Multiple sequence alignment - TraesCS6D01G070800

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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 TraesCS6D01G070800 chr6D 100.000 3515 0 0 1 3515 35668275 35664761 0.000000e+00 6492.0
1 TraesCS6D01G070800 chr6D 80.391 1739 244 60 664 2334 36106195 36104486 0.000000e+00 1232.0
2 TraesCS6D01G070800 chr6D 81.552 1366 191 38 784 2133 35717996 35716676 0.000000e+00 1070.0
3 TraesCS6D01G070800 chr6D 78.285 1423 226 44 751 2151 35642080 35640719 0.000000e+00 839.0
4 TraesCS6D01G070800 chr6D 76.070 1308 243 49 797 2076 36323919 36325184 4.990000e-173 617.0
5 TraesCS6D01G070800 chr6D 82.536 481 52 24 656 1111 35886366 35885893 9.150000e-106 394.0
6 TraesCS6D01G070800 chr6D 90.942 276 23 2 766 1040 36074173 36073899 1.540000e-98 370.0
7 TraesCS6D01G070800 chr6B 87.046 2393 209 42 15 2334 75269247 75266883 0.000000e+00 2608.0
8 TraesCS6D01G070800 chr6B 86.910 1505 153 18 765 2239 75514585 75513095 0.000000e+00 1648.0
9 TraesCS6D01G070800 chr6B 81.344 1399 199 31 764 2145 75423485 75422132 0.000000e+00 1081.0
10 TraesCS6D01G070800 chr6B 81.318 1290 206 17 764 2037 75510366 75509096 0.000000e+00 1014.0
11 TraesCS6D01G070800 chr6B 80.227 1411 205 48 765 2145 75526311 75524945 0.000000e+00 992.0
12 TraesCS6D01G070800 chr6B 84.413 494 52 13 3038 3515 75265744 75265260 2.470000e-126 462.0
13 TraesCS6D01G070800 chr6B 76.861 618 122 14 763 1371 75990631 75990026 2.620000e-86 329.0
14 TraesCS6D01G070800 chr6B 90.129 233 16 3 2727 2958 75266120 75265894 2.650000e-76 296.0
15 TraesCS6D01G070800 chr6B 91.071 112 4 5 2630 2735 75266425 75266314 2.830000e-31 147.0
16 TraesCS6D01G070800 chr6B 72.455 334 81 9 1579 1905 54149791 54150120 2.890000e-16 97.1
17 TraesCS6D01G070800 chr6A 80.979 1635 225 50 764 2334 39878003 39876391 0.000000e+00 1218.0
18 TraesCS6D01G070800 chr6A 79.126 1418 224 46 765 2150 39628973 39627596 0.000000e+00 913.0
19 TraesCS6D01G070800 chr6A 79.040 1417 224 45 767 2150 39581183 39579807 0.000000e+00 904.0
20 TraesCS6D01G070800 chr6A 81.148 732 109 15 1427 2151 39590373 39589664 8.520000e-156 560.0
21 TraesCS6D01G070800 chr6A 81.011 732 110 15 1427 2151 39548260 39547551 3.960000e-154 555.0
22 TraesCS6D01G070800 chr6A 81.818 671 96 12 1488 2151 39638109 39637458 1.110000e-149 540.0
23 TraesCS6D01G070800 chr6A 72.659 929 193 43 1207 2120 40529289 40528407 5.820000e-63 252.0
24 TraesCS6D01G070800 chr6A 87.097 62 6 1 1201 1260 33216079 33216018 6.300000e-08 69.4
25 TraesCS6D01G070800 chr1D 80.612 980 147 27 767 1741 37880021 37880962 0.000000e+00 717.0
26 TraesCS6D01G070800 chr1D 82.382 403 48 17 1757 2151 37881026 37881413 2.620000e-86 329.0
27 TraesCS6D01G070800 chr1B 80.450 977 153 23 770 1741 57615192 57616135 0.000000e+00 712.0
28 TraesCS6D01G070800 chr1B 80.299 401 60 12 1757 2151 57616196 57616583 5.740000e-73 285.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G070800 chr6D 35664761 35668275 3514 True 6492.00 6492 100.00000 1 3515 1 chr6D.!!$R2 3514
1 TraesCS6D01G070800 chr6D 36104486 36106195 1709 True 1232.00 1232 80.39100 664 2334 1 chr6D.!!$R6 1670
2 TraesCS6D01G070800 chr6D 35716676 35717996 1320 True 1070.00 1070 81.55200 784 2133 1 chr6D.!!$R3 1349
3 TraesCS6D01G070800 chr6D 35640719 35642080 1361 True 839.00 839 78.28500 751 2151 1 chr6D.!!$R1 1400
4 TraesCS6D01G070800 chr6D 36323919 36325184 1265 False 617.00 617 76.07000 797 2076 1 chr6D.!!$F1 1279
5 TraesCS6D01G070800 chr6B 75509096 75514585 5489 True 1331.00 1648 84.11400 764 2239 2 chr6B.!!$R5 1475
6 TraesCS6D01G070800 chr6B 75422132 75423485 1353 True 1081.00 1081 81.34400 764 2145 1 chr6B.!!$R1 1381
7 TraesCS6D01G070800 chr6B 75524945 75526311 1366 True 992.00 992 80.22700 765 2145 1 chr6B.!!$R2 1380
8 TraesCS6D01G070800 chr6B 75265260 75269247 3987 True 878.25 2608 88.16475 15 3515 4 chr6B.!!$R4 3500
9 TraesCS6D01G070800 chr6B 75990026 75990631 605 True 329.00 329 76.86100 763 1371 1 chr6B.!!$R3 608
10 TraesCS6D01G070800 chr6A 39876391 39878003 1612 True 1218.00 1218 80.97900 764 2334 1 chr6A.!!$R7 1570
11 TraesCS6D01G070800 chr6A 39627596 39628973 1377 True 913.00 913 79.12600 765 2150 1 chr6A.!!$R5 1385
12 TraesCS6D01G070800 chr6A 39579807 39581183 1376 True 904.00 904 79.04000 767 2150 1 chr6A.!!$R3 1383
13 TraesCS6D01G070800 chr6A 39589664 39590373 709 True 560.00 560 81.14800 1427 2151 1 chr6A.!!$R4 724
14 TraesCS6D01G070800 chr6A 39547551 39548260 709 True 555.00 555 81.01100 1427 2151 1 chr6A.!!$R2 724
15 TraesCS6D01G070800 chr6A 39637458 39638109 651 True 540.00 540 81.81800 1488 2151 1 chr6A.!!$R6 663
16 TraesCS6D01G070800 chr6A 40528407 40529289 882 True 252.00 252 72.65900 1207 2120 1 chr6A.!!$R8 913
17 TraesCS6D01G070800 chr1D 37880021 37881413 1392 False 523.00 717 81.49700 767 2151 2 chr1D.!!$F1 1384
18 TraesCS6D01G070800 chr1B 57615192 57616583 1391 False 498.50 712 80.37450 770 2151 2 chr1B.!!$F1 1381

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
638 675 0.036010 ATGGGCTTTCACCTCTCGTG 60.036 55.0 0.00 0.0 44.50 4.35 F
643 680 0.390472 CTTTCACCTCTCGTGGGCTC 60.390 60.0 0.00 0.0 43.23 4.70 F
2425 5898 0.179205 GCAGTGCAGATGTTTCTCGC 60.179 55.0 11.09 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2448 0.321034 GCTCGCTCCATGCCATATCA 60.321 55.000 0.0 0.0 38.78 2.15 R
2474 5947 1.133884 CAGCTCCATCATGTCCACCAT 60.134 52.381 0.0 0.0 0.00 3.55 R
3354 7616 0.907486 CCCATCTCTGCACCTCTTCA 59.093 55.000 0.0 0.0 0.00 3.02 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
110 112 4.522789 TGGGAAAGGAATAAGTGCACTTTC 59.477 41.667 35.20 26.28 43.71 2.62
129 131 0.108207 CAGGGAGCATTGGAGCTAGG 59.892 60.000 0.00 0.00 46.75 3.02
136 138 1.141881 ATTGGAGCTAGGTCGCGTG 59.858 57.895 15.43 0.00 34.40 5.34
152 154 3.454941 GTGCGCACACGAGATTTTT 57.545 47.368 34.52 0.00 43.93 1.94
158 160 1.195900 GCACACGAGATTTTTACCGCA 59.804 47.619 0.00 0.00 0.00 5.69
172 174 0.602638 ACCGCAAATCAGACGAGCAA 60.603 50.000 0.00 0.00 0.00 3.91
315 317 7.831193 CCTTTCCTTTCTCATCCTTGATCTTAA 59.169 37.037 0.00 0.00 0.00 1.85
317 319 7.502060 TCCTTTCTCATCCTTGATCTTAAGT 57.498 36.000 1.63 0.00 0.00 2.24
318 320 7.560368 TCCTTTCTCATCCTTGATCTTAAGTC 58.440 38.462 1.63 0.58 0.00 3.01
340 342 5.882557 GTCCACCATCATGTTATCTTCAGTT 59.117 40.000 0.00 0.00 0.00 3.16
348 350 8.886719 CATCATGTTATCTTCAGTTGCTTCTTA 58.113 33.333 0.00 0.00 0.00 2.10
369 371 8.442632 TCTTACTAATCATCAATCAAAGCCAG 57.557 34.615 0.00 0.00 0.00 4.85
378 380 2.103537 ATCAAAGCCAGCAATTTGCC 57.896 45.000 17.51 3.02 46.52 4.52
381 383 1.470996 AAAGCCAGCAATTTGCCGGA 61.471 50.000 24.57 0.00 43.51 5.14
392 394 4.083377 GCAATTTGCCGGATGTTTCAAAAT 60.083 37.500 5.05 0.00 37.42 1.82
396 398 7.920160 ATTTGCCGGATGTTTCAAAATAAAT 57.080 28.000 5.05 0.00 32.97 1.40
399 401 8.833231 TTGCCGGATGTTTCAAAATAAATAAA 57.167 26.923 5.05 0.00 0.00 1.40
400 402 9.442047 TTGCCGGATGTTTCAAAATAAATAAAT 57.558 25.926 5.05 0.00 0.00 1.40
422 424 6.830873 ATAACGTACTTAGTATGGCTAGGG 57.169 41.667 15.09 0.00 31.75 3.53
427 429 4.772886 ACTTAGTATGGCTAGGGTTTGG 57.227 45.455 0.00 0.00 31.75 3.28
430 432 1.844497 AGTATGGCTAGGGTTTGGACC 59.156 52.381 0.00 0.00 45.75 4.46
448 450 3.119566 GGACCGAATGACGTAGAAACTCT 60.120 47.826 0.00 0.00 40.78 3.24
449 451 4.483311 GACCGAATGACGTAGAAACTCTT 58.517 43.478 0.00 0.00 40.78 2.85
464 466 1.416401 ACTCTTTGTCACCATGACCGT 59.584 47.619 6.51 0.00 46.40 4.83
467 469 4.062293 CTCTTTGTCACCATGACCGTAAA 58.938 43.478 6.51 0.73 46.40 2.01
505 507 1.770294 ACAAGAGTTTCCCCGCAAAA 58.230 45.000 0.00 0.00 0.00 2.44
540 542 0.108615 CCGGGTCTAGCTTGTCACTG 60.109 60.000 0.00 0.00 0.00 3.66
636 673 0.250234 TGATGGGCTTTCACCTCTCG 59.750 55.000 0.00 0.00 0.00 4.04
637 674 0.250513 GATGGGCTTTCACCTCTCGT 59.749 55.000 0.00 0.00 0.00 4.18
638 675 0.036010 ATGGGCTTTCACCTCTCGTG 60.036 55.000 0.00 0.00 44.50 4.35
639 676 1.376037 GGGCTTTCACCTCTCGTGG 60.376 63.158 0.00 0.00 43.23 4.94
640 677 1.376037 GGCTTTCACCTCTCGTGGG 60.376 63.158 0.00 0.00 43.23 4.61
641 678 2.035442 GCTTTCACCTCTCGTGGGC 61.035 63.158 0.00 0.00 43.23 5.36
642 679 1.674057 CTTTCACCTCTCGTGGGCT 59.326 57.895 0.00 0.00 43.23 5.19
643 680 0.390472 CTTTCACCTCTCGTGGGCTC 60.390 60.000 0.00 0.00 43.23 4.70
644 681 1.118965 TTTCACCTCTCGTGGGCTCA 61.119 55.000 0.00 0.00 43.23 4.26
645 682 1.816863 TTCACCTCTCGTGGGCTCAC 61.817 60.000 6.66 6.66 43.23 3.51
646 683 2.118513 ACCTCTCGTGGGCTCACT 59.881 61.111 16.21 0.00 41.53 3.41
647 684 1.979693 ACCTCTCGTGGGCTCACTC 60.980 63.158 16.21 0.00 41.53 3.51
648 685 1.680651 CCTCTCGTGGGCTCACTCT 60.681 63.158 16.21 0.00 41.53 3.24
649 686 1.662438 CCTCTCGTGGGCTCACTCTC 61.662 65.000 16.21 0.00 41.53 3.20
650 687 0.679640 CTCTCGTGGGCTCACTCTCT 60.680 60.000 16.21 0.00 41.53 3.10
651 688 0.678366 TCTCGTGGGCTCACTCTCTC 60.678 60.000 16.21 0.00 41.53 3.20
652 689 1.662438 CTCGTGGGCTCACTCTCTCC 61.662 65.000 16.21 0.00 41.53 3.71
653 690 2.716017 CGTGGGCTCACTCTCTCCC 61.716 68.421 16.21 0.00 41.53 4.30
947 1019 3.636231 CTTCCGCCTCCACCACCA 61.636 66.667 0.00 0.00 0.00 4.17
957 1029 2.032987 CACCACCACCGTAACCCC 59.967 66.667 0.00 0.00 0.00 4.95
1006 1081 3.689649 GCACTTCGAACCTACAATGGATT 59.310 43.478 0.00 0.00 0.00 3.01
1266 1387 1.002502 GGTGGTCTTGGTAGGCACC 60.003 63.158 0.00 0.00 46.00 5.01
1384 1532 1.757699 AGGCTTCGAGTTCTATGGACC 59.242 52.381 0.00 0.00 0.00 4.46
1459 1607 3.244582 TCCCTTTACTGGTTGCTCACTA 58.755 45.455 0.00 0.00 0.00 2.74
1476 1624 4.566004 TCACTAATATATCGGCAGCAACC 58.434 43.478 0.00 0.00 0.00 3.77
1520 1683 3.416156 AGTTTGATTTGGAGAGGCAGAC 58.584 45.455 0.00 0.00 0.00 3.51
1575 1747 6.945218 TGCCAATAATTGTCTTAGCCAATTT 58.055 32.000 6.55 0.00 41.45 1.82
1602 1774 2.930019 CAGGCAGAGGGTGGTGGA 60.930 66.667 0.00 0.00 0.00 4.02
1639 1811 5.643379 TCTATCAAAATTCAGTGCCCAAC 57.357 39.130 0.00 0.00 0.00 3.77
1712 1884 1.680338 ACTGTTGAACTGGACAAGCC 58.320 50.000 7.13 0.00 37.10 4.35
1779 2006 5.185056 GGGGTTTGCTGAGTACAATAATGTT 59.815 40.000 0.00 0.00 41.05 2.71
1790 2017 8.151596 TGAGTACAATAATGTTGTGTTCCTACA 58.848 33.333 5.62 0.00 41.05 2.74
1853 2080 5.163622 TGCAGTTCAAGAAAGTTTCCAAGAG 60.164 40.000 12.05 0.00 0.00 2.85
1859 2086 4.907879 AGAAAGTTTCCAAGAGCAACAG 57.092 40.909 12.05 0.00 0.00 3.16
1873 2100 1.061711 GCAACAGCTTGACTCGCTATG 59.938 52.381 0.00 0.00 35.63 2.23
1931 2168 7.587629 AGCATATGCATATACATTGTGTGTTC 58.412 34.615 28.62 0.00 45.16 3.18
1932 2170 6.520790 GCATATGCATATACATTGTGTGTTCG 59.479 38.462 22.84 3.12 40.56 3.95
1933 2171 7.575365 CATATGCATATACATTGTGTGTTCGT 58.425 34.615 18.70 0.00 42.29 3.85
2001 2244 8.177119 TCACATCCTTTTGTGTTAAGCTAAAT 57.823 30.769 4.67 0.00 45.73 1.40
2151 2417 7.440856 TGATTTGGAAAAACATCTTTTAGTGGC 59.559 33.333 0.00 0.00 0.00 5.01
2168 2448 9.577222 TTTTAGTGGCTGTATTTAAGTTTACCT 57.423 29.630 0.00 0.00 0.00 3.08
2200 2482 6.541086 CATGGAGCGAGCTTAATCATAATTC 58.459 40.000 0.00 0.00 0.00 2.17
2205 2487 4.092091 GCGAGCTTAATCATAATTCGAGGG 59.908 45.833 0.00 0.00 33.41 4.30
2260 4224 8.722480 TGAGTGTGTATTCTTCATTTCTATGG 57.278 34.615 0.00 0.00 32.40 2.74
2280 4244 4.693283 TGGCACTAGTGAGTACATATTGC 58.307 43.478 27.08 6.04 33.32 3.56
2334 4344 7.898014 AGATGGGGTTTTGTTTATCTATTCC 57.102 36.000 0.00 0.00 0.00 3.01
2355 4395 4.646945 TCCTTATATCTCATCGATGCCCTC 59.353 45.833 20.81 0.00 33.48 4.30
2373 4413 6.925211 TGCCCTCTCGTATCTATTTTATCTG 58.075 40.000 0.00 0.00 0.00 2.90
2396 5869 7.233348 TCTGATATGAATGGTAGTATCAGTGCA 59.767 37.037 16.40 0.00 45.35 4.57
2397 5870 7.910584 TGATATGAATGGTAGTATCAGTGCAT 58.089 34.615 0.00 0.00 31.80 3.96
2398 5871 9.034800 TGATATGAATGGTAGTATCAGTGCATA 57.965 33.333 0.00 0.00 31.80 3.14
2425 5898 0.179205 GCAGTGCAGATGTTTCTCGC 60.179 55.000 11.09 0.00 0.00 5.03
2450 5923 7.330946 GCGCTGACATACATAATGGTTAGAATA 59.669 37.037 0.00 0.00 40.16 1.75
2474 5947 1.208535 CCTTGTAGGCACGGGTATTGA 59.791 52.381 0.00 0.00 31.08 2.57
2497 5970 2.422519 GGTGGACATGATGGAGCTGAAT 60.423 50.000 0.00 0.00 0.00 2.57
2542 6233 7.554211 TGATTGATCAGATGGATATGCTACTC 58.446 38.462 0.00 0.00 36.00 2.59
2547 6238 6.527057 TCAGATGGATATGCTACTCTGATG 57.473 41.667 15.45 0.17 35.46 3.07
2549 6240 6.496218 TCAGATGGATATGCTACTCTGATGTT 59.504 38.462 15.45 0.00 35.46 2.71
2553 6244 9.494271 GATGGATATGCTACTCTGATGTTTTAA 57.506 33.333 0.00 0.00 0.00 1.52
2628 6494 9.305925 CCCTTTCATTTGCTTAGTTGATATTTC 57.694 33.333 0.00 0.00 0.00 2.17
2679 6652 2.584835 TGGTGTTTTGCTGCTAGGAT 57.415 45.000 0.00 0.00 0.00 3.24
2680 6653 2.436417 TGGTGTTTTGCTGCTAGGATC 58.564 47.619 0.00 0.00 0.00 3.36
2681 6654 2.040278 TGGTGTTTTGCTGCTAGGATCT 59.960 45.455 0.00 0.00 0.00 2.75
2682 6655 3.263170 TGGTGTTTTGCTGCTAGGATCTA 59.737 43.478 0.00 0.00 0.00 1.98
2683 6656 4.080356 TGGTGTTTTGCTGCTAGGATCTAT 60.080 41.667 0.00 0.00 0.00 1.98
2684 6657 4.274459 GGTGTTTTGCTGCTAGGATCTATG 59.726 45.833 0.00 0.00 0.00 2.23
2690 6665 2.163412 GCTGCTAGGATCTATGAGTCCG 59.837 54.545 0.00 0.00 39.54 4.79
2710 6685 4.406326 TCCGGGTGCTATTTGTATCTTGTA 59.594 41.667 0.00 0.00 0.00 2.41
2745 6925 7.066525 ACAAGTAATTGATACCCAACAATACCG 59.933 37.037 10.35 0.00 37.63 4.02
2746 6926 6.655930 AGTAATTGATACCCAACAATACCGT 58.344 36.000 0.00 0.00 37.63 4.83
2747 6927 7.794041 AGTAATTGATACCCAACAATACCGTA 58.206 34.615 0.00 0.00 37.63 4.02
2748 6928 6.930667 AATTGATACCCAACAATACCGTAC 57.069 37.500 0.00 0.00 37.63 3.67
2749 6929 4.405116 TGATACCCAACAATACCGTACC 57.595 45.455 0.00 0.00 0.00 3.34
2792 6972 2.350498 CGTTTGTTAACTCGGGCCTATG 59.650 50.000 0.84 0.00 31.89 2.23
2811 6991 8.096414 GGCCTATGTAAATTGCCATTTCATATT 58.904 33.333 0.00 0.00 41.76 1.28
2849 7029 4.634349 TGTTGTAAAACGTAGTGATCGC 57.366 40.909 0.00 0.00 45.00 4.58
2852 7032 5.234757 TGTTGTAAAACGTAGTGATCGCTTT 59.765 36.000 15.16 4.75 45.00 3.51
2867 7047 7.867403 AGTGATCGCTTTCAATTTTTGTACAAT 59.133 29.630 9.56 0.00 0.00 2.71
2879 7059 9.906660 CAATTTTTGTACAATCTTAGCCTTGTA 57.093 29.630 9.56 4.05 36.92 2.41
2898 7078 4.771903 TGTAGGCGGTTTGCTCAAATATA 58.228 39.130 0.00 0.00 45.43 0.86
2905 7085 7.230510 AGGCGGTTTGCTCAAATATATTATCAA 59.769 33.333 0.00 0.00 45.43 2.57
2907 7087 7.860373 GCGGTTTGCTCAAATATATTATCAACA 59.140 33.333 0.00 0.00 41.73 3.33
2943 7123 7.149307 TGTCACTCGAACTCACATATGTAAAA 58.851 34.615 8.32 0.00 0.00 1.52
2950 7130 6.594159 CGAACTCACATATGTAAAACTCCCTT 59.406 38.462 8.32 0.00 0.00 3.95
2971 7151 1.265236 TTTTAACCATGGCTGCCTGG 58.735 50.000 25.81 25.81 38.55 4.45
2972 7152 0.407528 TTTAACCATGGCTGCCTGGA 59.592 50.000 30.94 15.44 36.35 3.86
2974 7154 0.630673 TAACCATGGCTGCCTGGATT 59.369 50.000 30.94 23.99 36.35 3.01
2975 7155 0.630673 AACCATGGCTGCCTGGATTA 59.369 50.000 30.94 9.90 36.35 1.75
2976 7156 0.106519 ACCATGGCTGCCTGGATTAC 60.107 55.000 30.94 3.25 36.35 1.89
2980 7160 1.523938 GGCTGCCTGGATTACGGTC 60.524 63.158 12.43 0.00 0.00 4.79
2981 7161 1.522569 GCTGCCTGGATTACGGTCT 59.477 57.895 0.00 0.00 0.00 3.85
2982 7162 0.107654 GCTGCCTGGATTACGGTCTT 60.108 55.000 0.00 0.00 0.00 3.01
2983 7163 1.941325 CTGCCTGGATTACGGTCTTC 58.059 55.000 0.00 0.00 0.00 2.87
2984 7164 0.539986 TGCCTGGATTACGGTCTTCC 59.460 55.000 0.00 3.05 0.00 3.46
2987 7167 1.200519 CTGGATTACGGTCTTCCCCA 58.799 55.000 6.77 0.00 0.00 4.96
2988 7168 1.557832 CTGGATTACGGTCTTCCCCAA 59.442 52.381 6.77 0.00 0.00 4.12
2989 7169 2.172717 CTGGATTACGGTCTTCCCCAAT 59.827 50.000 6.77 0.00 0.00 3.16
2991 7171 3.389983 TGGATTACGGTCTTCCCCAATAG 59.610 47.826 6.77 0.00 0.00 1.73
2992 7172 2.994186 TTACGGTCTTCCCCAATAGC 57.006 50.000 0.00 0.00 0.00 2.97
2993 7173 1.868713 TACGGTCTTCCCCAATAGCA 58.131 50.000 0.00 0.00 0.00 3.49
2994 7174 1.213296 ACGGTCTTCCCCAATAGCAT 58.787 50.000 0.00 0.00 0.00 3.79
2996 7176 1.949525 CGGTCTTCCCCAATAGCATTG 59.050 52.381 0.00 0.00 0.00 2.82
2998 7178 3.365472 GGTCTTCCCCAATAGCATTGTT 58.635 45.455 7.71 0.00 0.00 2.83
3000 7180 4.953579 GGTCTTCCCCAATAGCATTGTTAA 59.046 41.667 7.71 0.00 0.00 2.01
3001 7181 5.420739 GGTCTTCCCCAATAGCATTGTTAAA 59.579 40.000 7.71 0.61 0.00 1.52
3002 7182 6.330278 GTCTTCCCCAATAGCATTGTTAAAC 58.670 40.000 7.71 0.00 0.00 2.01
3003 7183 5.420739 TCTTCCCCAATAGCATTGTTAAACC 59.579 40.000 7.71 0.00 0.00 3.27
3004 7184 4.678256 TCCCCAATAGCATTGTTAAACCA 58.322 39.130 7.71 0.00 0.00 3.67
3005 7185 4.464597 TCCCCAATAGCATTGTTAAACCAC 59.535 41.667 7.71 0.00 0.00 4.16
3006 7186 4.466015 CCCCAATAGCATTGTTAAACCACT 59.534 41.667 7.71 0.00 0.00 4.00
3008 7188 6.463360 CCCAATAGCATTGTTAAACCACTTT 58.537 36.000 7.71 0.00 0.00 2.66
3009 7189 6.589907 CCCAATAGCATTGTTAAACCACTTTC 59.410 38.462 7.71 0.00 0.00 2.62
3014 7194 7.054491 AGCATTGTTAAACCACTTTCAAGAT 57.946 32.000 0.00 0.00 0.00 2.40
3017 7197 7.653311 GCATTGTTAAACCACTTTCAAGATTCT 59.347 33.333 0.00 0.00 0.00 2.40
3018 7198 8.971321 CATTGTTAAACCACTTTCAAGATTCTG 58.029 33.333 0.00 0.00 0.00 3.02
3019 7199 7.873719 TGTTAAACCACTTTCAAGATTCTGA 57.126 32.000 0.00 0.00 0.00 3.27
3020 7200 8.463930 TGTTAAACCACTTTCAAGATTCTGAT 57.536 30.769 0.00 0.00 0.00 2.90
3021 7201 8.352201 TGTTAAACCACTTTCAAGATTCTGATG 58.648 33.333 0.00 0.00 0.00 3.07
3023 7203 9.567776 TTAAACCACTTTCAAGATTCTGATGTA 57.432 29.630 0.00 0.00 0.00 2.29
3024 7204 7.678947 AACCACTTTCAAGATTCTGATGTAG 57.321 36.000 0.00 0.00 0.00 2.74
3025 7205 5.645497 ACCACTTTCAAGATTCTGATGTAGC 59.355 40.000 0.00 0.00 0.00 3.58
3026 7206 5.065731 CCACTTTCAAGATTCTGATGTAGCC 59.934 44.000 0.00 0.00 0.00 3.93
3027 7207 5.645067 CACTTTCAAGATTCTGATGTAGCCA 59.355 40.000 0.00 0.00 0.00 4.75
3029 7209 6.716628 ACTTTCAAGATTCTGATGTAGCCAAA 59.283 34.615 0.00 0.00 0.00 3.28
3031 7211 5.188434 TCAAGATTCTGATGTAGCCAAAGG 58.812 41.667 0.00 0.00 0.00 3.11
3032 7212 5.045651 TCAAGATTCTGATGTAGCCAAAGGA 60.046 40.000 0.00 0.00 0.00 3.36
3036 7216 6.995091 AGATTCTGATGTAGCCAAAGGATTAC 59.005 38.462 0.00 0.00 0.00 1.89
3037 7217 5.692115 TCTGATGTAGCCAAAGGATTACA 57.308 39.130 0.00 0.00 32.11 2.41
3039 7219 5.189736 TCTGATGTAGCCAAAGGATTACACT 59.810 40.000 0.00 0.00 31.00 3.55
3050 7300 7.565680 CCAAAGGATTACACTATGGTTAGTCT 58.434 38.462 0.00 0.00 36.50 3.24
3052 7302 6.980416 AGGATTACACTATGGTTAGTCTCC 57.020 41.667 0.00 0.00 36.50 3.71
3057 7307 4.684724 ACACTATGGTTAGTCTCCTTGGA 58.315 43.478 0.00 0.00 36.50 3.53
3060 7310 5.068460 CACTATGGTTAGTCTCCTTGGAGAG 59.932 48.000 18.69 7.29 36.50 3.20
3070 7320 1.205055 CCTTGGAGAGGGGACTAACC 58.795 60.000 0.00 0.00 44.43 2.85
3087 7337 3.994931 AACCGAACTAAGCCTAATGGT 57.005 42.857 0.00 0.00 35.27 3.55
3096 7346 6.074698 ACTAAGCCTAATGGTGGTATTTGT 57.925 37.500 0.00 0.00 35.27 2.83
3097 7347 5.885912 ACTAAGCCTAATGGTGGTATTTGTG 59.114 40.000 0.00 0.00 35.27 3.33
3098 7348 4.316025 AGCCTAATGGTGGTATTTGTGT 57.684 40.909 0.00 0.00 35.27 3.72
3099 7349 4.672899 AGCCTAATGGTGGTATTTGTGTT 58.327 39.130 0.00 0.00 35.27 3.32
3100 7350 5.083821 AGCCTAATGGTGGTATTTGTGTTT 58.916 37.500 0.00 0.00 35.27 2.83
3101 7351 5.542251 AGCCTAATGGTGGTATTTGTGTTTT 59.458 36.000 0.00 0.00 35.27 2.43
3193 7454 0.465460 GTTGAGGGTGTGCCACTTGA 60.465 55.000 0.00 0.00 34.40 3.02
3205 7466 6.460399 GGTGTGCCACTTGAAATTAACTGTTA 60.460 38.462 0.00 0.00 34.40 2.41
3206 7467 6.416750 GTGTGCCACTTGAAATTAACTGTTAC 59.583 38.462 0.00 0.00 0.00 2.50
3216 7477 8.395940 TGAAATTAACTGTTACGTTGGTTTTG 57.604 30.769 0.00 0.00 0.00 2.44
3231 7492 6.909550 TTGGTTTTGTCCAATAGCTTACAT 57.090 33.333 0.00 0.00 41.79 2.29
3232 7493 6.266168 TGGTTTTGTCCAATAGCTTACATG 57.734 37.500 0.00 0.00 34.24 3.21
3233 7494 6.007076 TGGTTTTGTCCAATAGCTTACATGA 58.993 36.000 0.00 0.00 34.24 3.07
3234 7495 6.072175 TGGTTTTGTCCAATAGCTTACATGAC 60.072 38.462 0.00 0.00 34.24 3.06
3237 7498 8.893727 GTTTTGTCCAATAGCTTACATGACTAT 58.106 33.333 0.00 0.00 0.00 2.12
3238 7499 9.461312 TTTTGTCCAATAGCTTACATGACTATT 57.539 29.630 0.00 4.65 37.13 1.73
3239 7500 8.437360 TTGTCCAATAGCTTACATGACTATTG 57.563 34.615 21.84 21.84 46.66 1.90
3243 7504 7.426929 CAATAGCTTACATGACTATTGGTCC 57.573 40.000 21.45 0.00 44.81 4.46
3246 7507 4.471386 AGCTTACATGACTATTGGTCCAGT 59.529 41.667 0.00 0.00 43.89 4.00
3250 7511 4.589908 ACATGACTATTGGTCCAGTTTCC 58.410 43.478 0.00 0.00 43.89 3.13
3251 7512 4.042809 ACATGACTATTGGTCCAGTTTCCA 59.957 41.667 0.00 0.00 43.89 3.53
3338 7600 9.121517 CTTGTTTGAACAGTGACATTGATTATC 57.878 33.333 4.78 0.00 40.50 1.75
3354 7616 5.793817 TGATTATCGCTGCACAGGTATTAT 58.206 37.500 0.00 0.00 0.00 1.28
3373 7635 0.907486 TGAAGAGGTGCAGAGATGGG 59.093 55.000 0.00 0.00 0.00 4.00
3377 7639 1.001641 AGGTGCAGAGATGGGTTGC 60.002 57.895 0.00 0.00 38.30 4.17
3406 7668 2.825861 AGCTTCTTCCGTTCCGTTTA 57.174 45.000 0.00 0.00 0.00 2.01
3407 7669 2.685100 AGCTTCTTCCGTTCCGTTTAG 58.315 47.619 0.00 0.00 0.00 1.85
3434 7696 0.037046 GCAGAAATGGCTTGTTGGGG 60.037 55.000 0.00 0.00 0.00 4.96
3435 7697 0.609662 CAGAAATGGCTTGTTGGGGG 59.390 55.000 0.00 0.00 0.00 5.40
3453 7715 1.477923 GGGTGTCCTTTTGGTGTGCTA 60.478 52.381 0.00 0.00 41.38 3.49
3469 7731 5.565592 TGTGCTACACATGGAAATTGATC 57.434 39.130 0.00 0.00 39.62 2.92
3475 7737 6.238593 GCTACACATGGAAATTGATCCTCTTC 60.239 42.308 0.00 0.00 40.35 2.87
3485 7747 7.980099 GGAAATTGATCCTCTTCGTTCTACTTA 59.020 37.037 0.00 0.00 36.50 2.24
3487 7749 5.502153 TGATCCTCTTCGTTCTACTTAGC 57.498 43.478 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.522804 GACTAATAGTGGTATGCTATTATGAGC 57.477 37.037 0.00 0.00 39.33 4.26
44 45 9.555727 GCAGTATTATTTTGGACTCTACCATTA 57.444 33.333 0.00 0.00 39.82 1.90
62 64 6.102615 ACCAAATCTCCCATAAGGCAGTATTA 59.897 38.462 0.00 0.00 34.51 0.98
86 88 3.421844 AGTGCACTTATTCCTTTCCCAC 58.578 45.455 15.25 0.00 0.00 4.61
87 89 3.806949 AGTGCACTTATTCCTTTCCCA 57.193 42.857 15.25 0.00 0.00 4.37
110 112 0.108207 CCTAGCTCCAATGCTCCCTG 59.892 60.000 0.00 0.00 42.97 4.45
136 138 1.785518 CGGTAAAAATCTCGTGTGCGC 60.786 52.381 0.00 0.00 38.14 6.09
140 142 4.214545 TGATTTGCGGTAAAAATCTCGTGT 59.785 37.500 9.54 0.00 42.17 4.49
150 152 1.730064 GCTCGTCTGATTTGCGGTAAA 59.270 47.619 0.00 0.00 0.00 2.01
152 154 0.245266 TGCTCGTCTGATTTGCGGTA 59.755 50.000 0.00 0.00 0.00 4.02
158 160 1.470098 GCACCATTGCTCGTCTGATTT 59.530 47.619 0.00 0.00 46.17 2.17
172 174 0.251922 ACAAGGCTTCATGGCACCAT 60.252 50.000 0.00 0.00 44.55 3.55
179 181 1.250328 TGCTCCAACAAGGCTTCATG 58.750 50.000 0.00 0.00 37.29 3.07
227 229 4.227538 GAGAAAACAATCTCTCACGACGA 58.772 43.478 0.00 0.00 42.12 4.20
281 283 5.770162 GGATGAGAAAGGAAAGGAACTCAAA 59.230 40.000 0.00 0.00 38.49 2.69
291 293 8.386264 ACTTAAGATCAAGGATGAGAAAGGAAA 58.614 33.333 10.09 0.00 39.39 3.13
299 301 5.104776 TGGTGGACTTAAGATCAAGGATGAG 60.105 44.000 10.09 0.00 39.39 2.90
315 317 5.190528 ACTGAAGATAACATGATGGTGGACT 59.809 40.000 0.00 0.00 0.00 3.85
317 319 5.698741 ACTGAAGATAACATGATGGTGGA 57.301 39.130 0.00 0.00 0.00 4.02
318 320 5.449588 GCAACTGAAGATAACATGATGGTGG 60.450 44.000 0.00 0.00 0.00 4.61
340 342 8.400947 GCTTTGATTGATGATTAGTAAGAAGCA 58.599 33.333 0.00 0.00 34.88 3.91
348 350 4.951715 TGCTGGCTTTGATTGATGATTAGT 59.048 37.500 0.00 0.00 0.00 2.24
369 371 2.077413 TGAAACATCCGGCAAATTGC 57.923 45.000 9.87 9.87 44.08 3.56
396 398 8.796475 CCCTAGCCATACTAAGTACGTTATTTA 58.204 37.037 0.00 0.00 0.00 1.40
399 401 6.310149 ACCCTAGCCATACTAAGTACGTTAT 58.690 40.000 0.00 0.00 0.00 1.89
400 402 5.694995 ACCCTAGCCATACTAAGTACGTTA 58.305 41.667 0.00 0.00 0.00 3.18
402 404 4.176120 ACCCTAGCCATACTAAGTACGT 57.824 45.455 0.00 0.00 0.00 3.57
403 405 5.287226 CAAACCCTAGCCATACTAAGTACG 58.713 45.833 0.00 0.00 0.00 3.67
404 406 5.364735 TCCAAACCCTAGCCATACTAAGTAC 59.635 44.000 0.00 0.00 0.00 2.73
405 407 5.364735 GTCCAAACCCTAGCCATACTAAGTA 59.635 44.000 0.00 0.00 0.00 2.24
406 408 4.163649 GTCCAAACCCTAGCCATACTAAGT 59.836 45.833 0.00 0.00 0.00 2.24
407 409 4.444449 GGTCCAAACCCTAGCCATACTAAG 60.444 50.000 0.00 0.00 39.93 2.18
408 410 3.457012 GGTCCAAACCCTAGCCATACTAA 59.543 47.826 0.00 0.00 39.93 2.24
409 411 3.043418 GGTCCAAACCCTAGCCATACTA 58.957 50.000 0.00 0.00 39.93 1.82
422 424 2.950433 TCTACGTCATTCGGTCCAAAC 58.050 47.619 0.00 0.00 44.69 2.93
427 429 4.094090 AGAGTTTCTACGTCATTCGGTC 57.906 45.455 0.00 0.00 44.69 4.79
430 432 5.401376 TGACAAAGAGTTTCTACGTCATTCG 59.599 40.000 0.00 0.00 46.00 3.34
432 434 5.465724 GGTGACAAAGAGTTTCTACGTCATT 59.534 40.000 0.00 0.00 38.89 2.57
464 466 9.474920 CTTGTATTGCTCAAAAATCAAGGTTTA 57.525 29.630 0.00 0.00 0.00 2.01
467 469 7.014615 ACTCTTGTATTGCTCAAAAATCAAGGT 59.985 33.333 0.00 0.00 34.01 3.50
606 643 2.425143 AGCCCATCACATACAACCAG 57.575 50.000 0.00 0.00 0.00 4.00
636 673 2.716017 CGGGAGAGAGTGAGCCCAC 61.716 68.421 0.00 0.00 40.71 4.61
637 674 2.363018 CGGGAGAGAGTGAGCCCA 60.363 66.667 0.00 0.00 40.71 5.36
638 675 1.258445 TTTCGGGAGAGAGTGAGCCC 61.258 60.000 0.00 0.00 41.75 5.19
639 676 0.174617 CTTTCGGGAGAGAGTGAGCC 59.825 60.000 0.00 0.00 41.75 4.70
640 677 0.174617 CCTTTCGGGAGAGAGTGAGC 59.825 60.000 0.00 0.00 39.29 4.26
641 678 1.840737 TCCTTTCGGGAGAGAGTGAG 58.159 55.000 0.00 0.00 39.29 3.51
650 687 0.538746 GCCCAAAACTCCTTTCGGGA 60.539 55.000 0.00 0.00 42.77 5.14
651 688 0.539669 AGCCCAAAACTCCTTTCGGG 60.540 55.000 0.00 0.00 37.92 5.14
652 689 1.269723 GAAGCCCAAAACTCCTTTCGG 59.730 52.381 0.00 0.00 0.00 4.30
653 690 1.953686 TGAAGCCCAAAACTCCTTTCG 59.046 47.619 0.00 0.00 0.00 3.46
957 1029 1.544691 TCGAAGAAACCGAGAAGAGGG 59.455 52.381 0.00 0.00 0.00 4.30
1140 1252 2.127758 CGCTTGTCGCCGTTGAAC 60.128 61.111 0.00 0.00 34.21 3.18
1266 1387 5.408299 TGTATGATGTTGGTTGTTTCTCTCG 59.592 40.000 0.00 0.00 0.00 4.04
1271 1392 4.472286 CCGTGTATGATGTTGGTTGTTTC 58.528 43.478 0.00 0.00 0.00 2.78
1384 1532 5.653769 ACATTCTAATCTTGGTGGGATGTTG 59.346 40.000 0.00 0.00 0.00 3.33
1459 1607 3.550820 TGTTGGTTGCTGCCGATATATT 58.449 40.909 0.00 0.00 0.00 1.28
1520 1683 2.223923 GGCACTGGTATCACAGCTAGAG 60.224 54.545 0.00 0.00 42.21 2.43
1575 1747 0.543277 CCTCTGCCTGCATAACCTGA 59.457 55.000 0.00 0.00 0.00 3.86
1639 1811 6.267242 TCAGAATCAGTCTCCATCTTCCATAG 59.733 42.308 0.00 0.00 32.70 2.23
1712 1884 4.260170 CTCTTCTGGATTCAGGGAAAGTG 58.740 47.826 0.00 0.00 41.23 3.16
1779 2006 2.895404 GGTAGGTGTCTGTAGGAACACA 59.105 50.000 7.80 0.00 35.03 3.72
1790 2017 4.263068 CCATGAAGAAGTTGGTAGGTGTCT 60.263 45.833 0.00 0.00 0.00 3.41
1853 2080 1.061711 CATAGCGAGTCAAGCTGTTGC 59.938 52.381 3.06 0.00 45.60 4.17
1859 2086 1.269309 ACGGATCATAGCGAGTCAAGC 60.269 52.381 0.00 0.00 0.00 4.01
1873 2100 6.307155 CAACATAGACACTTTCAAACGGATC 58.693 40.000 0.00 0.00 0.00 3.36
2072 2335 2.370349 TCCAGAAAGAGGACGCTAGAG 58.630 52.381 0.00 0.00 0.00 2.43
2151 2417 9.337396 TGCCATATCAGGTAAACTTAAATACAG 57.663 33.333 0.00 0.00 0.00 2.74
2159 2439 5.380043 CTCCATGCCATATCAGGTAAACTT 58.620 41.667 0.00 0.00 0.00 2.66
2161 2441 3.503748 GCTCCATGCCATATCAGGTAAAC 59.496 47.826 0.00 0.00 35.15 2.01
2168 2448 0.321034 GCTCGCTCCATGCCATATCA 60.321 55.000 0.00 0.00 38.78 2.15
2205 2487 3.197549 AGCTGATGAGAAGGGAGAAGTTC 59.802 47.826 0.00 0.00 0.00 3.01
2219 2501 6.701340 ACACACTCAAACTATTAGCTGATGA 58.299 36.000 0.32 0.00 0.00 2.92
2220 2502 6.974932 ACACACTCAAACTATTAGCTGATG 57.025 37.500 0.32 0.00 0.00 3.07
2260 4224 6.535150 TCAAAGCAATATGTACTCACTAGTGC 59.465 38.462 18.45 4.65 38.69 4.40
2334 4344 5.505489 CGAGAGGGCATCGATGAGATATAAG 60.505 48.000 29.20 9.11 42.76 1.73
2347 4387 7.704472 CAGATAAAATAGATACGAGAGGGCATC 59.296 40.741 0.00 0.00 0.00 3.91
2387 5860 6.335777 CACTGCAGCTATATATGCACTGATA 58.664 40.000 15.27 0.00 46.97 2.15
2425 5898 7.658179 ATTCTAACCATTATGTATGTCAGCG 57.342 36.000 0.00 0.00 31.99 5.18
2450 5923 3.327404 CCGTGCCTACAAGGGGGT 61.327 66.667 0.00 0.00 41.31 4.95
2474 5947 1.133884 CAGCTCCATCATGTCCACCAT 60.134 52.381 0.00 0.00 0.00 3.55
2502 5975 8.780249 TCTGATCAATCATCTTACGTATTACGA 58.220 33.333 22.18 4.01 38.99 3.43
2542 6233 9.209175 AGCTTACTTACTCAGTTAAAACATCAG 57.791 33.333 0.00 0.00 36.88 2.90
2628 6494 9.515020 AATGTTGCGACCAATAAATGTAAATAG 57.485 29.630 0.45 0.00 32.75 1.73
2634 6606 3.925913 GCAATGTTGCGACCAATAAATGT 59.074 39.130 0.45 0.00 45.11 2.71
2679 6652 2.677542 ATAGCACCCGGACTCATAGA 57.322 50.000 0.73 0.00 0.00 1.98
2680 6653 3.181465 ACAAATAGCACCCGGACTCATAG 60.181 47.826 0.73 0.00 0.00 2.23
2681 6654 2.769663 ACAAATAGCACCCGGACTCATA 59.230 45.455 0.73 0.00 0.00 2.15
2682 6655 1.559682 ACAAATAGCACCCGGACTCAT 59.440 47.619 0.73 0.00 0.00 2.90
2683 6656 0.981183 ACAAATAGCACCCGGACTCA 59.019 50.000 0.73 0.00 0.00 3.41
2684 6657 2.973694 TACAAATAGCACCCGGACTC 57.026 50.000 0.73 0.00 0.00 3.36
2690 6665 4.820173 GGGTACAAGATACAAATAGCACCC 59.180 45.833 0.00 0.00 35.48 4.61
2710 6685 6.126854 GGGTATCAATTACTTGTGTAGAGGGT 60.127 42.308 0.00 0.00 33.87 4.34
2816 6996 9.666626 CTACGTTTTACAACAATACCAAATGAA 57.333 29.630 0.00 0.00 32.54 2.57
2817 6997 8.838365 ACTACGTTTTACAACAATACCAAATGA 58.162 29.630 0.00 0.00 32.54 2.57
2818 6998 8.897809 CACTACGTTTTACAACAATACCAAATG 58.102 33.333 0.00 0.00 32.54 2.32
2826 7006 5.407387 AGCGATCACTACGTTTTACAACAAT 59.593 36.000 0.00 0.00 32.54 2.71
2838 7018 5.851177 ACAAAAATTGAAAGCGATCACTACG 59.149 36.000 0.00 0.00 0.00 3.51
2849 7029 9.696917 AGGCTAAGATTGTACAAAAATTGAAAG 57.303 29.630 13.23 4.10 0.00 2.62
2852 7032 8.637986 ACAAGGCTAAGATTGTACAAAAATTGA 58.362 29.630 13.23 0.00 37.85 2.57
2879 7059 6.714810 TGATAATATATTTGAGCAAACCGCCT 59.285 34.615 2.68 0.00 44.04 5.52
2905 7085 8.547967 AGTTCGAGTGACAAACAAATATATGT 57.452 30.769 0.00 0.00 34.24 2.29
2907 7087 8.656849 GTGAGTTCGAGTGACAAACAAATATAT 58.343 33.333 0.00 0.00 0.00 0.86
2911 7091 4.634004 TGTGAGTTCGAGTGACAAACAAAT 59.366 37.500 0.00 0.00 0.00 2.32
2956 7136 0.630673 TAATCCAGGCAGCCATGGTT 59.369 50.000 22.39 18.43 37.84 3.67
2958 7138 1.168407 CGTAATCCAGGCAGCCATGG 61.168 60.000 15.80 17.85 37.97 3.66
2959 7139 1.168407 CCGTAATCCAGGCAGCCATG 61.168 60.000 15.80 9.03 0.00 3.66
2960 7140 1.149174 CCGTAATCCAGGCAGCCAT 59.851 57.895 15.80 0.00 0.00 4.40
2961 7141 2.252072 GACCGTAATCCAGGCAGCCA 62.252 60.000 15.80 0.00 0.00 4.75
2962 7142 1.523938 GACCGTAATCCAGGCAGCC 60.524 63.158 1.84 1.84 0.00 4.85
2963 7143 0.107654 AAGACCGTAATCCAGGCAGC 60.108 55.000 0.00 0.00 0.00 5.25
2964 7144 1.473434 GGAAGACCGTAATCCAGGCAG 60.473 57.143 0.00 0.00 33.30 4.85
2965 7145 0.539986 GGAAGACCGTAATCCAGGCA 59.460 55.000 0.00 0.00 33.30 4.75
2966 7146 0.179054 GGGAAGACCGTAATCCAGGC 60.179 60.000 4.84 0.00 34.82 4.85
2967 7147 0.468648 GGGGAAGACCGTAATCCAGG 59.531 60.000 4.84 0.00 41.60 4.45
2968 7148 1.200519 TGGGGAAGACCGTAATCCAG 58.799 55.000 4.84 0.00 41.60 3.86
2969 7149 1.659022 TTGGGGAAGACCGTAATCCA 58.341 50.000 4.84 0.00 41.60 3.41
2970 7150 3.806157 GCTATTGGGGAAGACCGTAATCC 60.806 52.174 0.00 0.00 41.60 3.01
2971 7151 3.181458 TGCTATTGGGGAAGACCGTAATC 60.181 47.826 0.00 0.00 41.60 1.75
2972 7152 2.775384 TGCTATTGGGGAAGACCGTAAT 59.225 45.455 0.00 0.00 41.60 1.89
2974 7154 1.868713 TGCTATTGGGGAAGACCGTA 58.131 50.000 0.00 0.00 41.60 4.02
2975 7155 1.213296 ATGCTATTGGGGAAGACCGT 58.787 50.000 0.00 0.00 41.60 4.83
2976 7156 1.949525 CAATGCTATTGGGGAAGACCG 59.050 52.381 0.00 0.00 41.60 4.79
2980 7160 5.186797 TGGTTTAACAATGCTATTGGGGAAG 59.813 40.000 11.76 0.00 0.00 3.46
2981 7161 5.046950 GTGGTTTAACAATGCTATTGGGGAA 60.047 40.000 11.76 2.84 0.00 3.97
2982 7162 4.464597 GTGGTTTAACAATGCTATTGGGGA 59.535 41.667 11.76 0.00 0.00 4.81
2983 7163 4.466015 AGTGGTTTAACAATGCTATTGGGG 59.534 41.667 11.76 0.00 0.00 4.96
2984 7164 5.659440 AGTGGTTTAACAATGCTATTGGG 57.341 39.130 11.76 0.00 0.00 4.12
2987 7167 8.637986 TCTTGAAAGTGGTTTAACAATGCTATT 58.362 29.630 0.00 0.00 0.00 1.73
2988 7168 8.177119 TCTTGAAAGTGGTTTAACAATGCTAT 57.823 30.769 0.00 0.00 0.00 2.97
2989 7169 7.575414 TCTTGAAAGTGGTTTAACAATGCTA 57.425 32.000 0.00 0.00 0.00 3.49
2991 7171 7.653311 AGAATCTTGAAAGTGGTTTAACAATGC 59.347 33.333 0.00 0.00 0.00 3.56
2992 7172 8.971321 CAGAATCTTGAAAGTGGTTTAACAATG 58.029 33.333 0.00 0.00 0.00 2.82
2993 7173 8.912988 TCAGAATCTTGAAAGTGGTTTAACAAT 58.087 29.630 0.00 0.00 0.00 2.71
2994 7174 8.287439 TCAGAATCTTGAAAGTGGTTTAACAA 57.713 30.769 0.00 0.00 0.00 2.83
2996 7176 8.352942 ACATCAGAATCTTGAAAGTGGTTTAAC 58.647 33.333 0.00 0.00 0.00 2.01
2998 7178 9.219603 CTACATCAGAATCTTGAAAGTGGTTTA 57.780 33.333 0.00 0.00 0.00 2.01
3000 7180 6.150140 GCTACATCAGAATCTTGAAAGTGGTT 59.850 38.462 0.00 0.00 0.00 3.67
3001 7181 5.645497 GCTACATCAGAATCTTGAAAGTGGT 59.355 40.000 0.00 0.00 0.00 4.16
3002 7182 5.065731 GGCTACATCAGAATCTTGAAAGTGG 59.934 44.000 0.00 0.00 0.00 4.00
3003 7183 5.645067 TGGCTACATCAGAATCTTGAAAGTG 59.355 40.000 0.00 0.00 0.00 3.16
3004 7184 5.809001 TGGCTACATCAGAATCTTGAAAGT 58.191 37.500 0.00 0.00 0.00 2.66
3005 7185 6.748333 TTGGCTACATCAGAATCTTGAAAG 57.252 37.500 0.00 0.00 0.00 2.62
3006 7186 6.151648 CCTTTGGCTACATCAGAATCTTGAAA 59.848 38.462 0.00 0.00 0.00 2.69
3008 7188 5.045651 TCCTTTGGCTACATCAGAATCTTGA 60.046 40.000 0.00 0.00 0.00 3.02
3009 7189 5.188434 TCCTTTGGCTACATCAGAATCTTG 58.812 41.667 0.00 0.00 0.00 3.02
3014 7194 5.880332 GTGTAATCCTTTGGCTACATCAGAA 59.120 40.000 0.00 0.00 0.00 3.02
3017 7197 5.435686 AGTGTAATCCTTTGGCTACATCA 57.564 39.130 0.00 0.00 0.00 3.07
3018 7198 6.428159 CCATAGTGTAATCCTTTGGCTACATC 59.572 42.308 0.00 0.00 0.00 3.06
3019 7199 6.126478 ACCATAGTGTAATCCTTTGGCTACAT 60.126 38.462 0.00 0.00 35.25 2.29
3020 7200 5.190925 ACCATAGTGTAATCCTTTGGCTACA 59.809 40.000 0.00 0.00 35.25 2.74
3021 7201 5.681639 ACCATAGTGTAATCCTTTGGCTAC 58.318 41.667 0.00 0.00 35.25 3.58
3023 7203 4.862641 ACCATAGTGTAATCCTTTGGCT 57.137 40.909 0.00 0.00 35.25 4.75
3024 7204 6.120220 ACTAACCATAGTGTAATCCTTTGGC 58.880 40.000 0.00 0.00 40.88 4.52
3025 7205 7.565680 AGACTAACCATAGTGTAATCCTTTGG 58.434 38.462 0.00 0.00 42.47 3.28
3026 7206 7.711339 GGAGACTAACCATAGTGTAATCCTTTG 59.289 40.741 0.00 0.00 42.47 2.77
3027 7207 7.624077 AGGAGACTAACCATAGTGTAATCCTTT 59.376 37.037 0.00 0.00 42.47 3.11
3029 7209 6.684538 AGGAGACTAACCATAGTGTAATCCT 58.315 40.000 0.00 0.00 42.47 3.24
3031 7211 7.069578 TCCAAGGAGACTAACCATAGTGTAATC 59.930 40.741 0.00 0.00 42.47 1.75
3032 7212 6.901300 TCCAAGGAGACTAACCATAGTGTAAT 59.099 38.462 0.00 0.00 42.47 1.89
3036 7216 4.956700 TCTCCAAGGAGACTAACCATAGTG 59.043 45.833 14.66 0.00 45.26 2.74
3037 7217 5.205056 CTCTCCAAGGAGACTAACCATAGT 58.795 45.833 14.66 0.00 45.26 2.12
3052 7302 0.824759 CGGTTAGTCCCCTCTCCAAG 59.175 60.000 0.00 0.00 0.00 3.61
3057 7307 3.363627 CTTAGTTCGGTTAGTCCCCTCT 58.636 50.000 0.00 0.00 0.00 3.69
3060 7310 1.134580 GGCTTAGTTCGGTTAGTCCCC 60.135 57.143 0.00 0.00 0.00 4.81
3070 7320 3.261981 ACCACCATTAGGCTTAGTTCG 57.738 47.619 0.00 0.00 39.06 3.95
3134 7389 5.163353 ACCGAAAACCTTCCATTGTTGATTT 60.163 36.000 0.00 0.00 0.00 2.17
3135 7390 4.343814 ACCGAAAACCTTCCATTGTTGATT 59.656 37.500 0.00 0.00 0.00 2.57
3136 7391 3.895041 ACCGAAAACCTTCCATTGTTGAT 59.105 39.130 0.00 0.00 0.00 2.57
3165 7426 4.038642 TGGCACACCCTCAACTTATTTTTC 59.961 41.667 0.00 0.00 33.59 2.29
3166 7427 3.964031 TGGCACACCCTCAACTTATTTTT 59.036 39.130 0.00 0.00 33.59 1.94
3169 7430 2.969821 TGGCACACCCTCAACTTATT 57.030 45.000 0.00 0.00 33.59 1.40
3193 7454 7.488792 GGACAAAACCAACGTAACAGTTAATTT 59.511 33.333 0.00 0.00 32.35 1.82
3231 7492 9.911709 CCATCATGGAAACTGGACCAATAGTCA 62.912 44.444 0.00 0.00 43.53 3.41
3232 7493 4.843728 TCATGGAAACTGGACCAATAGTC 58.156 43.478 0.00 0.00 45.51 2.59
3233 7494 4.927267 TCATGGAAACTGGACCAATAGT 57.073 40.909 0.00 0.00 39.69 2.12
3234 7495 4.581824 CCATCATGGAAACTGGACCAATAG 59.418 45.833 0.00 0.00 40.96 1.73
3237 7498 2.378208 TCCATCATGGAAACTGGACCAA 59.622 45.455 2.95 0.00 45.00 3.67
3238 7499 1.991813 TCCATCATGGAAACTGGACCA 59.008 47.619 2.95 0.00 45.00 4.02
3239 7500 2.806945 TCCATCATGGAAACTGGACC 57.193 50.000 2.95 0.00 45.00 4.46
3282 7544 9.654663 GTACTATTCCTTATGTCTCACAACTTT 57.345 33.333 0.00 0.00 0.00 2.66
3288 7550 9.654663 AAGTTTGTACTATTCCTTATGTCTCAC 57.345 33.333 0.00 0.00 33.17 3.51
3322 7584 3.310501 TGCAGCGATAATCAATGTCACTG 59.689 43.478 0.00 0.00 0.00 3.66
3338 7600 3.457234 TCTTCATAATACCTGTGCAGCG 58.543 45.455 0.00 0.00 0.00 5.18
3342 7604 3.561725 GCACCTCTTCATAATACCTGTGC 59.438 47.826 0.00 0.00 39.61 4.57
3354 7616 0.907486 CCCATCTCTGCACCTCTTCA 59.093 55.000 0.00 0.00 0.00 3.02
3373 7635 3.920093 AAGCTACGCCCCCAGCAAC 62.920 63.158 0.00 0.00 44.04 4.17
3377 7639 1.153349 GAAGAAGCTACGCCCCCAG 60.153 63.158 0.00 0.00 0.00 4.45
3406 7668 1.099879 GCCATTTCTGCATCTCGGCT 61.100 55.000 6.96 0.00 35.17 5.52
3407 7669 1.099879 AGCCATTTCTGCATCTCGGC 61.100 55.000 6.26 6.26 38.36 5.54
3434 7696 1.607148 GTAGCACACCAAAAGGACACC 59.393 52.381 0.00 0.00 0.00 4.16
3435 7697 2.032924 GTGTAGCACACCAAAAGGACAC 59.967 50.000 7.86 0.00 43.05 3.67
3453 7715 4.637534 CGAAGAGGATCAATTTCCATGTGT 59.362 41.667 0.00 0.00 38.32 3.72
3469 7731 2.159421 TGCGCTAAGTAGAACGAAGAGG 60.159 50.000 9.73 0.00 0.00 3.69
3475 7737 1.624323 GCGTGCGCTAAGTAGAACG 59.376 57.895 9.73 8.76 38.26 3.95


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

AutoCloner maintained by Alex Coulton.