Multiple sequence alignment - TraesCS6D01G103400

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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 TraesCS6D01G103400 chr6D 100.000 6673 0 0 1 6673 67383321 67376649 0.000000e+00 12323.0
1 TraesCS6D01G103400 chr6D 100.000 63 0 0 2683 2745 67380575 67380513 4.230000e-22 117.0
2 TraesCS6D01G103400 chr6D 100.000 63 0 0 2747 2809 67380639 67380577 4.230000e-22 117.0
3 TraesCS6D01G103400 chr6A 91.930 2912 150 45 3827 6673 84924779 84921888 0.000000e+00 3997.0
4 TraesCS6D01G103400 chr6A 90.008 2582 119 40 241 2751 84928597 84926084 0.000000e+00 3210.0
5 TraesCS6D01G103400 chr6A 89.544 1119 59 22 2747 3825 84926151 84925051 0.000000e+00 1365.0
6 TraesCS6D01G103400 chr6B 92.157 2754 141 26 3827 6533 142231700 142228975 0.000000e+00 3819.0
7 TraesCS6D01G103400 chr6B 90.353 2778 134 56 51 2751 142235791 142233071 0.000000e+00 3522.0
8 TraesCS6D01G103400 chr6B 93.718 589 19 6 2747 3318 142233139 142232552 0.000000e+00 867.0
9 TraesCS6D01G103400 chr6B 94.647 467 19 3 3361 3825 142232436 142231974 0.000000e+00 719.0
10 TraesCS6D01G103400 chr6B 90.957 188 12 5 486 670 675922177 675921992 1.440000e-61 248.0
11 TraesCS6D01G103400 chr6B 82.946 129 21 1 4526 4654 213549323 213549450 1.520000e-21 115.0
12 TraesCS6D01G103400 chr6B 94.340 53 3 0 1 53 142238357 142238305 1.540000e-11 82.4
13 TraesCS6D01G103400 chr2A 83.761 1207 128 34 4526 5675 77166934 77165739 0.000000e+00 1081.0
14 TraesCS6D01G103400 chr2A 86.137 642 56 20 3196 3824 77168447 77167826 0.000000e+00 662.0
15 TraesCS6D01G103400 chr2A 81.698 754 102 23 995 1734 77170551 77169820 4.450000e-166 595.0
16 TraesCS6D01G103400 chr2A 89.068 311 22 6 1937 2246 77169609 77169310 6.320000e-100 375.0
17 TraesCS6D01G103400 chr2A 83.791 401 52 7 3827 4221 77167560 77167167 1.060000e-97 368.0
18 TraesCS6D01G103400 chr2A 87.814 279 29 3 2878 3154 77168720 77168445 8.350000e-84 322.0
19 TraesCS6D01G103400 chr2A 88.571 140 7 7 4276 4406 77167061 77166922 1.930000e-35 161.0
20 TraesCS6D01G103400 chr2A 81.295 139 18 2 1758 1896 77169743 77169613 9.150000e-19 106.0
21 TraesCS6D01G103400 chr2B 83.788 1209 122 35 4526 5675 117885916 117884723 0.000000e+00 1079.0
22 TraesCS6D01G103400 chr2B 86.217 653 61 19 3183 3823 117887424 117886789 0.000000e+00 680.0
23 TraesCS6D01G103400 chr2B 79.786 935 132 40 995 1896 117889968 117889058 1.580000e-175 627.0
24 TraesCS6D01G103400 chr2B 89.103 312 21 7 1937 2246 117889054 117888754 6.320000e-100 375.0
25 TraesCS6D01G103400 chr2B 82.294 401 51 10 3827 4221 117886537 117886151 4.990000e-86 329.0
26 TraesCS6D01G103400 chr2B 87.083 240 27 2 2912 3149 117887653 117887416 1.100000e-67 268.0
27 TraesCS6D01G103400 chr2B 90.052 191 11 6 486 670 614387895 614388083 2.400000e-59 241.0
28 TraesCS6D01G103400 chr2B 89.005 191 13 6 486 670 614493337 614493525 5.210000e-56 230.0
29 TraesCS6D01G103400 chr2B 87.770 139 9 5 4276 4406 117886042 117885904 8.960000e-34 156.0
30 TraesCS6D01G103400 chr2D 83.557 821 89 26 4893 5675 76640352 76639540 0.000000e+00 726.0
31 TraesCS6D01G103400 chr2D 86.250 640 55 20 3196 3823 76642546 76641928 0.000000e+00 664.0
32 TraesCS6D01G103400 chr2D 82.869 753 92 26 997 1734 76644687 76643957 5.640000e-180 641.0
33 TraesCS6D01G103400 chr2D 85.396 404 45 8 3827 4221 76641677 76641279 2.240000e-109 407.0
34 TraesCS6D01G103400 chr2D 91.525 295 21 4 4532 4823 76641039 76640746 2.900000e-108 403.0
35 TraesCS6D01G103400 chr2D 90.032 311 21 4 1937 2246 76643747 76643446 1.740000e-105 394.0
36 TraesCS6D01G103400 chr2D 89.286 280 23 5 2878 3154 76642819 76642544 1.780000e-90 344.0
37 TraesCS6D01G103400 chr2D 86.331 139 11 7 4276 4406 76641170 76641032 1.940000e-30 145.0
38 TraesCS6D01G103400 chr5B 83.066 437 35 17 6072 6492 150777270 150776857 1.770000e-95 361.0
39 TraesCS6D01G103400 chr5B 90.052 191 11 6 486 670 608166475 608166663 2.400000e-59 241.0
40 TraesCS6D01G103400 chr4B 90.052 191 11 6 486 670 27847420 27847232 2.400000e-59 241.0
41 TraesCS6D01G103400 chr4B 97.059 34 1 0 2634 2667 99015318 99015285 2.600000e-04 58.4
42 TraesCS6D01G103400 chr4A 89.529 191 12 6 486 670 648529648 648529836 1.120000e-57 235.0
43 TraesCS6D01G103400 chr4A 96.875 32 1 0 2640 2671 521308543 521308512 3.000000e-03 54.7
44 TraesCS6D01G103400 chr4A 100.000 29 0 0 2640 2668 625529179 625529151 3.000000e-03 54.7
45 TraesCS6D01G103400 chr7B 89.005 191 13 7 486 670 40819017 40819205 5.210000e-56 230.0
46 TraesCS6D01G103400 chr3B 89.005 191 13 6 486 670 316302623 316302811 5.210000e-56 230.0
47 TraesCS6D01G103400 chr3B 100.000 29 0 0 2639 2667 532227126 532227154 3.000000e-03 54.7
48 TraesCS6D01G103400 chr1A 100.000 30 0 0 2639 2668 177438082 177438111 1.000000e-03 56.5
49 TraesCS6D01G103400 chr5D 100.000 29 0 0 2640 2668 113376577 113376605 3.000000e-03 54.7
50 TraesCS6D01G103400 chr3A 96.970 33 0 1 2640 2671 113926986 113927018 3.000000e-03 54.7


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 TraesCS6D01G103400 chr6D 67376649 67383321 6672 True 4185.666667 12323 100.000000 1 6673 3 chr6D.!!$R1 6672
1 TraesCS6D01G103400 chr6A 84921888 84928597 6709 True 2857.333333 3997 90.494000 241 6673 3 chr6A.!!$R1 6432
2 TraesCS6D01G103400 chr6B 142228975 142238357 9382 True 1801.880000 3819 93.043000 1 6533 5 chr6B.!!$R2 6532
3 TraesCS6D01G103400 chr2A 77165739 77170551 4812 True 458.750000 1081 85.266875 995 5675 8 chr2A.!!$R1 4680
4 TraesCS6D01G103400 chr2B 117884723 117889968 5245 True 502.000000 1079 85.148714 995 5675 7 chr2B.!!$R1 4680
5 TraesCS6D01G103400 chr2D 76639540 76644687 5147 True 465.500000 726 86.905750 997 5675 8 chr2D.!!$R1 4678

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
40 41 0.028110 GGCGGAGATCGAATGTTTGC 59.972 55.000 0.00 0.0 42.43 3.68 F
210 2727 0.679640 GGAAACCGGTCCATCATGCA 60.680 55.000 8.04 0.0 37.65 3.96 F
230 2747 0.734942 TGCTTACGCTACGACCAAGC 60.735 55.000 14.20 14.2 38.75 4.01 F
1195 3827 0.736325 CCACGCTCTCAAAGGTACCG 60.736 60.000 6.18 0.0 0.00 4.02 F
2285 4992 1.819632 ATGTTGATTCGCTCGGGCC 60.820 57.895 0.00 0.0 34.44 5.80 F
2311 5018 1.267806 CCACACTCAACCATCAACAGC 59.732 52.381 0.00 0.0 0.00 4.40 F
2437 5158 1.405933 GGCAGCTTATTGGGCCTTTTG 60.406 52.381 4.53 0.0 43.09 2.44 F
2805 5778 1.812571 ACCCAAGATGCGTCATTTCAC 59.187 47.619 8.99 0.0 0.00 3.18 F
4322 8021 1.195115 CCTTGGACCGAGATTCTCCA 58.805 55.000 10.67 0.0 31.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 4090 0.179045 AGCTCCCACACAGACACAAC 60.179 55.000 0.00 0.00 0.00 3.32 R
2209 4916 1.251251 GCACAAAGCATCCTGAACCT 58.749 50.000 0.00 0.00 44.79 3.50 R
2210 4917 3.800628 GCACAAAGCATCCTGAACC 57.199 52.632 0.00 0.00 44.79 3.62 R
2310 5017 0.382158 GCTCCAGGATTAAAAGGCGC 59.618 55.000 0.00 0.00 0.00 6.53 R
3383 6734 0.750249 GTTGGGGTGGTTCAGTTTGG 59.250 55.000 0.00 0.00 0.00 3.28 R
3997 7632 2.939103 CCGCAAAAGGTCCTCTTCTATG 59.061 50.000 0.00 0.00 33.94 2.23 R
4125 7760 4.910458 ACTAACCTTGTAATCTGCAGGT 57.090 40.909 15.13 2.68 0.00 4.00 R
4684 8403 3.466836 GTCTTGTTGACTCACATGTCCA 58.533 45.455 0.00 0.00 42.21 4.02 R
6286 10395 0.321122 AACAGGGAGAAGCTTCTGCG 60.321 55.000 33.18 25.10 45.36 5.18 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
34 35 1.276421 CCTAATGGGCGGAGATCGAAT 59.724 52.381 0.00 0.00 42.43 3.34
40 41 0.028110 GGCGGAGATCGAATGTTTGC 59.972 55.000 0.00 0.00 42.43 3.68
44 45 0.726827 GAGATCGAATGTTTGCCGCA 59.273 50.000 0.00 0.00 0.00 5.69
54 2571 1.228094 TTTGCCGCACTCACCATGA 60.228 52.632 0.00 0.00 0.00 3.07
57 2574 1.210155 GCCGCACTCACCATGAAAC 59.790 57.895 0.00 0.00 0.00 2.78
67 2584 6.672147 CACTCACCATGAAACTTTTTAGAGG 58.328 40.000 0.00 0.00 0.00 3.69
73 2590 5.922544 CCATGAAACTTTTTAGAGGTTGCTG 59.077 40.000 0.00 0.00 0.00 4.41
82 2599 7.706607 ACTTTTTAGAGGTTGCTGAACATTTTC 59.293 33.333 0.00 0.00 33.27 2.29
83 2600 5.705609 TTAGAGGTTGCTGAACATTTTCC 57.294 39.130 0.00 0.00 33.27 3.13
84 2601 3.837355 AGAGGTTGCTGAACATTTTCCT 58.163 40.909 0.00 0.00 33.27 3.36
85 2602 4.985538 AGAGGTTGCTGAACATTTTCCTA 58.014 39.130 0.00 0.00 33.27 2.94
86 2603 5.574188 AGAGGTTGCTGAACATTTTCCTAT 58.426 37.500 0.00 0.00 33.27 2.57
87 2604 6.721318 AGAGGTTGCTGAACATTTTCCTATA 58.279 36.000 0.00 0.00 33.27 1.31
88 2605 7.349598 AGAGGTTGCTGAACATTTTCCTATAT 58.650 34.615 0.00 0.00 33.27 0.86
90 2607 7.775120 AGGTTGCTGAACATTTTCCTATATTG 58.225 34.615 0.00 0.00 33.27 1.90
91 2608 6.476706 GGTTGCTGAACATTTTCCTATATTGC 59.523 38.462 0.00 0.00 33.27 3.56
92 2609 6.772360 TGCTGAACATTTTCCTATATTGCA 57.228 33.333 0.00 0.00 0.00 4.08
93 2610 7.350744 TGCTGAACATTTTCCTATATTGCAT 57.649 32.000 0.00 0.00 0.00 3.96
94 2611 7.204604 TGCTGAACATTTTCCTATATTGCATG 58.795 34.615 0.00 0.00 0.00 4.06
95 2612 7.068470 TGCTGAACATTTTCCTATATTGCATGA 59.932 33.333 0.00 0.00 0.00 3.07
97 2614 9.976511 CTGAACATTTTCCTATATTGCATGAAT 57.023 29.630 0.00 0.00 0.00 2.57
210 2727 0.679640 GGAAACCGGTCCATCATGCA 60.680 55.000 8.04 0.00 37.65 3.96
212 2729 1.066002 GAAACCGGTCCATCATGCATG 59.934 52.381 21.07 21.07 0.00 4.06
214 2731 1.527611 CCGGTCCATCATGCATGCT 60.528 57.895 22.25 9.87 0.00 3.79
215 2732 1.105167 CCGGTCCATCATGCATGCTT 61.105 55.000 22.25 10.16 0.00 3.91
216 2733 1.596603 CGGTCCATCATGCATGCTTA 58.403 50.000 22.25 5.34 0.00 3.09
217 2734 1.265095 CGGTCCATCATGCATGCTTAC 59.735 52.381 22.25 15.41 0.00 2.34
218 2735 1.265095 GGTCCATCATGCATGCTTACG 59.735 52.381 22.25 7.61 0.00 3.18
220 2737 0.949397 CCATCATGCATGCTTACGCT 59.051 50.000 22.25 0.00 36.97 5.07
222 2739 2.096069 CCATCATGCATGCTTACGCTAC 60.096 50.000 22.25 0.00 36.97 3.58
224 2741 1.202359 TCATGCATGCTTACGCTACGA 60.202 47.619 22.25 1.37 36.97 3.43
225 2742 1.071239 CATGCATGCTTACGCTACGAC 60.071 52.381 20.33 0.00 36.97 4.34
226 2743 0.804544 TGCATGCTTACGCTACGACC 60.805 55.000 20.33 0.00 36.97 4.79
227 2744 0.804544 GCATGCTTACGCTACGACCA 60.805 55.000 11.37 0.00 36.97 4.02
228 2745 1.635844 CATGCTTACGCTACGACCAA 58.364 50.000 0.00 0.00 36.97 3.67
229 2746 1.588404 CATGCTTACGCTACGACCAAG 59.412 52.381 0.00 0.00 36.97 3.61
230 2747 0.734942 TGCTTACGCTACGACCAAGC 60.735 55.000 14.20 14.20 38.75 4.01
231 2748 1.419107 GCTTACGCTACGACCAAGCC 61.419 60.000 11.68 0.47 36.60 4.35
232 2749 1.138047 CTTACGCTACGACCAAGCCG 61.138 60.000 0.00 0.00 36.60 5.52
233 2750 2.546645 TTACGCTACGACCAAGCCGG 62.547 60.000 0.00 0.00 42.50 6.13
270 2787 2.358737 CCAAGTGACTGGGCCGAC 60.359 66.667 0.00 0.00 32.32 4.79
294 2811 2.124695 GGTCCACGAGGCAATCCC 60.125 66.667 0.00 0.00 33.74 3.85
348 2879 4.980903 GCCGTGTGCGCCAAGTTG 62.981 66.667 4.18 0.00 36.67 3.16
441 2972 2.956964 GCAACTCGATCTCCGCCG 60.957 66.667 0.00 0.00 38.37 6.46
519 3089 3.522731 CGCCCTCGACCTCTCCAG 61.523 72.222 0.00 0.00 38.10 3.86
520 3090 3.844090 GCCCTCGACCTCTCCAGC 61.844 72.222 0.00 0.00 0.00 4.85
521 3091 3.151022 CCCTCGACCTCTCCAGCC 61.151 72.222 0.00 0.00 0.00 4.85
522 3092 3.151022 CCTCGACCTCTCCAGCCC 61.151 72.222 0.00 0.00 0.00 5.19
523 3093 3.522731 CTCGACCTCTCCAGCCCG 61.523 72.222 0.00 0.00 0.00 6.13
540 3110 4.779733 GGAGCTCCTCCCCGACCA 62.780 72.222 26.25 0.00 44.36 4.02
541 3111 3.462678 GAGCTCCTCCCCGACCAC 61.463 72.222 0.87 0.00 0.00 4.16
584 3158 2.998279 GCCCAAGGTGAGCATGTGC 61.998 63.158 0.00 0.00 42.49 4.57
694 3301 4.966168 TGTGGATGTTCCTAGCCTAACATA 59.034 41.667 13.24 1.46 44.27 2.29
770 3379 9.935241 ACATAAAACTGCTATCTATATGACAGG 57.065 33.333 0.00 0.00 0.00 4.00
773 3382 7.618019 AAACTGCTATCTATATGACAGGGAA 57.382 36.000 0.00 0.00 0.00 3.97
775 3384 7.618019 ACTGCTATCTATATGACAGGGAAAA 57.382 36.000 0.00 0.00 0.00 2.29
851 3461 6.892658 TGTCCACTTATTTTGCTATGTGTT 57.107 33.333 0.00 0.00 0.00 3.32
909 3527 2.037511 AGGTTTGCCATGTCCACATTTG 59.962 45.455 0.00 0.00 37.19 2.32
911 3529 3.465871 GTTTGCCATGTCCACATTTGTT 58.534 40.909 0.00 0.00 33.61 2.83
955 3573 7.459795 TGCATGTTATGTCCACTTCATAAAA 57.540 32.000 0.00 0.00 38.78 1.52
969 3592 1.668751 CATAAAACTACCGTGCGCCAT 59.331 47.619 4.18 0.00 0.00 4.40
1163 3795 1.613630 AGCCCACGAAGATCCAGGT 60.614 57.895 0.00 0.00 0.00 4.00
1195 3827 0.736325 CCACGCTCTCAAAGGTACCG 60.736 60.000 6.18 0.00 0.00 4.02
1442 4085 6.038603 CCTTCTTGTGACACATTTTCTTCTCA 59.961 38.462 9.55 0.00 0.00 3.27
1447 4090 5.991606 TGTGACACATTTTCTTCTCAGTAGG 59.008 40.000 3.56 0.00 0.00 3.18
1583 4226 4.387862 GGTAAGTGGTGTTGATACAACTCG 59.612 45.833 14.19 0.00 42.66 4.18
1600 4244 5.527582 ACAACTCGCTCTTTATTTGTTCTGT 59.472 36.000 0.00 0.00 0.00 3.41
1649 4293 3.282021 GGATGCACATACTGGAACATGT 58.718 45.455 0.00 0.00 38.20 3.21
1681 4325 1.989165 GCGCGGATCATACTTCTCATC 59.011 52.381 8.83 0.00 0.00 2.92
1798 4495 8.122952 GCATAGTGAAACATGGTTGTATCTAAC 58.877 37.037 0.00 0.00 41.43 2.34
1802 4499 9.601217 AGTGAAACATGGTTGTATCTAACTATC 57.399 33.333 0.00 0.00 41.43 2.08
2285 4992 1.819632 ATGTTGATTCGCTCGGGCC 60.820 57.895 0.00 0.00 34.44 5.80
2310 5017 2.849942 TCCACACTCAACCATCAACAG 58.150 47.619 0.00 0.00 0.00 3.16
2311 5018 1.267806 CCACACTCAACCATCAACAGC 59.732 52.381 0.00 0.00 0.00 4.40
2413 5134 1.897560 CCAACCTGAACCTTCTCCAC 58.102 55.000 0.00 0.00 0.00 4.02
2418 5139 2.907042 ACCTGAACCTTCTCCACTTAGG 59.093 50.000 0.00 0.00 39.47 2.69
2437 5158 1.405933 GGCAGCTTATTGGGCCTTTTG 60.406 52.381 4.53 0.00 43.09 2.44
2454 5180 5.354513 GCCTTTTGACTTAGGTTACCATCTC 59.645 44.000 3.51 0.00 33.91 2.75
2455 5181 6.712276 CCTTTTGACTTAGGTTACCATCTCT 58.288 40.000 3.51 0.00 0.00 3.10
2456 5182 7.580882 GCCTTTTGACTTAGGTTACCATCTCTA 60.581 40.741 3.51 0.00 33.91 2.43
2457 5183 7.982354 CCTTTTGACTTAGGTTACCATCTCTAG 59.018 40.741 3.51 0.00 0.00 2.43
2458 5184 8.660295 TTTTGACTTAGGTTACCATCTCTAGA 57.340 34.615 3.51 0.00 0.00 2.43
2459 5185 7.642082 TTGACTTAGGTTACCATCTCTAGAC 57.358 40.000 3.51 0.00 0.00 2.59
2574 5304 7.224297 TGCATATAGATTTTGTCCTAACTCCC 58.776 38.462 0.00 0.00 0.00 4.30
2580 5310 4.781775 TTTTGTCCTAACTCCCAAGTCA 57.218 40.909 0.00 0.00 33.48 3.41
2751 5724 5.180367 TGCGTCATTTCACTGAATTTTGA 57.820 34.783 0.00 0.00 0.00 2.69
2753 5726 6.038985 TGCGTCATTTCACTGAATTTTGAAA 58.961 32.000 11.17 11.17 43.89 2.69
2754 5727 6.198778 TGCGTCATTTCACTGAATTTTGAAAG 59.801 34.615 13.19 8.07 43.21 2.62
2755 5728 6.575132 CGTCATTTCACTGAATTTTGAAAGC 58.425 36.000 13.19 7.72 43.21 3.51
2756 5729 6.418819 CGTCATTTCACTGAATTTTGAAAGCT 59.581 34.615 13.19 0.00 43.21 3.74
2757 5730 7.591057 CGTCATTTCACTGAATTTTGAAAGCTA 59.409 33.333 13.19 3.33 43.21 3.32
2758 5731 8.694394 GTCATTTCACTGAATTTTGAAAGCTAC 58.306 33.333 13.19 9.01 43.21 3.58
2759 5732 8.632679 TCATTTCACTGAATTTTGAAAGCTACT 58.367 29.630 13.19 0.00 43.21 2.57
2763 5736 6.542005 TCACTGAATTTTGAAAGCTACTGTGA 59.458 34.615 0.00 0.00 0.00 3.58
2764 5737 7.229306 TCACTGAATTTTGAAAGCTACTGTGAT 59.771 33.333 0.00 0.00 0.00 3.06
2765 5738 7.325338 CACTGAATTTTGAAAGCTACTGTGATG 59.675 37.037 0.00 0.00 0.00 3.07
2766 5739 7.229306 ACTGAATTTTGAAAGCTACTGTGATGA 59.771 33.333 0.00 0.00 0.00 2.92
2768 5741 6.882610 ATTTTGAAAGCTACTGTGATGACA 57.117 33.333 0.00 0.00 0.00 3.58
2771 5744 4.960938 TGAAAGCTACTGTGATGACAAGT 58.039 39.130 0.00 0.00 0.00 3.16
2773 5746 2.693069 AGCTACTGTGATGACAAGTGC 58.307 47.619 0.00 0.00 0.00 4.40
2774 5747 2.301296 AGCTACTGTGATGACAAGTGCT 59.699 45.455 0.00 1.12 0.00 4.40
2775 5748 3.511540 AGCTACTGTGATGACAAGTGCTA 59.488 43.478 4.37 0.00 0.00 3.49
2776 5749 3.614616 GCTACTGTGATGACAAGTGCTAC 59.385 47.826 0.00 0.00 0.00 3.58
2777 5750 3.045601 ACTGTGATGACAAGTGCTACC 57.954 47.619 0.00 0.00 0.00 3.18
2778 5751 2.634940 ACTGTGATGACAAGTGCTACCT 59.365 45.455 0.00 0.00 0.00 3.08
2779 5752 3.071602 ACTGTGATGACAAGTGCTACCTT 59.928 43.478 0.00 0.00 0.00 3.50
2780 5753 4.283467 ACTGTGATGACAAGTGCTACCTTA 59.717 41.667 0.00 0.00 0.00 2.69
2781 5754 5.046304 ACTGTGATGACAAGTGCTACCTTAT 60.046 40.000 0.00 0.00 0.00 1.73
2782 5755 6.154534 ACTGTGATGACAAGTGCTACCTTATA 59.845 38.462 0.00 0.00 0.00 0.98
2783 5756 6.941857 TGTGATGACAAGTGCTACCTTATAA 58.058 36.000 0.00 0.00 0.00 0.98
2784 5757 7.041721 TGTGATGACAAGTGCTACCTTATAAG 58.958 38.462 5.43 5.43 0.00 1.73
2785 5758 7.093509 TGTGATGACAAGTGCTACCTTATAAGA 60.094 37.037 14.28 0.00 0.00 2.10
2786 5759 7.222999 GTGATGACAAGTGCTACCTTATAAGAC 59.777 40.741 14.28 3.77 0.00 3.01
2787 5760 5.974108 TGACAAGTGCTACCTTATAAGACC 58.026 41.667 14.28 0.22 0.00 3.85
2788 5761 5.105064 TGACAAGTGCTACCTTATAAGACCC 60.105 44.000 14.28 0.55 0.00 4.46
2789 5762 4.781087 ACAAGTGCTACCTTATAAGACCCA 59.219 41.667 14.28 3.03 0.00 4.51
2790 5763 5.249852 ACAAGTGCTACCTTATAAGACCCAA 59.750 40.000 14.28 0.00 0.00 4.12
2791 5764 5.615925 AGTGCTACCTTATAAGACCCAAG 57.384 43.478 14.28 4.95 0.00 3.61
2792 5765 5.278061 AGTGCTACCTTATAAGACCCAAGA 58.722 41.667 14.28 0.00 0.00 3.02
2793 5766 5.905913 AGTGCTACCTTATAAGACCCAAGAT 59.094 40.000 14.28 0.00 0.00 2.40
2794 5767 5.992217 GTGCTACCTTATAAGACCCAAGATG 59.008 44.000 14.28 0.00 0.00 2.90
2795 5768 4.998033 GCTACCTTATAAGACCCAAGATGC 59.002 45.833 14.28 3.17 0.00 3.91
2796 5769 4.073293 ACCTTATAAGACCCAAGATGCG 57.927 45.455 14.28 0.00 0.00 4.73
2797 5770 3.454812 ACCTTATAAGACCCAAGATGCGT 59.545 43.478 14.28 0.00 0.00 5.24
2798 5771 4.058817 CCTTATAAGACCCAAGATGCGTC 58.941 47.826 14.28 0.00 0.00 5.19
2799 5772 4.442893 CCTTATAAGACCCAAGATGCGTCA 60.443 45.833 14.28 0.00 0.00 4.35
2800 5773 3.845781 ATAAGACCCAAGATGCGTCAT 57.154 42.857 8.99 0.00 0.00 3.06
2801 5774 2.496899 AAGACCCAAGATGCGTCATT 57.503 45.000 8.99 0.00 0.00 2.57
2802 5775 2.496899 AGACCCAAGATGCGTCATTT 57.503 45.000 8.99 0.00 0.00 2.32
2803 5776 2.359900 AGACCCAAGATGCGTCATTTC 58.640 47.619 8.99 0.00 0.00 2.17
2804 5777 2.083774 GACCCAAGATGCGTCATTTCA 58.916 47.619 8.99 0.00 0.00 2.69
2805 5778 1.812571 ACCCAAGATGCGTCATTTCAC 59.187 47.619 8.99 0.00 0.00 3.18
2806 5779 2.086869 CCCAAGATGCGTCATTTCACT 58.913 47.619 8.99 0.00 0.00 3.41
2807 5780 2.159476 CCCAAGATGCGTCATTTCACTG 60.159 50.000 8.99 0.00 0.00 3.66
2808 5781 2.743664 CCAAGATGCGTCATTTCACTGA 59.256 45.455 8.99 0.00 0.00 3.41
2809 5782 3.376234 CCAAGATGCGTCATTTCACTGAT 59.624 43.478 8.99 0.00 0.00 2.90
2810 5783 4.340263 CAAGATGCGTCATTTCACTGATG 58.660 43.478 8.99 0.00 35.64 3.07
2811 5784 3.865446 AGATGCGTCATTTCACTGATGA 58.135 40.909 8.99 0.00 34.67 2.92
2812 5785 3.620374 AGATGCGTCATTTCACTGATGAC 59.380 43.478 8.99 7.07 46.21 3.06
2821 5794 7.601073 TCATTTCACTGATGACAAGTGATAC 57.399 36.000 10.12 0.00 41.43 2.24
2822 5795 6.595326 TCATTTCACTGATGACAAGTGATACC 59.405 38.462 10.12 0.00 41.43 2.73
2823 5796 5.482163 TTCACTGATGACAAGTGATACCA 57.518 39.130 10.12 0.00 41.43 3.25
2824 5797 5.682234 TCACTGATGACAAGTGATACCAT 57.318 39.130 5.97 0.00 37.61 3.55
2825 5798 6.790232 TCACTGATGACAAGTGATACCATA 57.210 37.500 5.97 0.00 37.61 2.74
2834 5807 6.015095 TGACAAGTGATACCATATCTAGCAGG 60.015 42.308 0.00 0.00 0.00 4.85
2869 5842 2.040278 TGTGCAAGATAAGGCCAAGACT 59.960 45.455 5.01 0.00 0.00 3.24
3067 6325 6.581712 ACTTGGTACACATTCTTTGCATTTT 58.418 32.000 0.00 0.00 39.29 1.82
3324 6602 4.878397 GCAGTGCTATCCTGAAGTGTTAAT 59.122 41.667 8.18 0.00 31.38 1.40
3495 6849 7.868922 TGTAATAGTTTCTTCGTTGCAAGTAGA 59.131 33.333 0.00 0.00 0.00 2.59
3496 6850 7.724305 AATAGTTTCTTCGTTGCAAGTAGAA 57.276 32.000 0.00 6.56 0.00 2.10
3576 6930 7.308435 GGAACCTTCATTGTCAACTATTTCTG 58.692 38.462 0.00 0.00 0.00 3.02
3880 7515 5.698089 TGTGTTTTTGTTTGACTGAATGCAA 59.302 32.000 0.00 0.00 0.00 4.08
3953 7588 3.456644 TCAGAAACCCTGTCAAGGTAACA 59.543 43.478 0.00 0.00 42.74 2.41
3985 7620 9.733556 TCTTTGTAGTTTAGGCATTCAATAAGA 57.266 29.630 0.00 0.00 0.00 2.10
3997 7632 6.399986 GGCATTCAATAAGAAGCAAAACGTTC 60.400 38.462 0.00 0.00 40.15 3.95
4125 7760 8.362639 ACACTTAAAGAAGAGTGGTATTTCGTA 58.637 33.333 8.20 0.00 45.78 3.43
4150 7785 5.352569 CCTGCAGATTACAAGGTTAGTTCTG 59.647 44.000 17.39 0.00 33.86 3.02
4154 7789 5.705441 CAGATTACAAGGTTAGTTCTGGCAA 59.295 40.000 0.00 0.00 0.00 4.52
4322 8021 1.195115 CCTTGGACCGAGATTCTCCA 58.805 55.000 10.67 0.00 31.94 3.86
4447 8149 5.086104 ACCGTAGAGCAATTGTTCTATGT 57.914 39.130 32.34 26.81 40.82 2.29
4684 8403 2.093288 AGCATGACCATGATCTTCGTGT 60.093 45.455 13.67 0.00 41.20 4.49
4689 8408 1.623311 ACCATGATCTTCGTGTGGACA 59.377 47.619 0.00 0.00 31.62 4.02
4986 9037 5.516339 GGAATTCAACATCCTTATTTGCACG 59.484 40.000 7.93 0.00 32.75 5.34
5118 9191 3.064408 TGTCGAGAAGATCATGCATTTGC 59.936 43.478 0.00 0.00 42.50 3.68
5289 9364 6.616577 TCCTTGGTAATAGTTTCCCTTGTTT 58.383 36.000 0.00 0.00 0.00 2.83
5447 9522 5.130975 AGAGGATTGCACTGATGGTATGTAA 59.869 40.000 0.00 0.00 0.00 2.41
5453 9528 4.080638 TGCACTGATGGTATGTAATCCACA 60.081 41.667 0.00 0.00 42.69 4.17
5457 9532 5.070981 ACTGATGGTATGTAATCCACAGAGG 59.929 44.000 15.09 0.00 41.51 3.69
5468 9544 2.726821 TCCACAGAGGAATCCATTTGC 58.273 47.619 0.61 0.00 45.65 3.68
5518 9594 4.626081 ACAGCTGCACCGACACCC 62.626 66.667 15.27 0.00 0.00 4.61
5529 9605 1.641123 CCGACACCCGTTACCATTGC 61.641 60.000 0.00 0.00 36.31 3.56
5540 9617 7.012515 CACCCGTTACCATTGCTTGTTATTATA 59.987 37.037 0.00 0.00 0.00 0.98
5586 9666 2.372172 GGTCACAAGAGGAGGAGGAAAA 59.628 50.000 0.00 0.00 0.00 2.29
5588 9668 3.045634 TCACAAGAGGAGGAGGAAAACA 58.954 45.455 0.00 0.00 0.00 2.83
5598 9678 1.619332 GGAGGAAAACAGAGGACGAGT 59.381 52.381 0.00 0.00 0.00 4.18
5669 9752 1.153842 GAAATCAAAAGGGCGGCGG 60.154 57.895 9.78 0.00 0.00 6.13
5907 10003 7.078228 AGATTTCACTTTTACATCAAACTCGC 58.922 34.615 0.00 0.00 0.00 5.03
5963 10067 2.291217 ACCCTGCAATCTTCTTTCCCTC 60.291 50.000 0.00 0.00 0.00 4.30
5964 10068 2.373224 CCTGCAATCTTCTTTCCCTCC 58.627 52.381 0.00 0.00 0.00 4.30
6025 10129 1.445410 CCGGCGATGTCGAAAGTGA 60.445 57.895 9.30 0.00 43.02 3.41
6026 10130 1.011968 CCGGCGATGTCGAAAGTGAA 61.012 55.000 9.30 0.00 43.02 3.18
6034 10138 5.728507 GCGATGTCGAAAGTGAATTTTAGAC 59.271 40.000 6.60 7.59 43.02 2.59
6152 10256 2.892425 CGCGCCTCCATCTTCCAC 60.892 66.667 0.00 0.00 0.00 4.02
6213 10318 1.748122 CCTTCTGCAAGCATCGCCT 60.748 57.895 0.00 0.00 0.00 5.52
6218 10323 2.158559 TCTGCAAGCATCGCCTTAAAA 58.841 42.857 0.00 0.00 0.00 1.52
6239 10344 1.990160 AACGCCTGGAACTCCCAACA 61.990 55.000 0.00 0.00 46.07 3.33
6252 10357 3.223674 TCCCAACAGGGAGAAGAAAAC 57.776 47.619 0.00 0.00 46.79 2.43
6259 10366 4.777463 ACAGGGAGAAGAAAACGAAGAAA 58.223 39.130 0.00 0.00 0.00 2.52
6269 10376 6.234723 AGAAAACGAAGAAATGAAGAGAGC 57.765 37.500 0.00 0.00 0.00 4.09
6286 10395 2.093235 AGAGCAAGCTTACCCTGATGAC 60.093 50.000 0.00 0.00 0.00 3.06
6293 10402 2.544685 CTTACCCTGATGACGCAGAAG 58.455 52.381 0.00 0.00 38.14 2.85
6299 10413 1.925847 CTGATGACGCAGAAGCTTCTC 59.074 52.381 26.18 18.38 39.56 2.87
6301 10415 0.107945 ATGACGCAGAAGCTTCTCCC 60.108 55.000 26.18 17.92 39.56 4.30
6302 10416 1.188219 TGACGCAGAAGCTTCTCCCT 61.188 55.000 26.18 7.35 39.56 4.20
6303 10417 0.739112 GACGCAGAAGCTTCTCCCTG 60.739 60.000 26.18 16.56 36.22 4.45
6304 10418 1.294780 CGCAGAAGCTTCTCCCTGT 59.705 57.895 26.18 1.47 39.10 4.00
6306 10420 1.066858 CGCAGAAGCTTCTCCCTGTTA 60.067 52.381 26.18 0.00 39.10 2.41
6307 10421 2.351455 GCAGAAGCTTCTCCCTGTTAC 58.649 52.381 26.18 5.00 34.74 2.50
6310 10424 3.007398 CAGAAGCTTCTCCCTGTTACTGT 59.993 47.826 26.18 0.00 34.74 3.55
6311 10425 3.007398 AGAAGCTTCTCCCTGTTACTGTG 59.993 47.826 23.49 0.00 29.94 3.66
6312 10426 2.609747 AGCTTCTCCCTGTTACTGTGA 58.390 47.619 0.00 0.00 0.00 3.58
6317 10438 4.808414 TCTCCCTGTTACTGTGATGAAG 57.192 45.455 0.00 0.00 0.00 3.02
6351 10472 2.176798 AGGAATTGGTGTTGGGAGTTGA 59.823 45.455 0.00 0.00 0.00 3.18
6354 10475 2.638480 TTGGTGTTGGGAGTTGAGAG 57.362 50.000 0.00 0.00 0.00 3.20
6369 10490 0.174617 GAGAGCCTGCAGGTAGACAC 59.825 60.000 32.81 15.72 37.57 3.67
6395 10516 4.636206 AGAAATAGTTTGACGGAAGATGCC 59.364 41.667 0.00 0.00 0.00 4.40
6459 10587 2.601314 CGTCGCAACAAATATCTTCCGA 59.399 45.455 0.00 0.00 0.00 4.55
6465 10593 7.694784 GTCGCAACAAATATCTTCCGATTTTTA 59.305 33.333 0.00 0.00 32.09 1.52
6468 10596 8.268738 GCAACAAATATCTTCCGATTTTTATGC 58.731 33.333 0.00 0.00 36.58 3.14
6557 10697 4.584743 GCTATCCCCTACCAAAAATTCCAG 59.415 45.833 0.00 0.00 0.00 3.86
6605 10745 8.157476 AGTGAATAAGCCGAAATATCTGGTATT 58.843 33.333 0.00 0.00 34.46 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.528076 ATGGTGAGTGCGGCAAACA 60.528 52.632 3.23 5.17 0.00 2.83
40 41 1.238439 AAGTTTCATGGTGAGTGCGG 58.762 50.000 0.00 0.00 0.00 5.69
44 45 6.365520 ACCTCTAAAAAGTTTCATGGTGAGT 58.634 36.000 0.00 0.00 0.00 3.41
54 2571 6.524101 TGTTCAGCAACCTCTAAAAAGTTT 57.476 33.333 0.00 0.00 0.00 2.66
57 2574 7.169813 GGAAAATGTTCAGCAACCTCTAAAAAG 59.830 37.037 0.00 0.00 35.25 2.27
67 2584 7.035004 TGCAATATAGGAAAATGTTCAGCAAC 58.965 34.615 0.00 0.00 35.25 4.17
174 2691 5.276631 CGGTTTCCGTTCATTTTTCCTTTTG 60.277 40.000 0.00 0.00 42.73 2.44
184 2701 0.108963 TGGACCGGTTTCCGTTCATT 59.891 50.000 9.42 0.00 46.80 2.57
214 2731 1.153978 CGGCTTGGTCGTAGCGTAA 60.154 57.895 0.00 0.00 39.54 3.18
215 2732 2.486504 CGGCTTGGTCGTAGCGTA 59.513 61.111 0.00 0.00 39.54 4.42
216 2733 4.430765 CCGGCTTGGTCGTAGCGT 62.431 66.667 0.00 0.00 39.54 5.07
225 2742 4.760047 CCTCGTGGACCGGCTTGG 62.760 72.222 0.00 0.00 46.41 3.61
226 2743 4.760047 CCCTCGTGGACCGGCTTG 62.760 72.222 0.00 0.00 37.11 4.01
270 2787 4.760047 CCTCGTGGACCGGCTTGG 62.760 72.222 0.00 0.00 46.41 3.61
294 2811 1.384222 GGCATAAACCCCAGCGGAAG 61.384 60.000 0.00 0.00 34.64 3.46
295 2812 1.379309 GGCATAAACCCCAGCGGAA 60.379 57.895 0.00 0.00 34.64 4.30
348 2879 1.065709 TGGTTATGCGAGGGGAGAAAC 60.066 52.381 0.00 0.00 0.00 2.78
426 2957 4.208686 GGCGGCGGAGATCGAGTT 62.209 66.667 9.78 0.00 42.43 3.01
524 3094 3.462678 GTGGTCGGGGAGGAGCTC 61.463 72.222 4.71 4.71 35.52 4.09
527 3097 2.760385 GAGGTGGTCGGGGAGGAG 60.760 72.222 0.00 0.00 0.00 3.69
528 3098 4.393778 GGAGGTGGTCGGGGAGGA 62.394 72.222 0.00 0.00 0.00 3.71
541 3111 3.839432 GAACGAGCTCCGGGGAGG 61.839 72.222 4.80 0.00 43.93 4.30
625 3199 1.401409 CGAATTGCACACACATCCACC 60.401 52.381 0.00 0.00 0.00 4.61
694 3301 6.595716 GTCCTAGTTCTTGTTGTCATTAGCAT 59.404 38.462 0.00 0.00 0.00 3.79
817 3427 9.810231 GCAAAATAAGTGGACATAACAAAATTG 57.190 29.630 0.00 0.00 0.00 2.32
818 3428 9.777297 AGCAAAATAAGTGGACATAACAAAATT 57.223 25.926 0.00 0.00 0.00 1.82
821 3431 9.853555 CATAGCAAAATAAGTGGACATAACAAA 57.146 29.630 0.00 0.00 0.00 2.83
822 3432 9.019656 ACATAGCAAAATAAGTGGACATAACAA 57.980 29.630 0.00 0.00 0.00 2.83
823 3433 8.458052 CACATAGCAAAATAAGTGGACATAACA 58.542 33.333 0.00 0.00 0.00 2.41
826 3436 8.574251 AACACATAGCAAAATAAGTGGACATA 57.426 30.769 0.00 0.00 30.53 2.29
909 3527 6.035650 TGCAAGTGCTCTCGTATACATAAAAC 59.964 38.462 4.69 0.00 42.66 2.43
911 3529 5.656480 TGCAAGTGCTCTCGTATACATAAA 58.344 37.500 4.69 0.00 42.66 1.40
969 3592 3.294493 GTTTTGCTCTGCGGGGCA 61.294 61.111 18.43 18.43 36.92 5.36
973 3596 2.252260 CGTGGTTTTGCTCTGCGG 59.748 61.111 0.00 0.00 0.00 5.69
1195 3827 6.152323 ACATATAAATGGCTGAAGATGATGCC 59.848 38.462 0.00 0.00 45.10 4.40
1293 3929 2.650116 CCGACCCTGTCTGTCCCAG 61.650 68.421 0.00 0.00 0.00 4.45
1304 3940 2.284699 CCTGTCTTCCCCGACCCT 60.285 66.667 0.00 0.00 32.97 4.34
1442 4085 1.416401 CCCACACAGACACAACCTACT 59.584 52.381 0.00 0.00 0.00 2.57
1447 4090 0.179045 AGCTCCCACACAGACACAAC 60.179 55.000 0.00 0.00 0.00 3.32
1627 4271 3.281158 CATGTTCCAGTATGTGCATCCA 58.719 45.455 0.00 0.00 0.00 3.41
1649 4293 2.495366 ATCCGCGCAAGGACACGTAA 62.495 55.000 8.75 0.00 44.07 3.18
1681 4325 7.435068 ACCAGCAATTACAACAGTTAGTTAG 57.565 36.000 0.00 0.00 38.74 2.34
1850 4553 3.080300 TGAAATTGTCGGTATGGGCTT 57.920 42.857 0.00 0.00 0.00 4.35
2207 4914 3.019564 GCACAAAGCATCCTGAACCTAT 58.980 45.455 0.00 0.00 44.79 2.57
2208 4915 2.436417 GCACAAAGCATCCTGAACCTA 58.564 47.619 0.00 0.00 44.79 3.08
2209 4916 1.251251 GCACAAAGCATCCTGAACCT 58.749 50.000 0.00 0.00 44.79 3.50
2210 4917 3.800628 GCACAAAGCATCCTGAACC 57.199 52.632 0.00 0.00 44.79 3.62
2276 4983 2.749839 TGGATTTTGGCCCGAGCG 60.750 61.111 0.00 0.00 41.24 5.03
2285 4992 4.852134 TGATGGTTGAGTGTGGATTTTG 57.148 40.909 0.00 0.00 0.00 2.44
2310 5017 0.382158 GCTCCAGGATTAAAAGGCGC 59.618 55.000 0.00 0.00 0.00 6.53
2311 5018 1.750193 TGCTCCAGGATTAAAAGGCG 58.250 50.000 0.00 0.00 0.00 5.52
2413 5134 1.322442 GGCCCAATAAGCTGCCTAAG 58.678 55.000 3.33 0.00 40.77 2.18
2418 5139 1.550072 TCAAAAGGCCCAATAAGCTGC 59.450 47.619 0.00 0.00 0.00 5.25
2437 5158 6.367161 AGGTCTAGAGATGGTAACCTAAGTC 58.633 44.000 0.00 0.00 35.41 3.01
2454 5180 9.877178 ATTCACAAACAGAATTACTAGGTCTAG 57.123 33.333 3.65 3.65 34.55 2.43
2456 5182 9.654663 GTATTCACAAACAGAATTACTAGGTCT 57.345 33.333 0.00 0.00 37.02 3.85
2457 5183 9.431887 TGTATTCACAAACAGAATTACTAGGTC 57.568 33.333 0.00 0.00 37.02 3.85
2458 5184 9.216117 GTGTATTCACAAACAGAATTACTAGGT 57.784 33.333 0.00 0.00 43.37 3.08
2459 5185 9.436957 AGTGTATTCACAAACAGAATTACTAGG 57.563 33.333 5.21 0.00 46.01 3.02
2692 5582 3.832490 AGGTAGCACTTGTCATCACAGTA 59.168 43.478 0.00 0.00 32.71 2.74
2751 5724 3.499918 GCACTTGTCATCACAGTAGCTTT 59.500 43.478 0.00 0.00 32.71 3.51
2753 5726 2.301296 AGCACTTGTCATCACAGTAGCT 59.699 45.455 0.00 0.00 32.71 3.32
2754 5727 2.693069 AGCACTTGTCATCACAGTAGC 58.307 47.619 0.00 0.00 32.71 3.58
2755 5728 4.081972 AGGTAGCACTTGTCATCACAGTAG 60.082 45.833 0.00 0.00 32.71 2.57
2756 5729 3.832490 AGGTAGCACTTGTCATCACAGTA 59.168 43.478 0.00 0.00 32.71 2.74
2757 5730 2.634940 AGGTAGCACTTGTCATCACAGT 59.365 45.455 0.00 0.00 32.71 3.55
2758 5731 3.325293 AGGTAGCACTTGTCATCACAG 57.675 47.619 0.00 0.00 32.71 3.66
2759 5732 3.769739 AAGGTAGCACTTGTCATCACA 57.230 42.857 0.00 0.00 0.00 3.58
2763 5736 6.408206 GGGTCTTATAAGGTAGCACTTGTCAT 60.408 42.308 12.54 0.00 32.02 3.06
2764 5737 5.105064 GGGTCTTATAAGGTAGCACTTGTCA 60.105 44.000 12.54 0.00 32.02 3.58
2765 5738 5.105064 TGGGTCTTATAAGGTAGCACTTGTC 60.105 44.000 12.54 0.00 32.02 3.18
2766 5739 4.781087 TGGGTCTTATAAGGTAGCACTTGT 59.219 41.667 12.54 0.00 32.02 3.16
2768 5741 5.724854 TCTTGGGTCTTATAAGGTAGCACTT 59.275 40.000 12.54 0.00 34.52 3.16
2771 5744 5.454755 GCATCTTGGGTCTTATAAGGTAGCA 60.455 44.000 12.54 0.00 0.00 3.49
2773 5746 5.221461 ACGCATCTTGGGTCTTATAAGGTAG 60.221 44.000 12.54 3.92 39.47 3.18
2774 5747 4.652421 ACGCATCTTGGGTCTTATAAGGTA 59.348 41.667 12.54 0.00 39.47 3.08
2775 5748 3.454812 ACGCATCTTGGGTCTTATAAGGT 59.545 43.478 12.54 0.00 39.47 3.50
2776 5749 4.073293 ACGCATCTTGGGTCTTATAAGG 57.927 45.455 12.54 0.00 39.47 2.69
2785 5758 1.812571 GTGAAATGACGCATCTTGGGT 59.187 47.619 0.00 0.00 46.65 4.51
2786 5759 2.086869 AGTGAAATGACGCATCTTGGG 58.913 47.619 0.00 0.00 36.28 4.12
2787 5760 2.743664 TCAGTGAAATGACGCATCTTGG 59.256 45.455 0.00 0.00 0.00 3.61
2788 5761 4.093850 TCATCAGTGAAATGACGCATCTTG 59.906 41.667 0.00 0.00 30.46 3.02
2789 5762 4.093998 GTCATCAGTGAAATGACGCATCTT 59.906 41.667 10.34 0.00 42.44 2.40
2790 5763 3.620374 GTCATCAGTGAAATGACGCATCT 59.380 43.478 10.34 0.00 42.44 2.90
2791 5764 3.933031 GTCATCAGTGAAATGACGCATC 58.067 45.455 10.34 0.00 42.44 3.91
2797 5770 6.595326 GGTATCACTTGTCATCAGTGAAATGA 59.405 38.462 10.64 0.00 44.32 2.57
2798 5771 6.372381 TGGTATCACTTGTCATCAGTGAAATG 59.628 38.462 10.64 0.00 44.32 2.32
2799 5772 6.475504 TGGTATCACTTGTCATCAGTGAAAT 58.524 36.000 10.64 0.23 44.32 2.17
2800 5773 5.863965 TGGTATCACTTGTCATCAGTGAAA 58.136 37.500 10.64 0.00 44.32 2.69
2801 5774 5.482163 TGGTATCACTTGTCATCAGTGAA 57.518 39.130 10.64 0.42 44.32 3.18
2802 5775 5.682234 ATGGTATCACTTGTCATCAGTGA 57.318 39.130 9.30 9.30 45.07 3.41
2803 5776 7.440198 AGATATGGTATCACTTGTCATCAGTG 58.560 38.462 0.00 0.00 35.10 3.66
2804 5777 7.609097 AGATATGGTATCACTTGTCATCAGT 57.391 36.000 0.38 0.00 0.00 3.41
2805 5778 7.758980 GCTAGATATGGTATCACTTGTCATCAG 59.241 40.741 0.00 0.00 0.00 2.90
2806 5779 7.233348 TGCTAGATATGGTATCACTTGTCATCA 59.767 37.037 0.00 0.00 0.00 3.07
2807 5780 7.606349 TGCTAGATATGGTATCACTTGTCATC 58.394 38.462 0.00 0.00 0.00 2.92
2808 5781 7.310299 CCTGCTAGATATGGTATCACTTGTCAT 60.310 40.741 0.00 0.00 0.00 3.06
2809 5782 6.015095 CCTGCTAGATATGGTATCACTTGTCA 60.015 42.308 0.00 0.00 0.00 3.58
2810 5783 6.393990 CCTGCTAGATATGGTATCACTTGTC 58.606 44.000 0.00 0.00 0.00 3.18
2811 5784 5.279708 GCCTGCTAGATATGGTATCACTTGT 60.280 44.000 0.00 0.00 0.00 3.16
2812 5785 5.174395 GCCTGCTAGATATGGTATCACTTG 58.826 45.833 0.00 0.00 0.00 3.16
2813 5786 4.840680 TGCCTGCTAGATATGGTATCACTT 59.159 41.667 0.00 0.00 0.00 3.16
2814 5787 4.420206 TGCCTGCTAGATATGGTATCACT 58.580 43.478 0.00 0.00 0.00 3.41
2815 5788 4.808414 TGCCTGCTAGATATGGTATCAC 57.192 45.455 0.00 0.00 0.00 3.06
2816 5789 4.162888 CCATGCCTGCTAGATATGGTATCA 59.837 45.833 0.00 0.00 34.88 2.15
2817 5790 4.444022 CCCATGCCTGCTAGATATGGTATC 60.444 50.000 0.00 0.00 37.24 2.24
2818 5791 3.457380 CCCATGCCTGCTAGATATGGTAT 59.543 47.826 0.00 0.00 37.24 2.73
2819 5792 2.840038 CCCATGCCTGCTAGATATGGTA 59.160 50.000 0.00 0.00 37.24 3.25
2820 5793 1.632409 CCCATGCCTGCTAGATATGGT 59.368 52.381 0.00 0.00 37.24 3.55
2821 5794 1.911357 TCCCATGCCTGCTAGATATGG 59.089 52.381 0.00 0.00 38.37 2.74
2822 5795 2.570752 AGTCCCATGCCTGCTAGATATG 59.429 50.000 0.00 0.00 0.00 1.78
2823 5796 2.913203 AGTCCCATGCCTGCTAGATAT 58.087 47.619 0.00 0.00 0.00 1.63
2824 5797 2.369860 CAAGTCCCATGCCTGCTAGATA 59.630 50.000 0.00 0.00 0.00 1.98
2825 5798 1.142465 CAAGTCCCATGCCTGCTAGAT 59.858 52.381 0.00 0.00 0.00 1.98
2834 5807 2.639327 GCACACCCAAGTCCCATGC 61.639 63.158 0.00 0.00 0.00 4.06
2869 5842 3.304659 GCTCTTTTTGTCTGCGATGGAAA 60.305 43.478 0.00 0.00 0.00 3.13
3129 6389 3.885297 CCAAATCATGTACCTGACATCCC 59.115 47.826 2.71 0.00 46.33 3.85
3150 6410 7.330700 TGTCAAAAGTGAAAATTCAACTGAACC 59.669 33.333 0.00 0.00 39.21 3.62
3152 6412 8.087750 ACTGTCAAAAGTGAAAATTCAACTGAA 58.912 29.630 0.00 0.00 39.21 3.02
3154 6414 7.816945 ACTGTCAAAAGTGAAAATTCAACTG 57.183 32.000 0.00 0.00 39.21 3.16
3379 6730 1.047801 GGGTGGTTCAGTTTGGCAAT 58.952 50.000 0.00 0.00 0.00 3.56
3383 6734 0.750249 GTTGGGGTGGTTCAGTTTGG 59.250 55.000 0.00 0.00 0.00 3.28
3576 6930 6.205464 TGTGGAGGTATACGCTAGTTATGTAC 59.795 42.308 0.00 0.00 0.00 2.90
3825 7179 3.670627 GCCGTGAAGCACCAATTAGAAAG 60.671 47.826 0.00 0.00 0.00 2.62
3880 7515 5.010213 TGCAAAGAAAACCCGTAAGCTATTT 59.990 36.000 0.00 0.00 0.00 1.40
3953 7588 9.077885 TGAATGCCTAAACTACAAAGAAGAATT 57.922 29.630 0.00 0.00 0.00 2.17
3985 7620 5.179555 GTCCTCTTCTATGAACGTTTTGCTT 59.820 40.000 0.46 0.00 0.00 3.91
3997 7632 2.939103 CCGCAAAAGGTCCTCTTCTATG 59.061 50.000 0.00 0.00 33.94 2.23
4125 7760 4.910458 ACTAACCTTGTAATCTGCAGGT 57.090 40.909 15.13 2.68 0.00 4.00
4188 7826 7.336161 TGGTATTGAGAAAAAGAAACGGAAA 57.664 32.000 0.00 0.00 0.00 3.13
4684 8403 3.466836 GTCTTGTTGACTCACATGTCCA 58.533 45.455 0.00 0.00 42.21 4.02
4913 8964 6.173339 CCTAGTCTTTTGTCCTGATAAAGCA 58.827 40.000 0.00 0.00 0.00 3.91
4914 8965 5.065346 GCCTAGTCTTTTGTCCTGATAAAGC 59.935 44.000 0.00 0.00 0.00 3.51
5076 9127 5.514274 ACAATAAAGGCAATATCCGTTGG 57.486 39.130 0.00 0.00 0.00 3.77
5197 9272 4.478206 AGATACAGCATATCCCGATTGG 57.522 45.455 4.78 0.00 0.00 3.16
5289 9364 0.836606 TGTGTGCAAGGGAGACAAGA 59.163 50.000 0.00 0.00 0.00 3.02
5447 9522 3.294214 GCAAATGGATTCCTCTGTGGAT 58.706 45.455 3.95 0.00 45.68 3.41
5453 9528 3.350833 GACACTGCAAATGGATTCCTCT 58.649 45.455 3.95 0.00 0.00 3.69
5457 9532 5.581126 TTATGGACACTGCAAATGGATTC 57.419 39.130 2.90 0.00 0.00 2.52
5462 9537 5.957798 AGACAATTATGGACACTGCAAATG 58.042 37.500 0.00 0.00 0.00 2.32
5468 9544 4.253685 ACGGAAGACAATTATGGACACTG 58.746 43.478 0.00 0.00 0.00 3.66
5518 9594 9.594038 GTCATATAATAACAAGCAATGGTAACG 57.406 33.333 0.00 0.00 34.13 3.18
5540 9617 3.306364 CGTCCTCCTTCAGTTTCTGTCAT 60.306 47.826 0.00 0.00 32.61 3.06
5586 9666 4.590918 TCTTCTTCATACTCGTCCTCTGT 58.409 43.478 0.00 0.00 0.00 3.41
5588 9668 5.502079 TCTTCTTCTTCATACTCGTCCTCT 58.498 41.667 0.00 0.00 0.00 3.69
5598 9678 5.026121 TGGAGCTTCCTCTTCTTCTTCATA 58.974 41.667 0.00 0.00 37.46 2.15
5669 9752 5.071115 AGGAGGTTCTTCCAAGATATGCTAC 59.929 44.000 3.92 0.00 39.84 3.58
5754 9837 4.093408 GCTGCATCTGACGACTTTGATAAA 59.907 41.667 0.00 0.00 0.00 1.40
5848 9944 9.410556 GCATAGATGTAAAATTTTGTGTCAAGT 57.589 29.630 13.76 3.11 0.00 3.16
5907 10003 4.653341 AGACAGAGTTCATCCATAGAAGGG 59.347 45.833 0.00 0.00 0.00 3.95
5983 10087 0.733223 GAAGAACCGACGACTCTGCC 60.733 60.000 0.00 0.00 0.00 4.85
6025 10129 4.363999 CAGCGATCTCTCCGTCTAAAATT 58.636 43.478 0.00 0.00 0.00 1.82
6026 10130 3.797184 GCAGCGATCTCTCCGTCTAAAAT 60.797 47.826 0.00 0.00 0.00 1.82
6034 10138 0.594540 CAGAAGCAGCGATCTCTCCG 60.595 60.000 1.10 0.00 0.00 4.63
6152 10256 2.823593 TTGGATGCGATGGTGCCG 60.824 61.111 0.00 0.00 0.00 5.69
6192 10297 1.308069 GCGATGCTTGCAGAAGGGAA 61.308 55.000 0.87 0.00 0.00 3.97
6218 10323 1.534697 TGGGAGTTCCAGGCGTTTT 59.465 52.632 0.00 0.00 41.46 2.43
6239 10344 5.621193 TCATTTCTTCGTTTTCTTCTCCCT 58.379 37.500 0.00 0.00 0.00 4.20
6252 10357 3.683822 AGCTTGCTCTCTTCATTTCTTCG 59.316 43.478 0.00 0.00 0.00 3.79
6259 10366 2.843113 AGGGTAAGCTTGCTCTCTTCAT 59.157 45.455 11.64 0.00 0.00 2.57
6269 10376 1.009829 GCGTCATCAGGGTAAGCTTG 58.990 55.000 9.86 0.00 0.00 4.01
6286 10395 0.321122 AACAGGGAGAAGCTTCTGCG 60.321 55.000 33.18 25.10 45.36 5.18
6293 10402 3.055819 TCATCACAGTAACAGGGAGAAGC 60.056 47.826 0.00 0.00 0.00 3.86
6299 10413 4.637534 CCATTCTTCATCACAGTAACAGGG 59.362 45.833 0.00 0.00 0.00 4.45
6301 10415 6.402983 GCTTCCATTCTTCATCACAGTAACAG 60.403 42.308 0.00 0.00 0.00 3.16
6302 10416 5.412594 GCTTCCATTCTTCATCACAGTAACA 59.587 40.000 0.00 0.00 0.00 2.41
6303 10417 5.645497 AGCTTCCATTCTTCATCACAGTAAC 59.355 40.000 0.00 0.00 0.00 2.50
6304 10418 5.645067 CAGCTTCCATTCTTCATCACAGTAA 59.355 40.000 0.00 0.00 0.00 2.24
6306 10420 4.008330 CAGCTTCCATTCTTCATCACAGT 58.992 43.478 0.00 0.00 0.00 3.55
6307 10421 4.259356 TCAGCTTCCATTCTTCATCACAG 58.741 43.478 0.00 0.00 0.00 3.66
6310 10424 4.019051 TCCTTCAGCTTCCATTCTTCATCA 60.019 41.667 0.00 0.00 0.00 3.07
6311 10425 4.521146 TCCTTCAGCTTCCATTCTTCATC 58.479 43.478 0.00 0.00 0.00 2.92
6312 10426 4.581309 TCCTTCAGCTTCCATTCTTCAT 57.419 40.909 0.00 0.00 0.00 2.57
6317 10438 3.766051 ACCAATTCCTTCAGCTTCCATTC 59.234 43.478 0.00 0.00 0.00 2.67
6351 10472 1.599606 CGTGTCTACCTGCAGGCTCT 61.600 60.000 33.06 16.28 39.32 4.09
6354 10475 0.737715 CTTCGTGTCTACCTGCAGGC 60.738 60.000 33.06 16.73 39.32 4.85
6369 10490 6.470160 CATCTTCCGTCAAACTATTTCTTCG 58.530 40.000 0.00 0.00 0.00 3.79
6395 10516 1.302033 GATGGGGCTGATGGCTACG 60.302 63.158 0.00 0.00 41.46 3.51
6465 10593 6.091849 CGCATAGAGCTTGATATTTGTAGCAT 59.908 38.462 0.00 0.00 42.61 3.79
6468 10596 5.636965 AGCGCATAGAGCTTGATATTTGTAG 59.363 40.000 11.47 0.00 43.24 2.74
6471 10599 4.212847 ACAGCGCATAGAGCTTGATATTTG 59.787 41.667 11.47 0.00 44.06 2.32
6540 10680 1.831106 GGGCTGGAATTTTTGGTAGGG 59.169 52.381 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.