGAGTTTCT 59.933 43.478 20.86 5.21 45.87 2.52
1473 1771 4.997565 TGGCAGAAAGTTTGAGTTTCTTG 58.002 39.130 7.78 5.96 43.32 3.02
1504 1913 1.237285 ACAAGAATGGGCGCTCACAC 61.237 55.000 14.89 10.18 0.00 3.82
1505 1914 1.073025 AAGAATGGGCGCTCACACA 59.927 52.632 14.89 1.38 0.00 3.72
1506 1915 0.322816 AAGAATGGGCGCTCACACAT 60.323 50.000 14.89 0.00 0.00 3.21
1589 2009 8.089115 CTGAAAGTTTGAGTTCTACTAAAGGG 57.911 38.462 0.00 0.00 0.00 3.95
1591 2011 5.562298 AGTTTGAGTTCTACTAAAGGGCA 57.438 39.130 0.00 0.00 0.00 5.36
1592 2012 5.552178 AGTTTGAGTTCTACTAAAGGGCAG 58.448 41.667 0.00 0.00 0.00 4.85
1593 2013 3.611766 TGAGTTCTACTAAAGGGCAGC 57.388 47.619 0.00 0.00 0.00 5.25
1610 2030 4.235762 CCCGGTGCATAGGGTCCG 62.236 72.222 18.30 11.95 42.67 4.79
1611 2031 3.151710 CCGGTGCATAGGGTCCGA 61.152 66.667 12.32 0.00 44.86 4.55
1613 2033 2.504519 GGTGCATAGGGTCCGACC 59.495 66.667 9.30 9.30 37.60 4.79
1614 2034 2.363975 GGTGCATAGGGTCCGACCA 61.364 63.158 19.43 0.00 41.02 4.02
1615 2035 1.153429 GTGCATAGGGTCCGACCAC 60.153 63.158 19.43 8.70 41.02 4.16
1616 2036 1.305802 TGCATAGGGTCCGACCACT 60.306 57.895 19.43 15.07 41.02 4.00
1617 2037 0.907704 TGCATAGGGTCCGACCACTT 60.908 55.000 19.43 6.78 41.02 3.16
1618 2038 0.252197 GCATAGGGTCCGACCACTTT 59.748 55.000 19.43 6.55 41.02 2.66
1619 2039 2.012051 GCATAGGGTCCGACCACTTTG 61.012 57.143 19.43 17.15 41.02 2.77
1620 2040 0.909623 ATAGGGTCCGACCACTTTGG 59.090 55.000 19.43 0.00 41.02 3.28
1622 2042 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
1631 2051 3.672767 ACCACTTTGGGTCGTTAGTAG 57.327 47.619 0.00 0.00 43.37 2.57
1632 2052 2.301009 ACCACTTTGGGTCGTTAGTAGG 59.699 50.000 0.00 0.00 43.37 3.18
1633 2053 2.344025 CACTTTGGGTCGTTAGTAGGC 58.656 52.381 0.00 0.00 0.00 3.93
1634 2054 1.972795 ACTTTGGGTCGTTAGTAGGCA 59.027 47.619 0.00 0.00 0.00 4.75
1635 2055 2.028385 ACTTTGGGTCGTTAGTAGGCAG 60.028 50.000 0.00 0.00 0.00 4.85
1637 2057 0.974010 TGGGTCGTTAGTAGGCAGGG 60.974 60.000 0.00 0.00 0.00 4.45
1639 2059 0.459078 GGTCGTTAGTAGGCAGGGTC 59.541 60.000 0.00 0.00 0.00 4.46
1640 2060 0.459078 GTCGTTAGTAGGCAGGGTCC 59.541 60.000 0.00 0.00 0.00 4.46
1641 2061 1.033746 TCGTTAGTAGGCAGGGTCCG 61.034 60.000 0.00 0.00 0.00 4.79
1642 2062 1.821258 GTTAGTAGGCAGGGTCCGG 59.179 63.158 0.00 0.00 0.00 5.14
1655 2075 1.302993 GTCCGGGGCAACAGCTTTA 60.303 57.895 0.00 0.00 39.74 1.85
1656 2076 1.302993 TCCGGGGCAACAGCTTTAC 60.303 57.895 0.00 0.00 39.74 2.01
1657 2077 2.340328 CCGGGGCAACAGCTTTACC 61.340 63.158 0.00 0.00 39.74 2.85
1658 2078 1.602323 CGGGGCAACAGCTTTACCA 60.602 57.895 0.00 0.00 39.74 3.25
1659 2079 1.862602 CGGGGCAACAGCTTTACCAC 61.863 60.000 0.00 0.00 39.74 4.16
1660 2080 0.539669 GGGGCAACAGCTTTACCACT 60.540 55.000 0.00 0.00 39.74 4.00
1661 2081 0.598065 GGGCAACAGCTTTACCACTG 59.402 55.000 0.00 0.00 39.86 3.66
1662 2082 0.039165 GGCAACAGCTTTACCACTGC 60.039 55.000 0.00 0.00 37.42 4.40
1663 2083 0.385974 GCAACAGCTTTACCACTGCG 60.386 55.000 0.00 0.00 37.42 5.18
1664 2084 0.385974 CAACAGCTTTACCACTGCGC 60.386 55.000 0.00 0.00 37.42 6.09
1665 2085 1.515521 AACAGCTTTACCACTGCGCC 61.516 55.000 4.18 0.00 37.42 6.53
1666 2086 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
1667 2087 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
1668 2088 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
1671 2091 4.715523 TACCACTGCGCCAAGGCC 62.716 66.667 4.18 0.00 37.98 5.19
1690 2110 1.539157 CCCCCTTCTTGTTTGAGCTC 58.461 55.000 6.82 6.82 0.00 4.09
1697 2145 6.231211 CCCTTCTTGTTTGAGCTCTAGTAAA 58.769 40.000 16.19 3.97 0.00 2.01
1699 2147 7.148340 CCCTTCTTGTTTGAGCTCTAGTAAATG 60.148 40.741 16.19 2.73 0.00 2.32
1701 2149 5.643777 TCTTGTTTGAGCTCTAGTAAATGCC 59.356 40.000 16.19 0.00 0.00 4.40
1823 2471 0.465705 TGGATCGATGCACCCTCTTC 59.534 55.000 16.33 0.00 0.00 2.87
1941 2591 7.806180 ACTGATACTACTCCCATAATTGCTTT 58.194 34.615 0.00 0.00 0.00 3.51
1976 2626 4.261656 GGTGATCGATCTACCGAGTTCATT 60.262 45.833 25.02 0.00 42.21 2.57
2016 2666 3.028130 TCCAAAACAGACCAAAACCTCC 58.972 45.455 0.00 0.00 0.00 4.30
2080 2738 7.915923 GGAAATTGCCTACTTAATTACTTGCTC 59.084 37.037 0.00 0.00 0.00 4.26
2095 2753 5.033589 ACTTGCTCTCAATCTTATGGAGG 57.966 43.478 0.00 0.00 0.00 4.30
2149 2809 8.854979 TCACAATTGTTGATGAAGTTAAACAG 57.145 30.769 8.77 0.00 34.28 3.16
2179 2839 5.682862 GCAATTCATAAAACCGTGCATAGAG 59.317 40.000 0.00 0.00 0.00 2.43
2349 3017 3.144657 TCAAGTGCACCACTGAATGAT 57.855 42.857 14.63 0.00 44.62 2.45
2363 3032 5.688621 CACTGAATGATAATGGGCAATTTCG 59.311 40.000 0.00 0.00 0.00 3.46
2377 3046 5.358725 GGGCAATTTCGGGTTAATAAGAGAA 59.641 40.000 0.00 0.00 0.00 2.87
2419 3099 8.497910 ACAGGGAATATCAAGTACATATCTGT 57.502 34.615 0.00 0.00 39.49 3.41
2424 3104 9.355215 GGAATATCAAGTACATATCTGTTACCG 57.645 37.037 0.00 0.00 36.79 4.02
2453 3133 8.764524 AGAAAAGTACATAACTGCACTCTTAG 57.235 34.615 0.00 0.00 38.88 2.18
2530 3218 5.438117 CACTATTAGCAATGCAACGATCAG 58.562 41.667 8.35 0.00 0.00 2.90
2534 3222 0.804364 GCAATGCAACGATCAGGACA 59.196 50.000 0.00 0.00 0.00 4.02
2557 3245 3.758755 TGATACAGAGATGATGGTGGC 57.241 47.619 0.00 0.00 0.00 5.01
2726 3420 1.376812 CAAGGTACCCGAAGCCACC 60.377 63.158 8.74 0.00 0.00 4.61
2745 3439 4.402528 CGTCGCCATCACCCCCAA 62.403 66.667 0.00 0.00 0.00 4.12
2787 3481 1.645710 ACTTCACCTCGGATGGTTCT 58.354 50.000 0.00 0.00 38.45 3.01
2872 3634 6.707440 TTGACTATTTCAAAAGGTCAGCAA 57.293 33.333 8.06 0.00 41.51 3.91
2987 3831 8.126074 TGTGTATTTATTGTATGCAACCGATTC 58.874 33.333 0.00 0.00 37.44 2.52
2996 3840 4.789012 ATGCAACCGATTCAATCAAGTT 57.211 36.364 0.00 0.00 0.00 2.66
3008 3852 2.121116 ATCAAGTTATCGCCGACTCG 57.879 50.000 0.00 0.00 0.00 4.18
3087 3935 4.355549 TCTCTAGGGTGGAAAACGGATTA 58.644 43.478 0.00 0.00 0.00 1.75
3093 3941 3.268330 GGTGGAAAACGGATTAGGAGTC 58.732 50.000 0.00 0.00 0.00 3.36
3101 3949 6.732896 AAACGGATTAGGAGTCATGAGTAT 57.267 37.500 2.17 0.00 0.00 2.12
3102 3950 5.968528 ACGGATTAGGAGTCATGAGTATC 57.031 43.478 2.17 2.89 0.00 2.24
3161 4029 6.990798 TGCATTCACCAAATATGAGTTGAAA 58.009 32.000 0.00 0.00 0.00 2.69
3163 4031 6.867816 GCATTCACCAAATATGAGTTGAAACA 59.132 34.615 0.00 0.00 0.00 2.83
3202 4070 8.792830 ATATTACAAAGTTGTGTGTCAGCTAT 57.207 30.769 6.94 0.00 42.31 2.97
3294 4162 4.616802 GTCACGTTGCATGGAAAATTGTAG 59.383 41.667 0.00 0.00 0.00 2.74
3304 4180 7.037438 GCATGGAAAATTGTAGACATGTGAAT 58.963 34.615 1.15 0.00 38.29 2.57
3349 4225 7.497595 TCATCCAAAGCTCGTGTACTATATTT 58.502 34.615 0.00 0.00 0.00 1.40
3479 4614 5.480073 AGCTAGTTAATTTGTTTGGCCATCA 59.520 36.000 6.09 6.66 0.00 3.07
3630 4766 8.700051 AGCTATACAAGATAACAATGTCTGTCT 58.300 33.333 0.00 0.00 37.23 3.41
3653 4789 9.047371 GTCTAAGATAAAGGGAAGCTATTGTTC 57.953 37.037 0.00 0.00 0.00 3.18
3655 4791 9.396022 CTAAGATAAAGGGAAGCTATTGTTCAA 57.604 33.333 0.00 0.00 0.00 2.69
3660 4796 4.451900 AGGGAAGCTATTGTTCAATACCG 58.548 43.478 1.68 0.00 0.00 4.02
3687 5031 4.764823 TCCAACAAGTTGCCAAATACTAGG 59.235 41.667 1.81 0.00 39.16 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.504244 CCAAGAGACGTCGGCGAC 60.504 66.667 29.06 29.06 42.00 5.19
10 11 2.974489 GACCAAGAGACGTCGGCGA 61.974 63.158 20.03 4.99 42.00 5.54
11 12 2.504244 GACCAAGAGACGTCGGCG 60.504 66.667 8.42 8.42 44.93 6.46
12 13 1.444553 CAGACCAAGAGACGTCGGC 60.445 63.158 10.46 6.64 34.10 5.54
13 14 1.444553 GCAGACCAAGAGACGTCGG 60.445 63.158 10.46 7.82 34.10 4.79
14 15 0.109086 ATGCAGACCAAGAGACGTCG 60.109 55.000 10.46 0.00 34.10 5.12
15 16 1.728971 CAATGCAGACCAAGAGACGTC 59.271 52.381 7.70 7.70 0.00 4.34
16 17 1.344438 TCAATGCAGACCAAGAGACGT 59.656 47.619 0.00 0.00 0.00 4.34
17 18 1.728971 GTCAATGCAGACCAAGAGACG 59.271 52.381 0.00 0.00 32.36 4.18
18 19 1.728971 CGTCAATGCAGACCAAGAGAC 59.271 52.381 0.00 0.00 35.07 3.36
19 20 1.618343 TCGTCAATGCAGACCAAGAGA 59.382 47.619 0.00 0.00 35.07 3.10
20 21 1.728971 GTCGTCAATGCAGACCAAGAG 59.271 52.381 0.00 0.00 35.07 2.85
21 22 1.344438 AGTCGTCAATGCAGACCAAGA 59.656 47.619 0.00 0.00 35.65 3.02
22 23 1.800805 AGTCGTCAATGCAGACCAAG 58.199 50.000 0.00 0.00 35.65 3.61
23 24 2.143122 GAAGTCGTCAATGCAGACCAA 58.857 47.619 0.00 0.00 35.65 3.67
24 25 1.608025 GGAAGTCGTCAATGCAGACCA 60.608 52.381 0.00 0.00 35.65 4.02
25 26 1.079503 GGAAGTCGTCAATGCAGACC 58.920 55.000 0.00 0.00 35.65 3.85
26 27 1.079503 GGGAAGTCGTCAATGCAGAC 58.920 55.000 0.00 0.00 35.19 3.51
27 28 0.389817 CGGGAAGTCGTCAATGCAGA 60.390 55.000 0.00 0.00 0.00 4.26
28 29 1.970917 GCGGGAAGTCGTCAATGCAG 61.971 60.000 0.00 0.00 0.00 4.41
29 30 2.032634 GCGGGAAGTCGTCAATGCA 61.033 57.895 0.00 0.00 0.00 3.96
30 31 1.696832 GAGCGGGAAGTCGTCAATGC 61.697 60.000 0.00 0.00 0.00 3.56
31 32 1.413767 CGAGCGGGAAGTCGTCAATG 61.414 60.000 0.00 0.00 0.00 2.82
32 33 1.153823 CGAGCGGGAAGTCGTCAAT 60.154 57.895 0.00 0.00 0.00 2.57
33 34 2.257371 CGAGCGGGAAGTCGTCAA 59.743 61.111 0.00 0.00 0.00 3.18
34 35 2.981909 ACGAGCGGGAAGTCGTCA 60.982 61.111 0.00 0.00 46.17 4.35
37 38 2.809601 CCAACGAGCGGGAAGTCG 60.810 66.667 0.00 0.00 42.04 4.18
44 45 0.382515 TTTTGAAACCCAACGAGCGG 59.617 50.000 0.00 0.00 33.85 5.52
45 46 2.196295 TTTTTGAAACCCAACGAGCG 57.804 45.000 0.00 0.00 33.85 5.03
76 77 2.783135 TCTTTGTGCCTCCATCTTGAC 58.217 47.619 0.00 0.00 0.00 3.18
82 83 0.040058 TGCCATCTTTGTGCCTCCAT 59.960 50.000 0.00 0.00 0.00 3.41
83 84 0.609957 CTGCCATCTTTGTGCCTCCA 60.610 55.000 0.00 0.00 0.00 3.86
90 91 3.305608 GCAAAGCTTACTGCCATCTTTGT 60.306 43.478 11.37 0.00 43.10 2.83
97 98 1.238439 GTGAGCAAAGCTTACTGCCA 58.762 50.000 17.48 12.83 41.09 4.92
102 103 1.398960 CGCACTGTGAGCAAAGCTTAC 60.399 52.381 12.86 6.94 43.90 2.34
103 104 0.867746 CGCACTGTGAGCAAAGCTTA 59.132 50.000 12.86 0.00 39.88 3.09
104 105 1.650912 CGCACTGTGAGCAAAGCTT 59.349 52.632 12.86 0.00 39.88 3.74
184 185 8.241367 CCTTACAAACACACCCATATAGAAAAC 58.759 37.037 0.00 0.00 0.00 2.43
240 241 7.344441 GCGTGAATTTTATTTTTGCAAAGAGT 58.656 30.769 12.41 5.25 0.00 3.24
254 257 4.460731 TGAATGTCATGGGCGTGAATTTTA 59.539 37.500 0.00 0.00 0.00 1.52
264 268 9.715121 AATCATAAAAATATGAATGTCATGGGC 57.285 29.630 2.93 0.00 39.59 5.36
292 296 8.936070 ACATTTTTAGGTAACAAAAACACTCC 57.064 30.769 3.89 0.00 38.46 3.85
307 311 3.168193 CGTTTGGCGCTACATTTTTAGG 58.832 45.455 7.64 0.00 0.00 2.69
310 314 1.609555 TCCGTTTGGCGCTACATTTTT 59.390 42.857 7.64 0.00 39.71 1.94
322 326 6.483307 ACTCATCATGTTATGTATCCGTTTGG 59.517 38.462 0.00 0.00 0.00 3.28
337 341 2.346803 GCCACGTGTTACTCATCATGT 58.653 47.619 15.65 0.00 34.66 3.21
347 351 2.080693 CTATGCAAAGGCCACGTGTTA 58.919 47.619 15.65 0.00 40.13 2.41
377 381 4.431416 TTGACAGACAGTTGGTATTGGT 57.569 40.909 0.00 0.00 0.00 3.67
424 434 9.470399 TCGGTCCTATATATATGACTTTAGCAA 57.530 33.333 20.74 4.22 31.30 3.91
444 454 9.712359 GAACAATTAATTTTATAGTGTCGGTCC 57.288 33.333 0.00 0.00 0.00 4.46
446 456 9.233649 TGGAACAATTAATTTTATAGTGTCGGT 57.766 29.630 0.00 0.00 31.92 4.69
447 457 9.498307 GTGGAACAATTAATTTTATAGTGTCGG 57.502 33.333 0.00 0.00 44.16 4.79
530 543 1.892209 CTAACACAAAAGCCCGAGGT 58.108 50.000 0.00 0.00 0.00 3.85
656 673 3.160047 CGGAGGAGCTGGAGCCAT 61.160 66.667 0.00 0.00 43.38 4.40
728 746 5.186256 TCAAATAGGCCCAACTAATGACA 57.814 39.130 0.00 0.00 0.00 3.58
729 747 6.715347 AATCAAATAGGCCCAACTAATGAC 57.285 37.500 0.00 0.00 30.61 3.06
868 889 8.769359 ACTAACTACTAAGGCACCTTGAAATAT 58.231 33.333 12.29 0.00 37.47 1.28
934 968 2.842462 TGGTCTGGTGCGTGGAGT 60.842 61.111 0.00 0.00 0.00 3.85
962 996 1.256117 CGTTTGCTTGCTTGCTTGTTC 59.744 47.619 3.47 0.00 0.00 3.18
1052 1087 2.567169 TGATGATGAAGAACGGGTGAGT 59.433 45.455 0.00 0.00 0.00 3.41
1056 1091 3.535561 GTGATGATGATGAAGAACGGGT 58.464 45.455 0.00 0.00 0.00 5.28
1077 1118 1.208052 AGTCGGTGTTCCTGATGATGG 59.792 52.381 0.00 0.00 0.00 3.51
1099 1140 0.388134 GCGAAGAACTGGTACTCGCA 60.388 55.000 15.81 0.00 43.42 5.10
1128 1169 2.990967 CCATGGTGGTGGTGGTGC 60.991 66.667 2.57 0.00 34.46 5.01
1275 1328 1.523711 CAGGTGAGCCGTGTGTTGT 60.524 57.895 0.00 0.00 40.50 3.32
1308 1361 2.036256 ATGGTGGCTCTTGGTGGC 59.964 61.111 0.00 0.00 0.00 5.01
1310 1363 1.003355 ACGATGGTGGCTCTTGGTG 60.003 57.895 0.00 0.00 0.00 4.17
1311 1364 1.003355 CACGATGGTGGCTCTTGGT 60.003 57.895 0.00 0.00 40.58 3.67
1356 1412 1.043116 TCCCATCGATCGGCAAGAGT 61.043 55.000 16.41 0.00 0.00 3.24
1368 1424 0.105039 GTTAGCAGGAGGTCCCATCG 59.895 60.000 0.00 0.00 37.41 3.84
1373 1429 4.079253 TGATTTTTGTTAGCAGGAGGTCC 58.921 43.478 0.00 0.00 0.00 4.46
1375 1431 3.502211 CGTGATTTTTGTTAGCAGGAGGT 59.498 43.478 0.00 0.00 0.00 3.85
1378 1434 2.227865 GGCGTGATTTTTGTTAGCAGGA 59.772 45.455 0.00 0.00 0.00 3.86
1380 1436 3.559238 AGGCGTGATTTTTGTTAGCAG 57.441 42.857 0.00 0.00 0.00 4.24
1381 1437 4.069304 AGTAGGCGTGATTTTTGTTAGCA 58.931 39.130 0.00 0.00 0.00 3.49
1382 1438 4.680171 AGTAGGCGTGATTTTTGTTAGC 57.320 40.909 0.00 0.00 0.00 3.09
1383 1439 9.620660 AAATTAAGTAGGCGTGATTTTTGTTAG 57.379 29.630 0.00 0.00 0.00 2.34
1385 1441 7.597369 GGAAATTAAGTAGGCGTGATTTTTGTT 59.403 33.333 0.00 0.00 0.00 2.83
1386 1442 7.088272 GGAAATTAAGTAGGCGTGATTTTTGT 58.912 34.615 0.00 0.00 0.00 2.83
1387 1443 7.087639 TGGAAATTAAGTAGGCGTGATTTTTG 58.912 34.615 0.00 0.00 0.00 2.44
1392 1453 8.594550 AGTATATGGAAATTAAGTAGGCGTGAT 58.405 33.333 0.00 0.00 0.00 3.06
1393 1454 7.959175 AGTATATGGAAATTAAGTAGGCGTGA 58.041 34.615 0.00 0.00 0.00 4.35
1395 1456 7.384477 GGAGTATATGGAAATTAAGTAGGCGT 58.616 38.462 0.00 0.00 0.00 5.68
1397 1458 6.817140 CGGGAGTATATGGAAATTAAGTAGGC 59.183 42.308 0.00 0.00 0.00 3.93
1402 1463 5.556915 TGGCGGGAGTATATGGAAATTAAG 58.443 41.667 0.00 0.00 0.00 1.85
1408 1469 2.832129 GAGATGGCGGGAGTATATGGAA 59.168 50.000 0.00 0.00 0.00 3.53
1414 1475 3.644966 TTTTTGAGATGGCGGGAGTAT 57.355 42.857 0.00 0.00 0.00 2.12
1436 1497 3.221771 TCTGCCAGCATAAACACAAACT 58.778 40.909 0.00 0.00 0.00 2.66
1437 1498 3.641437 TCTGCCAGCATAAACACAAAC 57.359 42.857 0.00 0.00 0.00 2.93
1438 1499 4.099266 ACTTTCTGCCAGCATAAACACAAA 59.901 37.500 0.00 0.00 0.00 2.83
1439 1500 3.636300 ACTTTCTGCCAGCATAAACACAA 59.364 39.130 0.00 0.00 0.00 3.33
1440 1501 3.221771 ACTTTCTGCCAGCATAAACACA 58.778 40.909 0.00 0.00 0.00 3.72
1441 1502 3.923017 ACTTTCTGCCAGCATAAACAC 57.077 42.857 0.00 0.00 0.00 3.32
1443 1737 4.870363 TCAAACTTTCTGCCAGCATAAAC 58.130 39.130 0.00 0.00 0.00 2.01
1445 1739 4.144297 ACTCAAACTTTCTGCCAGCATAA 58.856 39.130 0.00 0.00 0.00 1.90
1450 1744 4.907879 AGAAACTCAAACTTTCTGCCAG 57.092 40.909 0.00 0.00 36.74 4.85
1451 1745 4.462483 ACAAGAAACTCAAACTTTCTGCCA 59.538 37.500 0.00 0.00 37.89 4.92
1465 1763 3.947196 TGTGCATCAACTGACAAGAAACT 59.053 39.130 0.00 0.00 0.00 2.66
1470 1768 4.556942 TTCTTGTGCATCAACTGACAAG 57.443 40.909 0.00 0.00 40.52 3.16
1471 1769 4.261698 CCATTCTTGTGCATCAACTGACAA 60.262 41.667 0.00 0.00 32.18 3.18
1473 1771 3.366679 CCCATTCTTGTGCATCAACTGAC 60.367 47.826 0.00 0.00 32.18 3.51
1570 1990 4.154375 GCTGCCCTTTAGTAGAACTCAAAC 59.846 45.833 0.00 0.00 0.00 2.93
1576 1996 1.742750 CGGGCTGCCCTTTAGTAGAAC 60.743 57.143 33.39 4.65 42.67 3.01
1579 1999 1.146263 CCGGGCTGCCCTTTAGTAG 59.854 63.158 33.39 16.86 42.67 2.57
1581 2001 2.933834 ACCGGGCTGCCCTTTAGT 60.934 61.111 33.39 21.92 42.67 2.24
1591 2011 3.480133 GACCCTATGCACCGGGCT 61.480 66.667 19.46 8.90 44.63 5.19
1592 2012 4.564110 GGACCCTATGCACCGGGC 62.564 72.222 19.46 7.25 44.63 6.13
1593 2013 4.235762 CGGACCCTATGCACCGGG 62.236 72.222 18.26 18.26 46.26 5.73
1596 2016 2.363975 TGGTCGGACCCTATGCACC 61.364 63.158 23.81 0.00 37.50 5.01
1597 2017 1.153429 GTGGTCGGACCCTATGCAC 60.153 63.158 23.81 10.68 37.50 4.57
1598 2018 0.907704 AAGTGGTCGGACCCTATGCA 60.908 55.000 23.81 1.39 37.50 3.96
1599 2019 0.252197 AAAGTGGTCGGACCCTATGC 59.748 55.000 23.81 9.21 37.50 3.14
1601 2021 0.909623 CCAAAGTGGTCGGACCCTAT 59.090 55.000 23.81 7.35 37.50 2.57
1602 2022 1.196104 CCCAAAGTGGTCGGACCCTA 61.196 60.000 23.81 3.76 37.50 3.53
1603 2023 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
1604 2024 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
1611 2031 2.301009 CCTACTAACGACCCAAAGTGGT 59.699 50.000 0.00 0.00 42.79 4.16
1613 2033 2.289195 TGCCTACTAACGACCCAAAGTG 60.289 50.000 0.00 0.00 0.00 3.16
1614 2034 1.972795 TGCCTACTAACGACCCAAAGT 59.027 47.619 0.00 0.00 0.00 2.66
1615 2035 2.618053 CTGCCTACTAACGACCCAAAG 58.382 52.381 0.00 0.00 0.00 2.77
1616 2036 1.276989 CCTGCCTACTAACGACCCAAA 59.723 52.381 0.00 0.00 0.00 3.28
1617 2037 0.899720 CCTGCCTACTAACGACCCAA 59.100 55.000 0.00 0.00 0.00 4.12
1618 2038 0.974010 CCCTGCCTACTAACGACCCA 60.974 60.000 0.00 0.00 0.00 4.51
1619 2039 0.974525 ACCCTGCCTACTAACGACCC 60.975 60.000 0.00 0.00 0.00 4.46
1620 2040 0.459078 GACCCTGCCTACTAACGACC 59.541 60.000 0.00 0.00 0.00 4.79
1622 2042 1.033746 CGGACCCTGCCTACTAACGA 61.034 60.000 0.00 0.00 0.00 3.85
1624 2044 1.683418 CCCGGACCCTGCCTACTAAC 61.683 65.000 0.73 0.00 0.00 2.34
1633 2053 4.722700 CTGTTGCCCCGGACCCTG 62.723 72.222 0.73 0.00 0.00 4.45
1637 2057 1.302993 TAAAGCTGTTGCCCCGGAC 60.303 57.895 0.73 0.00 40.80 4.79
1639 2059 2.340328 GGTAAAGCTGTTGCCCCGG 61.340 63.158 0.00 0.00 40.80 5.73
1640 2060 1.602323 TGGTAAAGCTGTTGCCCCG 60.602 57.895 11.25 0.00 40.80 5.73
1641 2061 0.539669 AGTGGTAAAGCTGTTGCCCC 60.540 55.000 11.25 3.01 40.80 5.80
1642 2062 0.598065 CAGTGGTAAAGCTGTTGCCC 59.402 55.000 11.25 0.00 40.80 5.36
1645 2065 0.385974 GCGCAGTGGTAAAGCTGTTG 60.386 55.000 0.30 0.00 35.33 3.33
1646 2066 1.515521 GGCGCAGTGGTAAAGCTGTT 61.516 55.000 10.83 0.00 35.33 3.16
1647 2067 1.966451 GGCGCAGTGGTAAAGCTGT 60.966 57.895 10.83 0.00 35.33 4.40
1648 2068 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
1651 2071 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
1652 2072 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
1671 2091 1.074566 AGAGCTCAAACAAGAAGGGGG 59.925 52.381 17.77 0.00 0.00 5.40
1672 2092 2.575805 AGAGCTCAAACAAGAAGGGG 57.424 50.000 17.77 0.00 0.00 4.79
1673 2093 4.278975 ACTAGAGCTCAAACAAGAAGGG 57.721 45.455 17.77 0.00 0.00 3.95
1674 2094 7.625185 GCATTTACTAGAGCTCAAACAAGAAGG 60.625 40.741 17.77 4.75 0.00 3.46
1675 2095 7.239972 GCATTTACTAGAGCTCAAACAAGAAG 58.760 38.462 17.77 2.59 0.00 2.85
1676 2096 6.149474 GGCATTTACTAGAGCTCAAACAAGAA 59.851 38.462 17.77 2.15 0.00 2.52
1677 2097 5.643777 GGCATTTACTAGAGCTCAAACAAGA 59.356 40.000 17.77 0.00 0.00 3.02
1678 2098 5.446473 CGGCATTTACTAGAGCTCAAACAAG 60.446 44.000 17.77 7.43 0.00 3.16
1679 2099 4.391830 CGGCATTTACTAGAGCTCAAACAA 59.608 41.667 17.77 2.15 0.00 2.83
1680 2100 3.932710 CGGCATTTACTAGAGCTCAAACA 59.067 43.478 17.77 0.00 0.00 2.83
1681 2101 4.181578 TCGGCATTTACTAGAGCTCAAAC 58.818 43.478 17.77 0.00 0.00 2.93
1684 2104 4.465632 TTTCGGCATTTACTAGAGCTCA 57.534 40.909 17.77 0.82 0.00 4.26
1685 2105 5.993106 ATTTTCGGCATTTACTAGAGCTC 57.007 39.130 5.27 5.27 0.00 4.09
1717 2329 2.852449 TGCTTGACCCCATAAGGAGATT 59.148 45.455 0.00 0.00 38.24 2.40
1723 2335 6.716628 ACATATGTATTGCTTGACCCCATAAG 59.283 38.462 6.56 0.00 0.00 1.73
1941 2591 2.363276 ATCACCCGGCCACTACGA 60.363 61.111 2.24 0.00 0.00 3.43
1976 2626 8.567948 GTTTTGGACTTGATCTCAATCAGTTTA 58.432 33.333 0.00 0.00 42.72 2.01
1985 2635 4.141505 TGGTCTGTTTTGGACTTGATCTCA 60.142 41.667 0.00 0.00 34.47 3.27
1993 2643 3.699538 GAGGTTTTGGTCTGTTTTGGACT 59.300 43.478 0.00 0.00 34.47 3.85
2016 2666 5.348164 ACAAAGAACTTGTTTCCATTTCGG 58.652 37.500 0.00 0.00 46.49 4.30
2032 2687 7.106439 TCCTGATGCAAACTAAAACAAAGAA 57.894 32.000 0.00 0.00 0.00 2.52
2035 2690 8.610896 CAATTTCCTGATGCAAACTAAAACAAA 58.389 29.630 0.00 0.00 0.00 2.83
2080 2738 3.565764 TGCCACCTCCATAAGATTGAG 57.434 47.619 0.00 0.00 0.00 3.02
2095 2753 2.353011 CCATTTGTGAGGAACATGCCAC 60.353 50.000 0.00 0.00 38.99 5.01
2149 2809 6.144724 TGCACGGTTTTATGAATTGCTAAAAC 59.855 34.615 16.67 16.67 42.77 2.43
2179 2839 1.537562 GCATACGTGTAGCCCTGTACC 60.538 57.143 0.00 0.00 0.00 3.34
2312 2980 7.962918 GTGCACTTGATTGTAATCGTTCTAATT 59.037 33.333 10.32 0.00 38.26 1.40
2313 2981 7.414098 GGTGCACTTGATTGTAATCGTTCTAAT 60.414 37.037 17.98 0.00 38.26 1.73
2314 2982 6.128391 GGTGCACTTGATTGTAATCGTTCTAA 60.128 38.462 17.98 0.00 38.26 2.10
2349 3017 6.834451 TCTTATTAACCCGAAATTGCCCATTA 59.166 34.615 0.00 0.00 0.00 1.90
2419 3099 7.095523 GCAGTTATGTACTTTTCTTGTCGGTAA 60.096 37.037 0.00 0.00 33.85 2.85
2453 3133 8.743714 ACCTGAACATCAAGAGAAAAATAATCC 58.256 33.333 0.00 0.00 0.00 3.01
2463 3147 1.699083 TGGCACCTGAACATCAAGAGA 59.301 47.619 0.00 0.00 0.00 3.10
2530 3218 6.204301 CACCATCATCTCTGTATCAATTGTCC 59.796 42.308 5.13 0.00 0.00 4.02
2534 3222 5.068636 GCCACCATCATCTCTGTATCAATT 58.931 41.667 0.00 0.00 0.00 2.32
2557 3245 1.961277 GTCGGATTATGGGCAGCCG 60.961 63.158 5.00 0.00 43.11 5.52
2745 3439 3.246416 ACTAGGATCATAGGGCGAAGT 57.754 47.619 18.05 0.00 0.00 3.01
2987 3831 2.216488 CGAGTCGGCGATAACTTGATTG 59.784 50.000 14.79 0.00 0.00 2.67
2996 3840 3.763097 TTTAACTTCGAGTCGGCGATA 57.237 42.857 14.79 0.00 40.35 2.92
3008 3852 5.774878 AAAGCTCGTCCGTATTTAACTTC 57.225 39.130 0.00 0.00 0.00 3.01
3087 3935 2.227626 CGCGATGATACTCATGACTCCT 59.772 50.000 0.00 0.00 37.20 3.69
3093 3941 2.991866 AGCATTCGCGATGATACTCATG 59.008 45.455 10.88 9.33 45.49 3.07
3101 3949 4.570369 TCTCAAAATAAGCATTCGCGATGA 59.430 37.500 10.88 5.52 45.49 2.92
3102 3950 4.836455 TCTCAAAATAAGCATTCGCGATG 58.164 39.130 10.88 11.83 45.49 3.84
3103 3951 4.811024 TCTCTCAAAATAAGCATTCGCGAT 59.189 37.500 10.88 0.00 45.49 4.58
3104 3952 4.180817 TCTCTCAAAATAAGCATTCGCGA 58.819 39.130 3.71 3.71 45.49 5.87
3105 3953 4.268644 TCTCTCTCAAAATAAGCATTCGCG 59.731 41.667 0.00 0.00 45.49 5.87
3106 3954 5.725110 TCTCTCTCAAAATAAGCATTCGC 57.275 39.130 0.00 0.00 38.99 4.70
3138 4006 6.867816 TGTTTCAACTCATATTTGGTGAATGC 59.132 34.615 6.15 4.41 0.00 3.56
3188 4056 6.595326 CCTCAAATTAGATAGCTGACACACAA 59.405 38.462 0.00 0.00 0.00 3.33
3202 4070 7.633018 ACCTATGATAAGGCCTCAAATTAGA 57.367 36.000 5.23 0.00 40.62 2.10
3294 4162 7.571983 GCAGCTATTATGGTGTATTCACATGTC 60.572 40.741 0.00 0.00 45.45 3.06
3304 4180 6.430925 GGATGATTTGCAGCTATTATGGTGTA 59.569 38.462 0.00 0.00 37.70 2.90
3349 4225 8.405531 GCAACAGCATAAGGAACTCATAATTAA 58.594 33.333 0.00 0.00 38.49 1.40
3467 4602 3.087781 TCGATCAAATGATGGCCAAACA 58.912 40.909 10.96 14.42 34.37 2.83
3479 4614 6.539826 ACACACATACACATGATCGATCAAAT 59.460 34.615 30.41 18.87 40.69 2.32
3568 4704 4.697756 TTGAGGTTGGAGGGCGCG 62.698 66.667 0.00 0.00 0.00 6.86
3571 4707 1.676967 CAGCTTGAGGTTGGAGGGC 60.677 63.158 0.00 0.00 0.00 5.19
3630 4766 9.920946 ATTGAACAATAGCTTCCCTTTATCTTA 57.079 29.630 0.00 0.00 0.00 2.10
3653 4789 4.722194 CAACTTGTTGGATCACGGTATTG 58.278 43.478 5.65 0.00 0.00 1.90
3655 4791 2.747446 GCAACTTGTTGGATCACGGTAT 59.253 45.455 14.30 0.00 0.00 2.73
3660 4796 3.451141 TTTGGCAACTTGTTGGATCAC 57.549 42.857 14.30 0.00 37.61 3.06
3687 5031 9.941664 CATTGGACTTAATAAATCTCATGACAC 57.058 33.333 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.