Multiple sequence alignment - TraesCS6A01G279700

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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 TraesCS6A01G279700 chr6A 100.000 2558 0 0 1 2558 507121719 507124276 0.000000e+00 4724
1 TraesCS6A01G279700 chr6D 82.112 2348 192 110 123 2358 366683649 366685880 0.000000e+00 1799
2 TraesCS6A01G279700 chr6D 86.628 172 15 5 2368 2538 366685941 366686105 1.560000e-42 183
3 TraesCS6A01G279700 chr6B 82.816 2095 167 84 381 2378 552404801 552406799 0.000000e+00 1696
4 TraesCS6A01G279700 chr6B 86.378 323 18 5 1152 1472 495540764 495541062 1.900000e-86 329
5 TraesCS6A01G279700 chr6B 82.095 296 31 17 70 352 552404209 552404495 1.530000e-57 233
6 TraesCS6A01G279700 chr6B 87.624 202 10 3 1152 1353 657261015 657261201 1.190000e-53 220
7 TraesCS6A01G279700 chr6B 82.581 155 14 7 2384 2538 552406854 552406995 9.610000e-25 124
8 TraesCS6A01G279700 chr2B 82.293 593 61 23 1815 2378 239860857 239861434 8.280000e-130 473
9 TraesCS6A01G279700 chr2B 81.677 322 17 9 1152 1472 5028976 5029256 1.980000e-56 230
10 TraesCS6A01G279700 chr2B 84.247 146 17 6 1417 1560 239858683 239858824 1.230000e-28 137
11 TraesCS6A01G279700 chrUn 82.095 592 63 23 1815 2378 311244763 311244187 1.390000e-127 466
12 TraesCS6A01G279700 chrUn 82.095 592 63 23 1815 2378 410091036 410091612 1.390000e-127 466
13 TraesCS6A01G279700 chrUn 84.932 146 16 6 1417 1560 287696463 287696604 2.650000e-30 143
14 TraesCS6A01G279700 chrUn 84.932 146 16 6 1417 1560 287708667 287708808 2.650000e-30 143
15 TraesCS6A01G279700 chrUn 84.932 146 16 6 1417 1560 294704680 294704821 2.650000e-30 143
16 TraesCS6A01G279700 chr1B 81.757 592 65 23 1815 2378 605568265 605568841 3.000000e-124 455
17 TraesCS6A01G279700 chr1B 86.646 322 19 3 1152 1472 32787996 32787698 4.080000e-88 335
18 TraesCS6A01G279700 chr1B 92.771 83 4 2 1479 1560 605566154 605566235 4.470000e-23 119
19 TraesCS6A01G279700 chr5A 81.399 586 61 17 1815 2378 49964387 49963828 3.910000e-118 435
20 TraesCS6A01G279700 chr5A 89.326 178 10 6 1392 1560 49965691 49965514 5.540000e-52 215
21 TraesCS6A01G279700 chr5A 88.360 189 7 3 1152 1340 600293964 600294137 1.990000e-51 213
22 TraesCS6A01G279700 chr3B 87.188 320 18 2 1153 1472 654436487 654436191 2.440000e-90 342
23 TraesCS6A01G279700 chr1D 87.147 319 18 4 1152 1470 35863005 35863300 8.770000e-90 340
24 TraesCS6A01G279700 chr1D 93.137 102 7 0 1271 1372 9855363 9855464 1.590000e-32 150
25 TraesCS6A01G279700 chr1A 87.065 201 11 3 1153 1353 96740289 96740474 1.990000e-51 213
26 TraesCS6A01G279700 chr7A 87.831 189 8 3 1152 1340 717181726 717181553 9.280000e-50 207
27 TraesCS6A01G279700 chr7D 90.411 146 12 2 1228 1372 138313023 138313167 9.340000e-45 191


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 TraesCS6A01G279700 chr6A 507121719 507124276 2557 False 4724.000000 4724 100.000000 1 2558 1 chr6A.!!$F1 2557
1 TraesCS6A01G279700 chr6D 366683649 366686105 2456 False 991.000000 1799 84.370000 123 2538 2 chr6D.!!$F1 2415
2 TraesCS6A01G279700 chr6B 552404209 552406995 2786 False 684.333333 1696 82.497333 70 2538 3 chr6B.!!$F3 2468
3 TraesCS6A01G279700 chr2B 239858683 239861434 2751 False 305.000000 473 83.270000 1417 2378 2 chr2B.!!$F2 961
4 TraesCS6A01G279700 chrUn 311244187 311244763 576 True 466.000000 466 82.095000 1815 2378 1 chrUn.!!$R1 563
5 TraesCS6A01G279700 chrUn 410091036 410091612 576 False 466.000000 466 82.095000 1815 2378 1 chrUn.!!$F4 563
6 TraesCS6A01G279700 chr1B 605566154 605568841 2687 False 287.000000 455 87.264000 1479 2378 2 chr1B.!!$F1 899
7 TraesCS6A01G279700 chr5A 49963828 49965691 1863 True 325.000000 435 85.362500 1392 2378 2 chr5A.!!$R1 986

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
67 68 0.034896 AGGCCTGGTACGTTGAAGTG 59.965 55.0 3.11 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2162 0.815734 TTCTTCCCCGTCGATCTCAC 59.184 55.0 0.0 0.0 0.0 3.51 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
45 46 2.887151 AGGAGAATTGTCCTTGTGGG 57.113 50.000 18.22 0.00 45.39 4.61
46 47 2.348472 AGGAGAATTGTCCTTGTGGGA 58.652 47.619 18.22 0.00 45.39 4.37
47 48 2.716424 AGGAGAATTGTCCTTGTGGGAA 59.284 45.455 18.22 0.00 45.39 3.97
48 49 3.140144 AGGAGAATTGTCCTTGTGGGAAA 59.860 43.478 18.22 0.00 45.39 3.13
49 50 4.751028 AGGAGAATTGTCCTTGTGGGAAAG 60.751 45.833 18.22 0.00 45.39 2.62
50 51 7.747922 AGGAGAATTGTCCTTGTGGGAAAGG 62.748 48.000 18.22 0.00 45.39 3.11
53 54 4.018195 TCCTTGTGGGAAAGGCCT 57.982 55.556 0.00 0.00 45.49 5.19
54 55 1.460255 TCCTTGTGGGAAAGGCCTG 59.540 57.895 5.69 0.00 45.49 4.85
55 56 1.607467 CCTTGTGGGAAAGGCCTGG 60.607 63.158 5.69 0.00 40.37 4.45
56 57 1.153756 CTTGTGGGAAAGGCCTGGT 59.846 57.895 5.69 0.00 36.66 4.00
57 58 0.404040 CTTGTGGGAAAGGCCTGGTA 59.596 55.000 5.69 0.00 36.66 3.25
58 59 0.111639 TTGTGGGAAAGGCCTGGTAC 59.888 55.000 5.69 0.00 36.66 3.34
59 60 1.376812 GTGGGAAAGGCCTGGTACG 60.377 63.158 5.69 0.00 36.66 3.67
60 61 1.844289 TGGGAAAGGCCTGGTACGT 60.844 57.895 5.69 0.00 36.66 3.57
61 62 1.377612 GGGAAAGGCCTGGTACGTT 59.622 57.895 5.69 0.00 36.66 3.99
62 63 0.958876 GGGAAAGGCCTGGTACGTTG 60.959 60.000 5.69 0.00 36.66 4.10
63 64 0.035739 GGAAAGGCCTGGTACGTTGA 59.964 55.000 5.69 0.00 0.00 3.18
64 65 1.543871 GGAAAGGCCTGGTACGTTGAA 60.544 52.381 5.69 0.00 0.00 2.69
65 66 1.804748 GAAAGGCCTGGTACGTTGAAG 59.195 52.381 5.69 0.00 0.00 3.02
66 67 0.763035 AAGGCCTGGTACGTTGAAGT 59.237 50.000 5.69 0.00 0.00 3.01
67 68 0.034896 AGGCCTGGTACGTTGAAGTG 59.965 55.000 3.11 0.00 0.00 3.16
68 69 0.250166 GGCCTGGTACGTTGAAGTGT 60.250 55.000 0.00 0.00 0.00 3.55
93 94 2.615493 CGGAAGGTGACAAATAGCTGGT 60.615 50.000 0.00 0.00 0.00 4.00
95 96 3.191371 GGAAGGTGACAAATAGCTGGTTG 59.809 47.826 0.00 2.77 0.00 3.77
98 99 3.821033 AGGTGACAAATAGCTGGTTGTTC 59.179 43.478 15.54 12.19 38.07 3.18
100 101 5.001232 GGTGACAAATAGCTGGTTGTTCTA 58.999 41.667 15.54 5.86 38.07 2.10
104 105 8.082242 GTGACAAATAGCTGGTTGTTCTATTTT 58.918 33.333 15.54 0.00 39.57 1.82
141 142 4.701956 AGAAACAGTTGGTTGTTCTGTG 57.298 40.909 0.00 0.00 40.24 3.66
142 143 3.443681 AGAAACAGTTGGTTGTTCTGTGG 59.556 43.478 0.00 0.00 40.24 4.17
249 256 7.694388 TGCTTATTACTACTAATCAAGCACG 57.306 36.000 2.21 0.00 36.02 5.34
250 257 7.262772 TGCTTATTACTACTAATCAAGCACGT 58.737 34.615 2.21 0.00 36.02 4.49
252 259 9.408069 GCTTATTACTACTAATCAAGCACGTAT 57.592 33.333 0.00 0.00 33.95 3.06
287 308 6.395426 TTTTATGTGAAGCATCCATCCATC 57.605 37.500 0.00 0.00 38.94 3.51
288 309 3.588210 ATGTGAAGCATCCATCCATCA 57.412 42.857 0.00 0.00 30.67 3.07
289 310 3.588210 TGTGAAGCATCCATCCATCAT 57.412 42.857 0.00 0.00 0.00 2.45
290 311 3.905968 TGTGAAGCATCCATCCATCATT 58.094 40.909 0.00 0.00 0.00 2.57
291 312 3.634910 TGTGAAGCATCCATCCATCATTG 59.365 43.478 0.00 0.00 0.00 2.82
292 313 3.887110 GTGAAGCATCCATCCATCATTGA 59.113 43.478 0.00 0.00 0.00 2.57
355 376 3.470888 CGGGGCCGTCCTCTCATT 61.471 66.667 0.00 0.00 35.33 2.57
363 666 3.367910 GGCCGTCCTCTCATTATGATCTC 60.368 52.174 0.00 0.00 0.00 2.75
375 678 6.226052 TCATTATGATCTCAAAGTAGCGCAT 58.774 36.000 11.47 0.00 0.00 4.73
376 679 6.367149 TCATTATGATCTCAAAGTAGCGCATC 59.633 38.462 11.47 1.13 0.00 3.91
377 680 2.463876 TGATCTCAAAGTAGCGCATCG 58.536 47.619 11.47 0.00 0.00 3.84
415 718 1.269621 GGTGTCCGGTTGATAGATCCG 60.270 57.143 0.00 0.00 43.30 4.18
425 731 4.202264 GGTTGATAGATCCGAGGACAACAT 60.202 45.833 18.14 2.39 38.14 2.71
436 742 4.025730 CCGAGGACAACATCAACGATAATG 60.026 45.833 0.00 0.00 31.87 1.90
441 747 5.447279 GGACAACATCAACGATAATGTCCAC 60.447 44.000 22.79 7.83 45.72 4.02
442 748 5.245531 ACAACATCAACGATAATGTCCACT 58.754 37.500 0.00 0.00 35.10 4.00
452 758 5.522460 ACGATAATGTCCACTCATTTTACCG 59.478 40.000 0.00 0.00 38.68 4.02
492 798 0.742281 CCCGTTCATCTCCTGCACTG 60.742 60.000 0.00 0.00 0.00 3.66
493 799 0.036952 CCGTTCATCTCCTGCACTGT 60.037 55.000 0.00 0.00 0.00 3.55
498 804 2.771089 TCATCTCCTGCACTGTCAAAC 58.229 47.619 0.00 0.00 0.00 2.93
499 805 2.369860 TCATCTCCTGCACTGTCAAACT 59.630 45.455 0.00 0.00 0.00 2.66
500 806 3.578282 TCATCTCCTGCACTGTCAAACTA 59.422 43.478 0.00 0.00 0.00 2.24
501 807 3.667497 TCTCCTGCACTGTCAAACTAG 57.333 47.619 0.00 0.00 0.00 2.57
502 808 2.965831 TCTCCTGCACTGTCAAACTAGT 59.034 45.455 0.00 0.00 0.00 2.57
503 809 4.149598 TCTCCTGCACTGTCAAACTAGTA 58.850 43.478 0.00 0.00 0.00 1.82
504 810 4.218635 TCTCCTGCACTGTCAAACTAGTAG 59.781 45.833 0.00 0.00 0.00 2.57
505 811 3.895656 TCCTGCACTGTCAAACTAGTAGT 59.104 43.478 0.00 0.00 0.00 2.73
506 812 5.074804 TCCTGCACTGTCAAACTAGTAGTA 58.925 41.667 2.50 0.00 0.00 1.82
507 813 5.183331 TCCTGCACTGTCAAACTAGTAGTAG 59.817 44.000 2.50 2.87 0.00 2.57
573 906 3.475566 TGGAGAACAAAGTCAGACAGG 57.524 47.619 2.66 0.00 0.00 4.00
581 914 2.421877 AAGTCAGACAGGTCGCCACG 62.422 60.000 2.66 0.00 34.09 4.94
582 915 2.910479 TCAGACAGGTCGCCACGT 60.910 61.111 0.00 0.00 34.09 4.49
583 916 2.734723 CAGACAGGTCGCCACGTG 60.735 66.667 9.08 9.08 42.97 4.49
647 988 3.667282 CACACAGCACAGGCAGGC 61.667 66.667 0.00 0.00 44.61 4.85
648 989 4.193893 ACACAGCACAGGCAGGCA 62.194 61.111 0.00 0.00 44.61 4.75
685 1026 0.101219 GACGCCCATCATTTGCCTTC 59.899 55.000 0.00 0.00 0.00 3.46
686 1027 1.322538 ACGCCCATCATTTGCCTTCC 61.323 55.000 0.00 0.00 0.00 3.46
687 1028 1.321805 CGCCCATCATTTGCCTTCCA 61.322 55.000 0.00 0.00 0.00 3.53
688 1029 1.125633 GCCCATCATTTGCCTTCCAT 58.874 50.000 0.00 0.00 0.00 3.41
689 1030 1.487558 GCCCATCATTTGCCTTCCATT 59.512 47.619 0.00 0.00 0.00 3.16
700 1041 1.186917 CCTTCCATTGCCAGCCAACA 61.187 55.000 0.00 0.00 35.99 3.33
731 1101 1.518056 CTGGCTGGAACAACACGCAT 61.518 55.000 0.00 0.00 38.70 4.73
733 1103 1.514678 GGCTGGAACAACACGCATCA 61.515 55.000 0.00 0.00 38.70 3.07
734 1104 0.110056 GCTGGAACAACACGCATCAG 60.110 55.000 0.00 0.00 38.70 2.90
735 1105 0.110056 CTGGAACAACACGCATCAGC 60.110 55.000 0.00 0.00 38.70 4.26
736 1106 1.210155 GGAACAACACGCATCAGCC 59.790 57.895 0.00 0.00 37.52 4.85
737 1107 1.237285 GGAACAACACGCATCAGCCT 61.237 55.000 0.00 0.00 37.52 4.58
738 1108 0.166814 GAACAACACGCATCAGCCTC 59.833 55.000 0.00 0.00 37.52 4.70
739 1109 1.237285 AACAACACGCATCAGCCTCC 61.237 55.000 0.00 0.00 37.52 4.30
740 1110 2.434884 AACACGCATCAGCCTCCG 60.435 61.111 0.00 0.00 37.52 4.63
825 1204 4.803426 CCTGTCCAGCCGCGACTC 62.803 72.222 8.23 0.00 0.00 3.36
831 1210 4.700365 CAGCCGCGACTCGACACA 62.700 66.667 8.23 0.00 41.67 3.72
832 1211 4.702081 AGCCGCGACTCGACACAC 62.702 66.667 8.23 0.00 41.67 3.82
833 1212 4.994201 GCCGCGACTCGACACACA 62.994 66.667 8.23 0.00 41.67 3.72
835 1214 3.097728 CGCGACTCGACACACACC 61.098 66.667 0.00 0.00 41.67 4.16
836 1215 3.097728 GCGACTCGACACACACCG 61.098 66.667 1.63 0.00 0.00 4.94
838 1217 3.097728 GACTCGACACACACCGCG 61.098 66.667 0.00 0.00 0.00 6.46
839 1218 4.640855 ACTCGACACACACCGCGG 62.641 66.667 26.86 26.86 0.00 6.46
866 1245 1.487482 CCGCCACTCACATATACACG 58.513 55.000 0.00 0.00 0.00 4.49
897 1287 0.324091 GTCCTACGACTTCCTCCCCA 60.324 60.000 0.00 0.00 35.99 4.96
898 1288 0.410663 TCCTACGACTTCCTCCCCAA 59.589 55.000 0.00 0.00 0.00 4.12
905 1300 0.547954 ACTTCCTCCCCAACTCCTCC 60.548 60.000 0.00 0.00 0.00 4.30
910 1305 2.124996 CCCCAACTCCTCCCCAGA 59.875 66.667 0.00 0.00 0.00 3.86
911 1306 1.997874 CCCCAACTCCTCCCCAGAG 60.998 68.421 0.00 0.00 40.09 3.35
913 1308 2.581354 CAACTCCTCCCCAGAGCG 59.419 66.667 0.00 0.00 38.96 5.03
935 1339 3.432046 GCCAAGAAGAGATCTGGAGAAGG 60.432 52.174 0.00 0.00 38.79 3.46
942 1346 2.365293 GAGATCTGGAGAAGGGAGAAGC 59.635 54.545 0.00 0.00 0.00 3.86
943 1347 1.068434 GATCTGGAGAAGGGAGAAGCG 59.932 57.143 0.00 0.00 0.00 4.68
955 1359 1.997928 GAGAAGCGGAAGGCCATTGC 61.998 60.000 5.01 2.86 45.17 3.56
957 1361 0.748005 GAAGCGGAAGGCCATTGCTA 60.748 55.000 5.01 0.00 45.17 3.49
972 1376 3.675563 CTAGCTAGCTCCCCGCCG 61.676 72.222 23.26 0.00 40.39 6.46
987 1391 2.517402 CCGTCTCCTCCCTCCTCG 60.517 72.222 0.00 0.00 0.00 4.63
988 1392 3.213402 CGTCTCCTCCCTCCTCGC 61.213 72.222 0.00 0.00 0.00 5.03
990 1394 1.380650 GTCTCCTCCCTCCTCGCTT 60.381 63.158 0.00 0.00 0.00 4.68
991 1395 1.380515 TCTCCTCCCTCCTCGCTTG 60.381 63.158 0.00 0.00 0.00 4.01
993 1397 2.685380 CCTCCCTCCTCGCTTGGT 60.685 66.667 0.00 0.00 0.00 3.67
1335 1755 1.045911 AGATGAACGAGGAGGAGGCC 61.046 60.000 0.00 0.00 0.00 5.19
1560 1989 2.409870 GGCAATGGCGCACTAAGCT 61.410 57.895 10.83 0.00 42.61 3.74
1561 1990 1.095228 GGCAATGGCGCACTAAGCTA 61.095 55.000 10.83 0.00 42.61 3.32
1563 1992 1.368641 CAATGGCGCACTAAGCTACA 58.631 50.000 10.83 0.00 42.61 2.74
1565 1994 3.130633 CAATGGCGCACTAAGCTACATA 58.869 45.455 10.83 0.00 42.61 2.29
1566 1995 3.685139 ATGGCGCACTAAGCTACATAT 57.315 42.857 10.83 0.00 42.61 1.78
1567 1996 3.026630 TGGCGCACTAAGCTACATATC 57.973 47.619 10.83 0.00 42.61 1.63
1571 2000 4.051922 GCGCACTAAGCTACATATCTTGT 58.948 43.478 0.30 0.00 42.61 3.16
1572 2001 4.084849 GCGCACTAAGCTACATATCTTGTG 60.085 45.833 0.30 0.00 42.61 3.33
1574 2003 5.520288 CGCACTAAGCTACATATCTTGTGTT 59.480 40.000 0.00 0.00 42.61 3.32
1575 2004 6.291849 CGCACTAAGCTACATATCTTGTGTTC 60.292 42.308 0.00 0.00 42.61 3.18
1577 2006 7.278868 GCACTAAGCTACATATCTTGTGTTCTT 59.721 37.037 0.00 0.00 39.48 2.52
1579 2008 9.155975 ACTAAGCTACATATCTTGTGTTCTTTG 57.844 33.333 0.00 0.00 39.48 2.77
1580 2009 6.992063 AGCTACATATCTTGTGTTCTTTGG 57.008 37.500 0.00 0.00 39.48 3.28
1581 2010 6.476378 AGCTACATATCTTGTGTTCTTTGGT 58.524 36.000 0.00 0.00 39.48 3.67
1582 2011 6.942576 AGCTACATATCTTGTGTTCTTTGGTT 59.057 34.615 0.00 0.00 39.48 3.67
1583 2012 7.023575 GCTACATATCTTGTGTTCTTTGGTTG 58.976 38.462 0.00 0.00 39.48 3.77
1584 2013 6.331369 ACATATCTTGTGTTCTTTGGTTGG 57.669 37.500 0.00 0.00 37.11 3.77
1585 2014 6.068010 ACATATCTTGTGTTCTTTGGTTGGA 58.932 36.000 0.00 0.00 37.11 3.53
1586 2015 6.549364 ACATATCTTGTGTTCTTTGGTTGGAA 59.451 34.615 0.00 0.00 37.11 3.53
1587 2016 4.712122 TCTTGTGTTCTTTGGTTGGAAC 57.288 40.909 0.00 0.00 41.28 3.62
1588 2017 4.082845 TCTTGTGTTCTTTGGTTGGAACA 58.917 39.130 4.69 4.69 46.08 3.18
1594 2023 3.374042 TCTTTGGTTGGAACAAGACCA 57.626 42.857 0.00 0.00 46.26 4.02
1596 2025 3.819245 TGGTTGGAACAAGACCAGG 57.181 52.632 0.00 0.00 43.48 4.45
1597 2026 1.217916 TGGTTGGAACAAGACCAGGA 58.782 50.000 0.00 0.00 43.48 3.86
1603 2032 4.270756 TGGAACAAGACCAGGATCTGGC 62.271 54.545 13.35 6.99 46.71 4.85
1624 2102 4.867599 GTCGTCCGCGGGATCCAC 62.868 72.222 27.83 14.96 38.89 4.02
1637 2131 2.163815 GGGATCCACATAGATACGACGG 59.836 54.545 15.23 0.00 0.00 4.79
1641 2135 3.289836 TCCACATAGATACGACGGGAAA 58.710 45.455 0.00 0.00 0.00 3.13
1667 2161 2.836981 AGAAGATTCAGGTCTCAGGTGG 59.163 50.000 0.00 0.00 0.00 4.61
1668 2162 1.577736 AGATTCAGGTCTCAGGTGGG 58.422 55.000 0.00 0.00 0.00 4.61
1669 2163 1.203364 AGATTCAGGTCTCAGGTGGGT 60.203 52.381 0.00 0.00 0.00 4.51
1670 2164 0.987294 ATTCAGGTCTCAGGTGGGTG 59.013 55.000 0.00 0.00 0.00 4.61
1678 2172 0.457851 CTCAGGTGGGTGAGATCGAC 59.542 60.000 0.00 0.00 46.02 4.20
1687 2181 0.815734 GTGAGATCGACGGGGAAGAA 59.184 55.000 0.00 0.00 0.00 2.52
1689 2183 1.340697 TGAGATCGACGGGGAAGAAGA 60.341 52.381 0.00 0.00 0.00 2.87
1690 2184 1.749634 GAGATCGACGGGGAAGAAGAA 59.250 52.381 0.00 0.00 0.00 2.52
1691 2185 1.751924 AGATCGACGGGGAAGAAGAAG 59.248 52.381 0.00 0.00 0.00 2.85
1692 2186 1.749634 GATCGACGGGGAAGAAGAAGA 59.250 52.381 0.00 0.00 0.00 2.87
1693 2187 1.848652 TCGACGGGGAAGAAGAAGAT 58.151 50.000 0.00 0.00 0.00 2.40
1717 2211 8.938801 ATGCAACACAATTATATCTGGGAATA 57.061 30.769 0.00 0.00 0.00 1.75
1733 2228 8.701908 TCTGGGAATATAGAATTGTACTACGT 57.298 34.615 0.00 0.00 0.00 3.57
1734 2229 9.797642 TCTGGGAATATAGAATTGTACTACGTA 57.202 33.333 0.00 0.00 0.00 3.57
1794 2291 6.092944 GGGTAGATCTGATGTCTCTACGTATG 59.907 46.154 5.18 0.00 41.38 2.39
1813 4181 6.315642 ACGTATGATAGATACCGAGTGTATGG 59.684 42.308 0.00 0.00 40.31 2.74
1866 4238 2.353605 GGTGCCATGTAAATGTTGGTGG 60.354 50.000 0.00 0.00 0.00 4.61
1867 4239 2.560542 GTGCCATGTAAATGTTGGTGGA 59.439 45.455 0.00 0.00 0.00 4.02
1868 4240 3.195396 GTGCCATGTAAATGTTGGTGGAT 59.805 43.478 0.00 0.00 0.00 3.41
1869 4241 3.446873 TGCCATGTAAATGTTGGTGGATC 59.553 43.478 0.00 0.00 0.00 3.36
1935 4334 4.740205 GCAGATTCGTGATTCGTCTTGATA 59.260 41.667 0.00 0.00 40.80 2.15
1947 4346 8.531146 TGATTCGTCTTGATAATATAGATGCCA 58.469 33.333 0.00 0.00 0.00 4.92
1949 4348 8.707938 TTCGTCTTGATAATATAGATGCCATG 57.292 34.615 0.00 0.00 0.00 3.66
1952 4351 9.242477 CGTCTTGATAATATAGATGCCATGTAG 57.758 37.037 0.00 0.00 0.00 2.74
1959 4358 1.945387 AGATGCCATGTAGTGCTTCG 58.055 50.000 0.00 0.00 36.92 3.79
1971 4371 3.229276 AGTGCTTCGTTCAGATCTGAG 57.771 47.619 23.92 14.59 41.13 3.35
1995 4395 2.229784 GCTGAACCATCTTTCCAGTTGG 59.770 50.000 0.00 0.00 43.35 3.77
2026 4426 1.542472 TGGTTCATGCAGCTCACAATG 59.458 47.619 0.00 0.00 0.00 2.82
2045 4445 3.371087 GCTGGTGGAGCTAGCTAAC 57.629 57.895 19.38 18.42 46.57 2.34
2066 4466 4.021229 ACGAGGGTTTTGTTTTCCTTTCT 58.979 39.130 0.00 0.00 0.00 2.52
2131 4531 3.550437 AGAAAGCAGCTCCGTATGATT 57.450 42.857 0.00 0.00 0.00 2.57
2145 4545 3.001026 CGTATGATTGAAGTGCTGCTCAG 59.999 47.826 0.00 0.00 0.00 3.35
2146 4546 1.817357 TGATTGAAGTGCTGCTCAGG 58.183 50.000 0.00 0.00 0.00 3.86
2164 4564 8.114331 TGCTCAGGCAGATAAAATAATAATGG 57.886 34.615 0.00 0.00 44.28 3.16
2166 4566 8.796475 GCTCAGGCAGATAAAATAATAATGGAA 58.204 33.333 0.00 0.00 38.54 3.53
2172 4572 9.617975 GCAGATAAAATAATAATGGAAGTGCTC 57.382 33.333 0.00 0.00 0.00 4.26
2183 4583 0.659957 GAAGTGCTCCGATGGAATGC 59.340 55.000 0.00 0.00 0.00 3.56
2240 4643 9.754382 AATAATAAGAACGTGTCGGTGTATTAT 57.246 29.630 0.00 6.79 0.00 1.28
2243 4646 9.754382 AATAAGAACGTGTCGGTGTATTATATT 57.246 29.630 0.00 0.00 0.00 1.28
2250 4653 7.492020 ACGTGTCGGTGTATTATATTAGCAAAA 59.508 33.333 0.00 0.00 0.00 2.44
2284 4688 8.595362 AAACAATTATAAAAAGGAGGAGGAGG 57.405 34.615 0.00 0.00 0.00 4.30
2286 4690 7.578203 ACAATTATAAAAAGGAGGAGGAGGAG 58.422 38.462 0.00 0.00 0.00 3.69
2289 4693 2.262266 AAAAGGAGGAGGAGGAGGAG 57.738 55.000 0.00 0.00 0.00 3.69
2298 4702 2.666317 GAGGAGGAGGAGGAAGAAGAG 58.334 57.143 0.00 0.00 0.00 2.85
2310 4714 2.342179 GAAGAAGAGGCAAAGGAGACG 58.658 52.381 0.00 0.00 0.00 4.18
2322 4728 0.959553 AGGAGACGACACACACGAAT 59.040 50.000 0.00 0.00 34.70 3.34
2323 4729 1.068472 AGGAGACGACACACACGAATC 60.068 52.381 0.00 0.00 34.70 2.52
2326 4732 2.394708 AGACGACACACACGAATCTTG 58.605 47.619 0.00 0.00 34.70 3.02
2328 4734 0.179275 CGACACACACGAATCTTGCG 60.179 55.000 0.00 0.00 0.00 4.85
2329 4735 0.859232 GACACACACGAATCTTGCGT 59.141 50.000 0.00 0.00 43.67 5.24
2330 4736 2.055838 GACACACACGAATCTTGCGTA 58.944 47.619 0.00 0.00 40.44 4.42
2331 4737 2.666508 GACACACACGAATCTTGCGTAT 59.333 45.455 0.00 0.00 40.44 3.06
2333 4739 3.122948 ACACACACGAATCTTGCGTATTC 59.877 43.478 0.00 0.00 40.44 1.75
2335 4741 3.994392 ACACACGAATCTTGCGTATTCTT 59.006 39.130 0.00 0.00 40.44 2.52
2338 4744 6.146510 ACACACGAATCTTGCGTATTCTTTTA 59.853 34.615 0.00 0.00 40.44 1.52
2339 4745 6.461698 CACACGAATCTTGCGTATTCTTTTAC 59.538 38.462 0.00 0.00 40.44 2.01
2340 4746 6.146510 ACACGAATCTTGCGTATTCTTTTACA 59.853 34.615 0.00 0.00 40.44 2.41
2341 4747 6.678663 CACGAATCTTGCGTATTCTTTTACAG 59.321 38.462 0.00 0.00 40.44 2.74
2342 4748 6.183360 ACGAATCTTGCGTATTCTTTTACAGG 60.183 38.462 0.00 0.00 40.65 4.00
2347 4753 6.708949 TCTTGCGTATTCTTTTACAGGAGTTT 59.291 34.615 0.00 0.00 0.00 2.66
2361 4770 3.502211 CAGGAGTTTGGCGTATGTTTCTT 59.498 43.478 0.00 0.00 0.00 2.52
2362 4771 3.502211 AGGAGTTTGGCGTATGTTTCTTG 59.498 43.478 0.00 0.00 0.00 3.02
2378 4787 4.330944 TTCTTGAGCTACCGTCTTTTCA 57.669 40.909 0.00 0.00 0.00 2.69
2379 4788 3.914312 TCTTGAGCTACCGTCTTTTCAG 58.086 45.455 0.00 0.00 0.00 3.02
2380 4789 2.080286 TGAGCTACCGTCTTTTCAGC 57.920 50.000 0.00 0.00 0.00 4.26
2381 4790 0.992802 GAGCTACCGTCTTTTCAGCG 59.007 55.000 0.00 0.00 37.32 5.18
2388 4845 2.116366 CCGTCTTTTCAGCGGTTTTTG 58.884 47.619 0.00 0.00 40.53 2.44
2389 4846 2.223386 CCGTCTTTTCAGCGGTTTTTGA 60.223 45.455 0.00 0.00 40.53 2.69
2391 4848 3.372060 GTCTTTTCAGCGGTTTTTGAGG 58.628 45.455 0.00 0.00 0.00 3.86
2395 4852 1.878953 TCAGCGGTTTTTGAGGAGAC 58.121 50.000 0.00 0.00 0.00 3.36
2401 4858 3.848554 GCGGTTTTTGAGGAGACTTTTCG 60.849 47.826 0.00 0.00 44.43 3.46
2409 4866 2.801111 GAGGAGACTTTTCGAGCGTTTT 59.199 45.455 0.00 0.00 44.43 2.43
2410 4867 3.203716 AGGAGACTTTTCGAGCGTTTTT 58.796 40.909 0.00 0.00 37.44 1.94
2429 4886 5.740290 TTTTTGTGTTTAGGGTGTTTCCA 57.260 34.783 0.00 0.00 38.11 3.53
2452 4909 6.860023 CCAAAAAGTGACATTAGAGCAGAAAG 59.140 38.462 0.00 0.00 0.00 2.62
2453 4910 7.420800 CAAAAAGTGACATTAGAGCAGAAAGT 58.579 34.615 0.00 0.00 0.00 2.66
2454 4911 8.559536 CAAAAAGTGACATTAGAGCAGAAAGTA 58.440 33.333 0.00 0.00 0.00 2.24
2460 4917 7.275999 GTGACATTAGAGCAGAAAGTAGTAACC 59.724 40.741 0.00 0.00 0.00 2.85
2463 4920 7.819900 ACATTAGAGCAGAAAGTAGTAACCAAG 59.180 37.037 0.00 0.00 0.00 3.61
2478 4935 2.100631 CAAGGAGTAGGCGCGGTTG 61.101 63.158 8.83 0.00 0.00 3.77
2516 4973 1.444553 GCGACGAGGAGAACAGGTG 60.445 63.158 0.00 0.00 0.00 4.00
2518 4975 1.241990 CGACGAGGAGAACAGGTGGA 61.242 60.000 0.00 0.00 0.00 4.02
2538 4995 3.441572 GGAAGGTCCAAATCTGTGACATG 59.558 47.826 0.00 0.00 36.28 3.21
2539 4996 3.795688 AGGTCCAAATCTGTGACATGT 57.204 42.857 0.00 0.00 0.00 3.21
2540 4997 3.415212 AGGTCCAAATCTGTGACATGTG 58.585 45.455 1.15 0.00 0.00 3.21
2541 4998 2.095059 GGTCCAAATCTGTGACATGTGC 60.095 50.000 1.15 0.00 0.00 4.57
2542 4999 1.805943 TCCAAATCTGTGACATGTGCG 59.194 47.619 1.15 0.00 0.00 5.34
2543 5000 1.609932 CAAATCTGTGACATGTGCGC 58.390 50.000 1.15 0.00 0.00 6.09
2544 5001 0.523072 AAATCTGTGACATGTGCGCC 59.477 50.000 1.15 0.00 0.00 6.53
2545 5002 0.606130 AATCTGTGACATGTGCGCCA 60.606 50.000 1.15 2.31 0.00 5.69
2546 5003 1.300971 ATCTGTGACATGTGCGCCAC 61.301 55.000 1.15 5.70 34.56 5.01
2547 5004 2.969806 CTGTGACATGTGCGCCACC 61.970 63.158 1.15 0.00 32.73 4.61
2548 5005 2.977456 GTGACATGTGCGCCACCA 60.977 61.111 1.15 0.00 32.73 4.17
2549 5006 2.669229 TGACATGTGCGCCACCAG 60.669 61.111 1.15 1.36 32.73 4.00
2550 5007 2.358615 GACATGTGCGCCACCAGA 60.359 61.111 1.15 0.00 32.73 3.86
2551 5008 2.359107 ACATGTGCGCCACCAGAG 60.359 61.111 4.18 0.00 32.73 3.35
2552 5009 2.046988 CATGTGCGCCACCAGAGA 60.047 61.111 4.18 0.00 32.73 3.10
2553 5010 2.046892 ATGTGCGCCACCAGAGAC 60.047 61.111 4.18 0.00 32.73 3.36
2554 5011 3.939837 ATGTGCGCCACCAGAGACG 62.940 63.158 4.18 0.00 32.73 4.18
2555 5012 4.357947 GTGCGCCACCAGAGACGA 62.358 66.667 4.18 0.00 0.00 4.20
2556 5013 3.611674 TGCGCCACCAGAGACGAA 61.612 61.111 4.18 0.00 0.00 3.85
2557 5014 2.357034 GCGCCACCAGAGACGAAA 60.357 61.111 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.344968 CCCACAAGGACAATTCTCCTTTTT 59.655 41.667 11.94 0.62 46.89 1.94
23 24 3.897505 CCCACAAGGACAATTCTCCTTTT 59.102 43.478 11.94 3.95 46.89 2.27
24 25 3.140144 TCCCACAAGGACAATTCTCCTTT 59.860 43.478 11.94 2.64 46.89 3.11
26 27 2.348472 TCCCACAAGGACAATTCTCCT 58.652 47.619 0.00 0.00 43.08 3.69
27 28 2.879103 TCCCACAAGGACAATTCTCC 57.121 50.000 0.00 0.00 40.93 3.71
36 37 1.460255 CAGGCCTTTCCCACAAGGA 59.540 57.895 0.00 0.00 45.79 3.36
37 38 1.607467 CCAGGCCTTTCCCACAAGG 60.607 63.158 0.00 0.00 45.70 3.61
38 39 0.404040 TACCAGGCCTTTCCCACAAG 59.596 55.000 0.00 0.00 34.51 3.16
39 40 0.111639 GTACCAGGCCTTTCCCACAA 59.888 55.000 0.00 0.00 34.51 3.33
40 41 1.765074 GTACCAGGCCTTTCCCACA 59.235 57.895 0.00 0.00 34.51 4.17
41 42 1.376812 CGTACCAGGCCTTTCCCAC 60.377 63.158 0.00 0.00 34.51 4.61
42 43 1.420532 AACGTACCAGGCCTTTCCCA 61.421 55.000 0.00 0.00 34.51 4.37
43 44 0.958876 CAACGTACCAGGCCTTTCCC 60.959 60.000 0.00 0.00 34.51 3.97
44 45 0.035739 TCAACGTACCAGGCCTTTCC 59.964 55.000 0.00 0.00 0.00 3.13
45 46 1.804748 CTTCAACGTACCAGGCCTTTC 59.195 52.381 0.00 0.00 0.00 2.62
46 47 1.142262 ACTTCAACGTACCAGGCCTTT 59.858 47.619 0.00 0.00 0.00 3.11
47 48 0.763035 ACTTCAACGTACCAGGCCTT 59.237 50.000 0.00 0.00 0.00 4.35
48 49 0.034896 CACTTCAACGTACCAGGCCT 59.965 55.000 0.00 0.00 0.00 5.19
49 50 0.250166 ACACTTCAACGTACCAGGCC 60.250 55.000 0.00 0.00 0.00 5.19
50 51 0.865769 CACACTTCAACGTACCAGGC 59.134 55.000 0.00 0.00 0.00 4.85
51 52 1.508632 CCACACTTCAACGTACCAGG 58.491 55.000 0.00 0.00 0.00 4.45
52 53 0.865769 GCCACACTTCAACGTACCAG 59.134 55.000 0.00 0.00 0.00 4.00
53 54 0.533308 GGCCACACTTCAACGTACCA 60.533 55.000 0.00 0.00 0.00 3.25
54 55 1.562575 CGGCCACACTTCAACGTACC 61.563 60.000 2.24 0.00 0.00 3.34
55 56 1.562575 CCGGCCACACTTCAACGTAC 61.563 60.000 2.24 0.00 0.00 3.67
56 57 1.301087 CCGGCCACACTTCAACGTA 60.301 57.895 2.24 0.00 0.00 3.57
57 58 2.590575 CCGGCCACACTTCAACGT 60.591 61.111 2.24 0.00 0.00 3.99
58 59 1.841663 CTTCCGGCCACACTTCAACG 61.842 60.000 2.24 0.00 0.00 4.10
59 60 1.515521 CCTTCCGGCCACACTTCAAC 61.516 60.000 2.24 0.00 0.00 3.18
60 61 1.228124 CCTTCCGGCCACACTTCAA 60.228 57.895 2.24 0.00 0.00 2.69
61 62 2.429930 CCTTCCGGCCACACTTCA 59.570 61.111 2.24 0.00 0.00 3.02
62 63 1.966451 CACCTTCCGGCCACACTTC 60.966 63.158 2.24 0.00 0.00 3.01
63 64 2.113139 CACCTTCCGGCCACACTT 59.887 61.111 2.24 0.00 0.00 3.16
64 65 2.847234 TCACCTTCCGGCCACACT 60.847 61.111 2.24 0.00 0.00 3.55
65 66 2.668550 GTCACCTTCCGGCCACAC 60.669 66.667 2.24 0.00 0.00 3.82
66 67 2.272230 TTTGTCACCTTCCGGCCACA 62.272 55.000 2.24 0.00 0.00 4.17
67 68 0.893727 ATTTGTCACCTTCCGGCCAC 60.894 55.000 2.24 0.00 0.00 5.01
68 69 0.693622 TATTTGTCACCTTCCGGCCA 59.306 50.000 2.24 0.00 0.00 5.36
78 79 6.743575 ATAGAACAACCAGCTATTTGTCAC 57.256 37.500 11.49 9.39 34.82 3.67
104 105 6.276847 ACTGTTTCTTTCACACACACAAAAA 58.723 32.000 0.00 0.00 0.00 1.94
106 107 5.446143 ACTGTTTCTTTCACACACACAAA 57.554 34.783 0.00 0.00 0.00 2.83
110 111 3.823873 ACCAACTGTTTCTTTCACACACA 59.176 39.130 0.00 0.00 0.00 3.72
111 112 4.434713 ACCAACTGTTTCTTTCACACAC 57.565 40.909 0.00 0.00 0.00 3.82
112 113 4.279671 ACAACCAACTGTTTCTTTCACACA 59.720 37.500 0.00 0.00 34.00 3.72
113 114 4.805219 ACAACCAACTGTTTCTTTCACAC 58.195 39.130 0.00 0.00 34.00 3.82
114 115 5.242838 AGAACAACCAACTGTTTCTTTCACA 59.757 36.000 0.00 0.00 39.63 3.58
115 116 5.572896 CAGAACAACCAACTGTTTCTTTCAC 59.427 40.000 0.00 0.00 39.63 3.18
116 117 5.242838 ACAGAACAACCAACTGTTTCTTTCA 59.757 36.000 0.00 0.00 41.21 2.69
141 142 1.339727 ACGAAACAATGCTCCTACCCC 60.340 52.381 0.00 0.00 0.00 4.95
142 143 1.737793 CACGAAACAATGCTCCTACCC 59.262 52.381 0.00 0.00 0.00 3.69
220 221 9.937175 GCTTGATTAGTAGTAATAAGCAAAAGG 57.063 33.333 18.32 10.53 37.87 3.11
271 289 4.141344 TCTCAATGATGGATGGATGCTTCA 60.141 41.667 1.64 0.25 36.89 3.02
275 296 4.004314 CTCTCTCAATGATGGATGGATGC 58.996 47.826 0.00 0.00 0.00 3.91
284 305 6.428465 CCTTTGATGATCCTCTCTCAATGATG 59.572 42.308 0.00 0.00 0.00 3.07
285 306 6.101442 ACCTTTGATGATCCTCTCTCAATGAT 59.899 38.462 0.00 0.00 0.00 2.45
287 308 5.682659 ACCTTTGATGATCCTCTCTCAATG 58.317 41.667 0.00 0.00 0.00 2.82
288 309 5.972327 ACCTTTGATGATCCTCTCTCAAT 57.028 39.130 0.00 0.00 0.00 2.57
289 310 5.338708 GGAACCTTTGATGATCCTCTCTCAA 60.339 44.000 0.00 0.00 0.00 3.02
290 311 4.163078 GGAACCTTTGATGATCCTCTCTCA 59.837 45.833 0.00 0.00 0.00 3.27
291 312 4.163078 TGGAACCTTTGATGATCCTCTCTC 59.837 45.833 0.00 0.00 0.00 3.20
292 313 4.107072 TGGAACCTTTGATGATCCTCTCT 58.893 43.478 0.00 0.00 0.00 3.10
338 359 1.472662 ATAATGAGAGGACGGCCCCG 61.473 60.000 1.76 4.96 46.03 5.73
352 373 5.912360 TGCGCTACTTTGAGATCATAATG 57.088 39.130 9.73 0.00 0.00 1.90
355 376 4.229876 CGATGCGCTACTTTGAGATCATA 58.770 43.478 9.73 0.00 0.00 2.15
415 718 5.006746 GGACATTATCGTTGATGTTGTCCTC 59.993 44.000 22.56 8.63 43.74 3.71
425 731 7.065324 GGTAAAATGAGTGGACATTATCGTTGA 59.935 37.037 0.00 0.00 39.19 3.18
436 742 1.092348 GGGCGGTAAAATGAGTGGAC 58.908 55.000 0.00 0.00 0.00 4.02
441 747 1.476488 CCTTTGGGGCGGTAAAATGAG 59.524 52.381 0.00 0.00 0.00 2.90
442 748 1.551452 CCTTTGGGGCGGTAAAATGA 58.449 50.000 0.00 0.00 0.00 2.57
468 774 0.458543 CAGGAGATGAACGGGTCGTG 60.459 60.000 0.00 0.00 39.99 4.35
498 804 6.800892 ACGCGAGAAAGTTTTTCTACTACTAG 59.199 38.462 15.93 0.00 0.00 2.57
499 805 6.672147 ACGCGAGAAAGTTTTTCTACTACTA 58.328 36.000 15.93 0.00 0.00 1.82
500 806 5.527033 ACGCGAGAAAGTTTTTCTACTACT 58.473 37.500 15.93 0.00 0.00 2.57
501 807 5.819270 ACGCGAGAAAGTTTTTCTACTAC 57.181 39.130 15.93 0.00 0.00 2.73
502 808 5.403466 GGAACGCGAGAAAGTTTTTCTACTA 59.597 40.000 15.93 0.00 0.00 1.82
503 809 4.210746 GGAACGCGAGAAAGTTTTTCTACT 59.789 41.667 15.93 0.00 0.00 2.57
504 810 4.025480 TGGAACGCGAGAAAGTTTTTCTAC 60.025 41.667 15.93 0.39 0.00 2.59
505 811 4.025480 GTGGAACGCGAGAAAGTTTTTCTA 60.025 41.667 15.93 0.00 0.00 2.10
506 812 2.940410 TGGAACGCGAGAAAGTTTTTCT 59.060 40.909 15.93 3.86 0.00 2.52
507 813 3.033873 GTGGAACGCGAGAAAGTTTTTC 58.966 45.455 15.93 1.86 0.00 2.29
552 867 3.392616 ACCTGTCTGACTTTGTTCTCCAT 59.607 43.478 9.51 0.00 0.00 3.41
581 914 0.598065 GCTTTGACATCCACCACCAC 59.402 55.000 0.00 0.00 0.00 4.16
582 915 0.184692 TGCTTTGACATCCACCACCA 59.815 50.000 0.00 0.00 0.00 4.17
583 916 0.883833 CTGCTTTGACATCCACCACC 59.116 55.000 0.00 0.00 0.00 4.61
615 948 1.149627 TGTGTACCACCTGGCAACC 59.850 57.895 0.00 0.00 39.32 3.77
616 949 0.464735 TGTGTGTACCACCTGGCAAC 60.465 55.000 10.70 0.00 43.85 4.17
685 1026 2.259204 CGTGTTGGCTGGCAATGG 59.741 61.111 19.92 8.45 0.00 3.16
686 1027 2.259204 CCGTGTTGGCTGGCAATG 59.741 61.111 19.92 12.34 0.00 2.82
687 1028 2.203480 ACCGTGTTGGCTGGCAAT 60.203 55.556 19.92 0.23 43.94 3.56
688 1029 2.904866 GACCGTGTTGGCTGGCAA 60.905 61.111 13.06 13.06 43.94 4.52
740 1110 4.424566 TTCGTACACCGCCGGAGC 62.425 66.667 11.71 0.00 36.19 4.70
789 1164 2.918802 TGGCTGGCTGGCTTTTGG 60.919 61.111 18.27 0.00 42.34 3.28
842 1221 2.329539 ATATGTGAGTGGCGGGCTGG 62.330 60.000 2.38 0.00 0.00 4.85
843 1222 0.392706 TATATGTGAGTGGCGGGCTG 59.607 55.000 2.38 0.00 0.00 4.85
844 1223 0.393077 GTATATGTGAGTGGCGGGCT 59.607 55.000 2.38 0.00 0.00 5.19
845 1224 0.105964 TGTATATGTGAGTGGCGGGC 59.894 55.000 0.00 0.00 0.00 6.13
846 1225 1.865865 GTGTATATGTGAGTGGCGGG 58.134 55.000 0.00 0.00 0.00 6.13
847 1226 1.487482 CGTGTATATGTGAGTGGCGG 58.513 55.000 0.00 0.00 0.00 6.13
848 1227 0.852777 GCGTGTATATGTGAGTGGCG 59.147 55.000 0.00 0.00 0.00 5.69
849 1228 1.217882 GGCGTGTATATGTGAGTGGC 58.782 55.000 0.00 0.00 0.00 5.01
854 1233 1.066454 CGTCTGGGCGTGTATATGTGA 59.934 52.381 0.00 0.00 0.00 3.58
880 1259 0.535797 GTTGGGGAGGAAGTCGTAGG 59.464 60.000 0.00 0.00 0.00 3.18
897 1287 3.394836 GCGCTCTGGGGAGGAGTT 61.395 66.667 0.00 0.00 39.80 3.01
905 1300 1.449246 CTCTTCTTGGCGCTCTGGG 60.449 63.158 7.64 0.00 0.00 4.45
910 1305 0.177604 CCAGATCTCTTCTTGGCGCT 59.822 55.000 7.64 0.00 29.93 5.92
911 1306 0.176680 TCCAGATCTCTTCTTGGCGC 59.823 55.000 0.00 0.00 29.93 6.53
913 1308 3.432046 CCTTCTCCAGATCTCTTCTTGGC 60.432 52.174 0.00 0.00 29.93 4.52
935 1339 1.077429 AATGGCCTTCCGCTTCTCC 60.077 57.895 3.32 0.00 37.74 3.71
942 1346 0.106708 TAGCTAGCAATGGCCTTCCG 59.893 55.000 18.83 0.00 42.56 4.30
943 1347 1.889545 CTAGCTAGCAATGGCCTTCC 58.110 55.000 18.83 0.00 42.56 3.46
969 1373 2.835895 GAGGAGGGAGGAGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
972 1376 1.380650 AAGCGAGGAGGGAGGAGAC 60.381 63.158 0.00 0.00 0.00 3.36
979 1383 2.266055 GACACCAAGCGAGGAGGG 59.734 66.667 4.39 0.00 0.00 4.30
981 1385 2.811317 GCGACACCAAGCGAGGAG 60.811 66.667 4.39 0.00 0.00 3.69
982 1386 4.373116 GGCGACACCAAGCGAGGA 62.373 66.667 4.39 0.00 38.86 3.71
1515 1944 1.958288 ACTGGAAGCTCTGGGTGTAT 58.042 50.000 0.00 0.00 37.60 2.29
1560 1989 7.227873 TCCAACCAAAGAACACAAGATATGTA 58.772 34.615 0.00 0.00 41.46 2.29
1561 1990 6.068010 TCCAACCAAAGAACACAAGATATGT 58.932 36.000 0.00 0.00 45.34 2.29
1563 1992 6.549364 TGTTCCAACCAAAGAACACAAGATAT 59.451 34.615 1.63 0.00 45.53 1.63
1565 1994 4.709397 TGTTCCAACCAAAGAACACAAGAT 59.291 37.500 1.63 0.00 45.53 2.40
1566 1995 4.082845 TGTTCCAACCAAAGAACACAAGA 58.917 39.130 1.63 0.00 45.53 3.02
1567 1996 4.448537 TGTTCCAACCAAAGAACACAAG 57.551 40.909 1.63 0.00 45.53 3.16
1572 2001 3.445805 TGGTCTTGTTCCAACCAAAGAAC 59.554 43.478 0.00 0.00 40.04 3.01
1574 2003 3.287222 CTGGTCTTGTTCCAACCAAAGA 58.713 45.455 0.00 0.00 42.28 2.52
1575 2004 2.362077 CCTGGTCTTGTTCCAACCAAAG 59.638 50.000 0.00 0.00 42.28 2.77
1577 2006 1.566703 TCCTGGTCTTGTTCCAACCAA 59.433 47.619 0.00 0.00 42.28 3.67
1579 2008 2.040412 AGATCCTGGTCTTGTTCCAACC 59.960 50.000 0.00 0.00 34.35 3.77
1580 2009 3.077359 CAGATCCTGGTCTTGTTCCAAC 58.923 50.000 0.00 0.00 34.35 3.77
1581 2010 2.040278 CCAGATCCTGGTCTTGTTCCAA 59.960 50.000 4.88 0.00 45.82 3.53
1582 2011 1.630369 CCAGATCCTGGTCTTGTTCCA 59.370 52.381 4.88 0.00 45.82 3.53
1583 2012 2.409948 CCAGATCCTGGTCTTGTTCC 57.590 55.000 4.88 0.00 45.82 3.62
1593 2022 2.202797 CGACACCGCCAGATCCTG 60.203 66.667 0.00 0.00 0.00 3.86
1594 2023 2.680352 ACGACACCGCCAGATCCT 60.680 61.111 0.00 0.00 39.95 3.24
1595 2024 2.202756 GACGACACCGCCAGATCC 60.203 66.667 0.00 0.00 39.95 3.36
1596 2025 2.202756 GGACGACACCGCCAGATC 60.203 66.667 0.00 0.00 39.95 2.75
1597 2026 4.129737 CGGACGACACCGCCAGAT 62.130 66.667 7.36 0.00 46.20 2.90
1617 2095 2.163815 CCCGTCGTATCTATGTGGATCC 59.836 54.545 4.20 4.20 0.00 3.36
1624 2102 4.940463 TCCTTTTTCCCGTCGTATCTATG 58.060 43.478 0.00 0.00 0.00 2.23
1637 2131 5.565509 AGACCTGAATCTTCTCCTTTTTCC 58.434 41.667 0.00 0.00 0.00 3.13
1641 2135 4.224818 CCTGAGACCTGAATCTTCTCCTTT 59.775 45.833 0.00 0.00 35.81 3.11
1667 2161 1.035932 TCTTCCCCGTCGATCTCACC 61.036 60.000 0.00 0.00 0.00 4.02
1668 2162 0.815734 TTCTTCCCCGTCGATCTCAC 59.184 55.000 0.00 0.00 0.00 3.51
1669 2163 1.103803 CTTCTTCCCCGTCGATCTCA 58.896 55.000 0.00 0.00 0.00 3.27
1670 2164 1.390565 TCTTCTTCCCCGTCGATCTC 58.609 55.000 0.00 0.00 0.00 2.75
1678 2172 1.740025 GTTGCATCTTCTTCTTCCCCG 59.260 52.381 0.00 0.00 0.00 5.73
1687 2181 7.230108 CCCAGATATAATTGTGTTGCATCTTCT 59.770 37.037 0.00 0.00 0.00 2.85
1689 2183 7.062322 TCCCAGATATAATTGTGTTGCATCTT 58.938 34.615 0.00 0.00 0.00 2.40
1690 2184 6.604171 TCCCAGATATAATTGTGTTGCATCT 58.396 36.000 0.00 0.00 0.00 2.90
1691 2185 6.882610 TCCCAGATATAATTGTGTTGCATC 57.117 37.500 0.00 0.00 0.00 3.91
1692 2186 7.844493 ATTCCCAGATATAATTGTGTTGCAT 57.156 32.000 0.00 0.00 0.00 3.96
1693 2187 8.938801 ATATTCCCAGATATAATTGTGTTGCA 57.061 30.769 0.00 0.00 0.00 4.08
1728 2223 4.337763 CAGCACGGTAAACTACTACGTAG 58.662 47.826 20.97 20.97 41.43 3.51
1729 2224 3.426159 GCAGCACGGTAAACTACTACGTA 60.426 47.826 0.00 0.00 35.85 3.57
1730 2225 2.669391 GCAGCACGGTAAACTACTACGT 60.669 50.000 0.00 0.00 38.43 3.57
1731 2226 1.916000 GCAGCACGGTAAACTACTACG 59.084 52.381 0.00 0.00 0.00 3.51
1732 2227 3.227810 AGCAGCACGGTAAACTACTAC 57.772 47.619 0.00 0.00 0.00 2.73
1733 2228 3.947910 AAGCAGCACGGTAAACTACTA 57.052 42.857 0.00 0.00 0.00 1.82
1734 2229 2.833631 AAGCAGCACGGTAAACTACT 57.166 45.000 0.00 0.00 0.00 2.57
1735 2230 3.064931 AGAAAGCAGCACGGTAAACTAC 58.935 45.455 0.00 0.00 0.00 2.73
1736 2231 3.396260 AGAAAGCAGCACGGTAAACTA 57.604 42.857 0.00 0.00 0.00 2.24
1737 2232 2.256117 AGAAAGCAGCACGGTAAACT 57.744 45.000 0.00 0.00 0.00 2.66
1794 2291 4.765856 ACCACCATACACTCGGTATCTATC 59.234 45.833 0.00 0.00 40.76 2.08
1813 4181 4.937201 AAAGAATGGAAAGAACCACCAC 57.063 40.909 0.00 0.00 43.03 4.16
1866 4238 6.136541 AGGCAAAAACATAAGGAATCGATC 57.863 37.500 0.00 0.00 0.00 3.69
1867 4239 5.067805 GGAGGCAAAAACATAAGGAATCGAT 59.932 40.000 0.00 0.00 0.00 3.59
1868 4240 4.398044 GGAGGCAAAAACATAAGGAATCGA 59.602 41.667 0.00 0.00 0.00 3.59
1869 4241 4.399303 AGGAGGCAAAAACATAAGGAATCG 59.601 41.667 0.00 0.00 0.00 3.34
1935 4334 5.871524 CGAAGCACTACATGGCATCTATATT 59.128 40.000 0.00 0.00 0.00 1.28
1947 4346 4.158579 TCAGATCTGAACGAAGCACTACAT 59.841 41.667 23.17 0.00 36.53 2.29
1949 4348 4.098055 TCAGATCTGAACGAAGCACTAC 57.902 45.455 23.17 0.00 36.53 2.73
1952 4351 2.094494 TCCTCAGATCTGAACGAAGCAC 60.094 50.000 25.09 0.00 39.39 4.40
1959 4358 3.883830 TTCAGCTCCTCAGATCTGAAC 57.116 47.619 25.09 14.88 45.64 3.18
1971 4371 2.290577 ACTGGAAAGATGGTTCAGCTCC 60.291 50.000 0.00 0.00 0.00 4.70
1977 4377 3.756963 GGTACCAACTGGAAAGATGGTTC 59.243 47.826 12.19 7.84 41.31 3.62
2045 4445 4.649088 AGAAAGGAAAACAAAACCCTCG 57.351 40.909 0.00 0.00 0.00 4.63
2066 4466 6.174720 CCATCTGTGGTATTAAGCCTCTAA 57.825 41.667 1.31 0.00 40.83 2.10
2120 4520 2.286294 GCAGCACTTCAATCATACGGAG 59.714 50.000 0.00 0.00 0.00 4.63
2131 4531 2.831043 TGCCTGAGCAGCACTTCA 59.169 55.556 0.00 0.00 46.52 3.02
2145 4545 8.579863 AGCACTTCCATTATTATTTTATCTGCC 58.420 33.333 0.00 0.00 0.00 4.85
2146 4546 9.617975 GAGCACTTCCATTATTATTTTATCTGC 57.382 33.333 0.00 0.00 0.00 4.26
2164 4564 0.659957 GCATTCCATCGGAGCACTTC 59.340 55.000 0.00 0.00 31.21 3.01
2166 4566 0.463295 CTGCATTCCATCGGAGCACT 60.463 55.000 0.00 0.00 31.23 4.40
2167 4567 0.745845 ACTGCATTCCATCGGAGCAC 60.746 55.000 0.00 0.00 31.23 4.40
2172 4572 1.431488 CCGACACTGCATTCCATCGG 61.431 60.000 9.65 9.65 42.69 4.18
2183 4583 1.668793 TGCTGATGCACCGACACTG 60.669 57.895 0.00 0.00 45.31 3.66
2205 4605 9.250986 CGACACGTTCTTATTATTTTTCTTCTG 57.749 33.333 0.00 0.00 0.00 3.02
2266 4669 5.468658 CTCCTCCTCCTCCTCCTTTTTATA 58.531 45.833 0.00 0.00 0.00 0.98
2268 4672 3.569004 CCTCCTCCTCCTCCTCCTTTTTA 60.569 52.174 0.00 0.00 0.00 1.52
2273 4677 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
2278 4682 2.666317 CTCTTCTTCCTCCTCCTCCTC 58.334 57.143 0.00 0.00 0.00 3.71
2281 4685 1.119684 GCCTCTTCTTCCTCCTCCTC 58.880 60.000 0.00 0.00 0.00 3.71
2284 4688 2.355615 CCTTTGCCTCTTCTTCCTCCTC 60.356 54.545 0.00 0.00 0.00 3.71
2286 4690 1.630878 TCCTTTGCCTCTTCTTCCTCC 59.369 52.381 0.00 0.00 0.00 4.30
2289 4693 2.705730 GTCTCCTTTGCCTCTTCTTCC 58.294 52.381 0.00 0.00 0.00 3.46
2298 4702 0.531974 TGTGTGTCGTCTCCTTTGCC 60.532 55.000 0.00 0.00 0.00 4.52
2310 4714 0.859232 ACGCAAGATTCGTGTGTGTC 59.141 50.000 16.28 0.00 38.27 3.67
2322 4728 5.790593 ACTCCTGTAAAAGAATACGCAAGA 58.209 37.500 0.00 0.00 43.62 3.02
2326 4732 5.628134 CCAAACTCCTGTAAAAGAATACGC 58.372 41.667 0.00 0.00 0.00 4.42
2328 4734 5.180680 ACGCCAAACTCCTGTAAAAGAATAC 59.819 40.000 0.00 0.00 0.00 1.89
2329 4735 5.310451 ACGCCAAACTCCTGTAAAAGAATA 58.690 37.500 0.00 0.00 0.00 1.75
2330 4736 4.142038 ACGCCAAACTCCTGTAAAAGAAT 58.858 39.130 0.00 0.00 0.00 2.40
2331 4737 3.547746 ACGCCAAACTCCTGTAAAAGAA 58.452 40.909 0.00 0.00 0.00 2.52
2333 4739 4.454504 ACATACGCCAAACTCCTGTAAAAG 59.545 41.667 0.00 0.00 0.00 2.27
2335 4741 4.010667 ACATACGCCAAACTCCTGTAAA 57.989 40.909 0.00 0.00 0.00 2.01
2338 4744 2.561478 AACATACGCCAAACTCCTGT 57.439 45.000 0.00 0.00 0.00 4.00
2339 4745 3.074412 AGAAACATACGCCAAACTCCTG 58.926 45.455 0.00 0.00 0.00 3.86
2340 4746 3.418684 AGAAACATACGCCAAACTCCT 57.581 42.857 0.00 0.00 0.00 3.69
2341 4747 3.500680 TCAAGAAACATACGCCAAACTCC 59.499 43.478 0.00 0.00 0.00 3.85
2342 4748 4.712763 CTCAAGAAACATACGCCAAACTC 58.287 43.478 0.00 0.00 0.00 3.01
2347 4753 2.472695 AGCTCAAGAAACATACGCCA 57.527 45.000 0.00 0.00 0.00 5.69
2361 4770 1.668919 CGCTGAAAAGACGGTAGCTCA 60.669 52.381 0.00 0.00 32.43 4.26
2362 4771 0.992802 CGCTGAAAAGACGGTAGCTC 59.007 55.000 0.00 0.00 32.43 4.09
2378 4787 2.640316 AAGTCTCCTCAAAAACCGCT 57.360 45.000 0.00 0.00 0.00 5.52
2379 4788 3.629058 GAAAAGTCTCCTCAAAAACCGC 58.371 45.455 0.00 0.00 0.00 5.68
2380 4789 3.558418 TCGAAAAGTCTCCTCAAAAACCG 59.442 43.478 0.00 0.00 0.00 4.44
2381 4790 4.554919 GCTCGAAAAGTCTCCTCAAAAACC 60.555 45.833 0.00 0.00 0.00 3.27
2382 4791 4.528504 GCTCGAAAAGTCTCCTCAAAAAC 58.471 43.478 0.00 0.00 0.00 2.43
2388 4845 2.067414 AACGCTCGAAAAGTCTCCTC 57.933 50.000 0.00 0.00 0.00 3.71
2389 4846 2.528041 AAACGCTCGAAAAGTCTCCT 57.472 45.000 0.00 0.00 0.00 3.69
2409 4866 5.740290 TTTGGAAACACCCTAAACACAAA 57.260 34.783 0.00 0.00 42.67 2.83
2410 4867 5.740290 TTTTGGAAACACCCTAAACACAA 57.260 34.783 0.00 0.00 42.67 3.33
2428 4885 7.420800 ACTTTCTGCTCTAATGTCACTTTTTG 58.579 34.615 0.00 0.00 0.00 2.44
2429 4886 7.573968 ACTTTCTGCTCTAATGTCACTTTTT 57.426 32.000 0.00 0.00 0.00 1.94
2452 4909 2.480932 GCGCCTACTCCTTGGTTACTAC 60.481 54.545 0.00 0.00 0.00 2.73
2453 4910 1.753073 GCGCCTACTCCTTGGTTACTA 59.247 52.381 0.00 0.00 0.00 1.82
2454 4911 0.535797 GCGCCTACTCCTTGGTTACT 59.464 55.000 0.00 0.00 0.00 2.24
2460 4917 2.100631 CAACCGCGCCTACTCCTTG 61.101 63.158 0.00 0.00 0.00 3.61
2463 4920 4.832608 CCCAACCGCGCCTACTCC 62.833 72.222 0.00 0.00 0.00 3.85
2478 4935 0.530870 GACGCTTCACCTATGCTCCC 60.531 60.000 0.00 0.00 0.00 4.30
2516 4973 3.140325 TGTCACAGATTTGGACCTTCC 57.860 47.619 0.00 0.00 36.96 3.46
2518 4975 3.822735 CACATGTCACAGATTTGGACCTT 59.177 43.478 0.00 0.00 0.00 3.50
2534 4991 2.359107 CTCTGGTGGCGCACATGT 60.359 61.111 10.83 0.00 35.86 3.21
2538 4995 3.858868 TTCGTCTCTGGTGGCGCAC 62.859 63.158 10.83 5.50 0.00 5.34
2539 4996 3.158537 TTTCGTCTCTGGTGGCGCA 62.159 57.895 10.83 0.00 0.00 6.09
2540 4997 2.357034 TTTCGTCTCTGGTGGCGC 60.357 61.111 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.