Multiple sequence alignment - TraesCS1D01G257600

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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 TraesCS1D01G257600 chr1D 100.000 6116 0 0 1 6116 349796443 349790328 0.000000e+00 11295.0
1 TraesCS1D01G257600 chr1D 84.507 71 6 5 3622 3691 415987229 415987163 1.420000e-06 65.8
2 TraesCS1D01G257600 chr1A 96.006 1903 69 4 1724 3625 450096473 450094577 0.000000e+00 3086.0
3 TraesCS1D01G257600 chr1A 93.026 1864 89 21 3671 5511 450094574 450092729 0.000000e+00 2684.0
4 TraesCS1D01G257600 chr1A 89.598 1740 85 28 1 1677 450098164 450096458 0.000000e+00 2122.0
5 TraesCS1D01G257600 chr1A 95.868 121 5 0 5978 6098 450092684 450092564 4.840000e-46 196.0
6 TraesCS1D01G257600 chr1B 96.930 1824 55 1 1796 3619 471763396 471761574 0.000000e+00 3057.0
7 TraesCS1D01G257600 chr1B 91.449 2070 108 31 3671 5702 471761567 471759529 0.000000e+00 2778.0
8 TraesCS1D01G257600 chr1B 91.839 772 49 8 3749 4512 683421608 683422373 0.000000e+00 1064.0
9 TraesCS1D01G257600 chr1B 85.768 1061 69 33 750 1763 471764608 471763583 0.000000e+00 1048.0
10 TraesCS1D01G257600 chr1B 88.649 370 10 13 5751 6116 471759528 471759187 7.330000e-114 422.0
11 TraesCS1D01G257600 chr1B 78.055 401 66 15 273 666 471765174 471764789 3.690000e-57 233.0
12 TraesCS1D01G257600 chr1B 97.260 73 1 1 1 72 471766157 471766085 8.330000e-24 122.0
13 TraesCS1D01G257600 chr7B 83.658 1799 255 34 1804 3587 47003544 47001770 0.000000e+00 1657.0
14 TraesCS1D01G257600 chr7B 92.727 55 1 3 3614 3667 588501270 588501322 6.570000e-10 76.8
15 TraesCS1D01G257600 chr7B 84.507 71 6 5 3622 3691 676008854 676008788 1.420000e-06 65.8
16 TraesCS1D01G257600 chr7D 83.324 1799 261 34 1804 3587 93791572 93789798 0.000000e+00 1624.0
17 TraesCS1D01G257600 chr7D 82.531 1225 188 23 2370 3587 606636170 606637375 0.000000e+00 1053.0
18 TraesCS1D01G257600 chr7D 87.589 564 63 5 1801 2362 606635498 606636056 0.000000e+00 647.0
19 TraesCS1D01G257600 chr7A 83.213 1799 263 34 1804 3587 96570408 96568634 0.000000e+00 1613.0
20 TraesCS1D01G257600 chr7A 82.993 1223 180 24 2373 3587 698679361 698678159 0.000000e+00 1081.0
21 TraesCS1D01G257600 chr6B 82.934 1793 277 26 1805 3587 668250519 668248746 0.000000e+00 1589.0
22 TraesCS1D01G257600 chr6B 83.333 96 12 4 435 529 135892710 135892802 1.090000e-12 86.1
23 TraesCS1D01G257600 chr6D 82.618 1795 279 28 1805 3587 443849859 443848086 0.000000e+00 1555.0
24 TraesCS1D01G257600 chr6D 94.231 52 2 1 3614 3664 89352161 89352212 1.830000e-10 78.7
25 TraesCS1D01G257600 chr6A 82.618 1795 279 28 1805 3587 591439927 591438154 0.000000e+00 1555.0
26 TraesCS1D01G257600 chr5B 91.969 772 49 7 3749 4512 679583217 679582451 0.000000e+00 1070.0
27 TraesCS1D01G257600 chr5B 95.918 49 1 1 3623 3671 372109467 372109514 1.830000e-10 78.7
28 TraesCS1D01G257600 chr2B 91.192 772 50 10 3749 4512 44986116 44985355 0.000000e+00 1033.0
29 TraesCS1D01G257600 chr4B 90.933 772 57 7 3749 4512 365085312 365084546 0.000000e+00 1026.0
30 TraesCS1D01G257600 chr4A 93.286 566 32 4 3959 4524 558669042 558669601 0.000000e+00 830.0
31 TraesCS1D01G257600 chr3A 97.872 47 0 1 3624 3670 416192338 416192293 5.080000e-11 80.5
32 TraesCS1D01G257600 chr3A 89.655 58 3 3 3607 3664 12779145 12779199 3.060000e-08 71.3
33 TraesCS1D01G257600 chr2A 95.556 45 0 2 3622 3665 402689285 402689328 3.060000e-08 71.3
34 TraesCS1D01G257600 chr3D 84.507 71 7 4 3622 3691 587947466 587947399 3.960000e-07 67.6


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 TraesCS1D01G257600 chr1D 349790328 349796443 6115 True 11295.000000 11295 100.000000 1 6116 1 chr1D.!!$R1 6115
1 TraesCS1D01G257600 chr1A 450092564 450098164 5600 True 2022.000000 3086 93.624500 1 6098 4 chr1A.!!$R1 6097
2 TraesCS1D01G257600 chr1B 471759187 471766157 6970 True 1276.666667 3057 89.685167 1 6116 6 chr1B.!!$R1 6115
3 TraesCS1D01G257600 chr1B 683421608 683422373 765 False 1064.000000 1064 91.839000 3749 4512 1 chr1B.!!$F1 763
4 TraesCS1D01G257600 chr7B 47001770 47003544 1774 True 1657.000000 1657 83.658000 1804 3587 1 chr7B.!!$R1 1783
5 TraesCS1D01G257600 chr7D 93789798 93791572 1774 True 1624.000000 1624 83.324000 1804 3587 1 chr7D.!!$R1 1783
6 TraesCS1D01G257600 chr7D 606635498 606637375 1877 False 850.000000 1053 85.060000 1801 3587 2 chr7D.!!$F1 1786
7 TraesCS1D01G257600 chr7A 96568634 96570408 1774 True 1613.000000 1613 83.213000 1804 3587 1 chr7A.!!$R1 1783
8 TraesCS1D01G257600 chr7A 698678159 698679361 1202 True 1081.000000 1081 82.993000 2373 3587 1 chr7A.!!$R2 1214
9 TraesCS1D01G257600 chr6B 668248746 668250519 1773 True 1589.000000 1589 82.934000 1805 3587 1 chr6B.!!$R1 1782
10 TraesCS1D01G257600 chr6D 443848086 443849859 1773 True 1555.000000 1555 82.618000 1805 3587 1 chr6D.!!$R1 1782
11 TraesCS1D01G257600 chr6A 591438154 591439927 1773 True 1555.000000 1555 82.618000 1805 3587 1 chr6A.!!$R1 1782
12 TraesCS1D01G257600 chr5B 679582451 679583217 766 True 1070.000000 1070 91.969000 3749 4512 1 chr5B.!!$R1 763
13 TraesCS1D01G257600 chr2B 44985355 44986116 761 True 1033.000000 1033 91.192000 3749 4512 1 chr2B.!!$R1 763
14 TraesCS1D01G257600 chr4B 365084546 365085312 766 True 1026.000000 1026 90.933000 3749 4512 1 chr4B.!!$R1 763
15 TraesCS1D01G257600 chr4A 558669042 558669601 559 False 830.000000 830 93.286000 3959 4524 1 chr4A.!!$F1 565

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
309 1031 0.039256 CATGTTTCGGCCTTGGTGTG 60.039 55.000 0.00 0.0 0.00 3.82 F
379 1107 0.106708 TGGGAGCTCATATTCCACGC 59.893 55.000 17.19 0.0 35.09 5.34 F
434 1163 0.251787 ATCAGCCCACAAAGTTCCCC 60.252 55.000 0.00 0.0 0.00 4.81 F
1317 2204 0.757512 AGATGCATCGATCTGGCTGT 59.242 50.000 20.67 0.0 31.14 4.40 F
1963 3040 1.004080 GCTGCTCCTGCTCAACTCA 60.004 57.895 0.00 0.0 40.48 3.41 F
2886 4069 1.585006 CGCTCACCTACCAAGACGT 59.415 57.895 0.00 0.0 0.00 4.34 F
3637 4820 0.257039 TACAGTACTCCCTCCGTCCC 59.743 60.000 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 2695 0.584396 TGCCGTTAGAAACTTGCACG 59.416 50.000 0.00 0.00 33.69 5.34 R
1777 2700 1.199097 CGCCATTGCCGTTAGAAACTT 59.801 47.619 0.00 0.00 0.00 2.66 R
1912 2989 2.526873 AAGTCCTGCCAGTCCGGT 60.527 61.111 0.00 0.00 36.97 5.28 R
2746 3929 0.842030 TGGCATCCTGGTTCTCCACT 60.842 55.000 0.00 0.00 39.03 4.00 R
3340 4523 0.320073 CGTACTTGTGCTCGGGGAAA 60.320 55.000 0.00 0.00 0.00 3.13 R
4788 6009 0.390735 CCGGGGTCACCTAAGAAACG 60.391 60.000 0.00 0.00 36.97 3.60 R
5614 6842 0.106819 GGAACCAGATGGAGCATGCT 60.107 55.000 22.92 22.92 38.94 3.79 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
87 365 3.387947 AGCCATGCTTTGCTGCCC 61.388 61.111 0.00 0.00 33.89 5.36
110 388 2.401583 TCTTCATTGGTGGGATGTCG 57.598 50.000 0.00 0.00 0.00 4.35
147 426 5.234972 CGGGTTAGTATGGTCGGTATTTTTC 59.765 44.000 0.00 0.00 0.00 2.29
163 448 7.540745 CGGTATTTTTCTTTTATCTGTGTTGGG 59.459 37.037 0.00 0.00 0.00 4.12
174 459 3.917300 TCTGTGTTGGGTTGGGTTTAAT 58.083 40.909 0.00 0.00 0.00 1.40
188 473 7.256012 GGTTGGGTTTAATTTATGTTCTGACCA 60.256 37.037 0.00 0.00 0.00 4.02
219 504 7.402811 TTTCATTCGTATATCGTGATGAACC 57.597 36.000 17.23 0.00 44.00 3.62
255 542 9.985318 GATATTGTTTGTTCTGAAATGAGAGAG 57.015 33.333 0.00 0.00 0.00 3.20
262 549 6.169094 TGTTCTGAAATGAGAGAGTGGAATC 58.831 40.000 0.00 0.00 0.00 2.52
275 997 2.501316 AGTGGAATCGGATGATGTGTGA 59.499 45.455 0.00 0.00 34.24 3.58
286 1008 5.423015 GGATGATGTGTGATTGTAGTGTCT 58.577 41.667 0.00 0.00 0.00 3.41
289 1011 6.544038 TGATGTGTGATTGTAGTGTCTTTG 57.456 37.500 0.00 0.00 0.00 2.77
309 1031 0.039256 CATGTTTCGGCCTTGGTGTG 60.039 55.000 0.00 0.00 0.00 3.82
338 1066 2.288666 GTTGTTGTGTGAGCCTCTTGA 58.711 47.619 0.00 0.00 0.00 3.02
349 1077 3.319122 TGAGCCTCTTGAAAGCCTTTTTC 59.681 43.478 0.00 0.00 0.00 2.29
357 1085 7.338957 CCTCTTGAAAGCCTTTTTCTAGATCAT 59.661 37.037 11.97 0.00 38.73 2.45
379 1107 0.106708 TGGGAGCTCATATTCCACGC 59.893 55.000 17.19 0.00 35.09 5.34
389 1117 5.926542 GCTCATATTCCACGCTGAAATAGTA 59.073 40.000 0.00 0.00 0.00 1.82
402 1131 7.134815 CGCTGAAATAGTAAATTGCTGCTATT 58.865 34.615 3.47 3.47 36.17 1.73
432 1161 1.177401 GGATCAGCCCACAAAGTTCC 58.823 55.000 0.00 0.00 0.00 3.62
434 1163 0.251787 ATCAGCCCACAAAGTTCCCC 60.252 55.000 0.00 0.00 0.00 4.81
435 1164 1.153756 CAGCCCACAAAGTTCCCCT 59.846 57.895 0.00 0.00 0.00 4.79
436 1165 0.895559 CAGCCCACAAAGTTCCCCTC 60.896 60.000 0.00 0.00 0.00 4.30
437 1166 1.971695 GCCCACAAAGTTCCCCTCG 60.972 63.158 0.00 0.00 0.00 4.63
438 1167 1.971695 CCCACAAAGTTCCCCTCGC 60.972 63.158 0.00 0.00 0.00 5.03
452 1184 2.176045 CCCTCGCCCAGGTTTTATTTT 58.824 47.619 0.00 0.00 41.51 1.82
503 1236 5.839621 AGCCGGCTACCGTATTATTATATG 58.160 41.667 31.86 0.00 46.80 1.78
532 1265 9.683069 AAGTTCATCAAATCAAAAGATGTACAC 57.317 29.630 0.00 0.00 40.38 2.90
703 1438 5.954150 AGGAATTGACATCATGGCTTACTTT 59.046 36.000 0.00 0.00 0.00 2.66
740 1475 6.299604 CAGACTTACATCGTCAATCAACAAC 58.700 40.000 0.00 0.00 33.89 3.32
753 1604 7.304622 CGTCAATCAACAACGACAAAGTAAAAG 60.305 37.037 0.00 0.00 38.65 2.27
776 1628 8.876303 AAGCAGAAGAAGAGATAAGGAATTTT 57.124 30.769 0.00 0.00 0.00 1.82
963 1825 4.552572 CGTATACGTACGTGCATAGTTGGA 60.553 45.833 30.25 6.91 46.51 3.53
1116 1981 2.033424 AGCGAGTTCTTGCCAACTTTTC 59.967 45.455 8.26 0.00 36.71 2.29
1137 2002 9.820229 CTTTTCTATGCGTGTTTTTATCTGTTA 57.180 29.630 0.00 0.00 0.00 2.41
1163 2033 6.349973 AGTTGTTACATGTTCTATGCATCG 57.650 37.500 2.30 0.00 0.00 3.84
1187 2057 7.333423 TCGTGTAAAGATCATTAGGAAAACCTG 59.667 37.037 0.00 0.00 0.00 4.00
1192 2065 8.650143 AAAGATCATTAGGAAAACCTGCTAAA 57.350 30.769 0.00 0.00 40.86 1.85
1203 2076 9.920946 AGGAAAACCTGCTAAATGATAATTCTA 57.079 29.630 0.00 0.00 0.00 2.10
1208 2081 9.700831 AACCTGCTAAATGATAATTCTAAACCT 57.299 29.630 0.00 0.00 0.00 3.50
1315 2202 1.542767 CCAAGATGCATCGATCTGGCT 60.543 52.381 20.67 0.00 32.77 4.75
1317 2204 0.757512 AGATGCATCGATCTGGCTGT 59.242 50.000 20.67 0.00 31.14 4.40
1381 2274 2.924290 CCGATCGTCTTTGTTTCTCTCC 59.076 50.000 15.09 0.00 0.00 3.71
1447 2342 8.782144 GCTTTTTCCCATCTAATCTCTTATCAG 58.218 37.037 0.00 0.00 0.00 2.90
1451 2346 4.180057 CCATCTAATCTCTTATCAGCGCC 58.820 47.826 2.29 0.00 0.00 6.53
1508 2427 1.939974 TAGTGCATGCGAATCCAGTC 58.060 50.000 14.09 0.00 0.00 3.51
1669 2588 2.870411 CGAAGAGAAAAAGGTTCGGTGT 59.130 45.455 0.00 0.00 38.47 4.16
1717 2640 7.858052 ATTGTTTGAAGCGAATTAGTTCTTG 57.142 32.000 0.00 0.00 32.00 3.02
1739 2662 9.554724 TCTTGATTTCGTTGCTGAAATTTATAC 57.445 29.630 11.57 2.77 45.90 1.47
1763 2686 8.707796 ACCATCTTCGTTAGGATTTCTAGATA 57.292 34.615 0.00 0.00 0.00 1.98
1765 2688 9.015367 CCATCTTCGTTAGGATTTCTAGATAGA 57.985 37.037 0.00 0.00 0.00 1.98
1769 2692 9.134734 CTTCGTTAGGATTTCTAGATAGATTGC 57.865 37.037 0.00 0.00 31.40 3.56
1770 2693 7.306213 TCGTTAGGATTTCTAGATAGATTGCG 58.694 38.462 0.00 0.00 31.40 4.85
1771 2694 7.040617 TCGTTAGGATTTCTAGATAGATTGCGT 60.041 37.037 0.00 0.00 31.40 5.24
1772 2695 7.271653 CGTTAGGATTTCTAGATAGATTGCGTC 59.728 40.741 0.00 0.00 31.40 5.19
1773 2696 5.704888 AGGATTTCTAGATAGATTGCGTCG 58.295 41.667 0.00 0.00 31.40 5.12
1774 2697 5.241949 AGGATTTCTAGATAGATTGCGTCGT 59.758 40.000 0.00 0.00 31.40 4.34
1775 2698 5.343593 GGATTTCTAGATAGATTGCGTCGTG 59.656 44.000 0.00 0.00 31.40 4.35
1776 2699 3.269486 TCTAGATAGATTGCGTCGTGC 57.731 47.619 0.00 0.00 46.70 5.34
1963 3040 1.004080 GCTGCTCCTGCTCAACTCA 60.004 57.895 0.00 0.00 40.48 3.41
2125 3202 1.709147 GCATCAAGCTCGGCGACATT 61.709 55.000 4.99 0.00 41.15 2.71
2476 3659 4.278956 GACGGCATCGACAACCTT 57.721 55.556 0.00 0.00 40.11 3.50
2578 3761 3.984193 GAAGCAGGGCGCCATCACT 62.984 63.158 30.85 18.42 44.04 3.41
2886 4069 1.585006 CGCTCACCTACCAAGACGT 59.415 57.895 0.00 0.00 0.00 4.34
3259 4442 2.070650 GTACCCCTCATCCGCCCTT 61.071 63.158 0.00 0.00 0.00 3.95
3340 4523 2.359478 GATGGGTTCGCCGGTGTT 60.359 61.111 16.01 0.00 38.45 3.32
3603 4786 0.400213 ACCGTGAGCATTCTCCCAAA 59.600 50.000 0.00 0.00 38.58 3.28
3609 4792 3.057946 GTGAGCATTCTCCCAAAACTCAC 60.058 47.826 0.00 0.00 43.80 3.51
3611 4794 4.041567 TGAGCATTCTCCCAAAACTCACTA 59.958 41.667 0.00 0.00 38.58 2.74
3620 4803 7.159372 TCTCCCAAAACTCACTAACATTCTAC 58.841 38.462 0.00 0.00 0.00 2.59
3621 4804 6.833041 TCCCAAAACTCACTAACATTCTACA 58.167 36.000 0.00 0.00 0.00 2.74
3622 4805 6.934645 TCCCAAAACTCACTAACATTCTACAG 59.065 38.462 0.00 0.00 0.00 2.74
3623 4806 6.710744 CCCAAAACTCACTAACATTCTACAGT 59.289 38.462 0.00 0.00 0.00 3.55
3626 4809 9.477484 CAAAACTCACTAACATTCTACAGTACT 57.523 33.333 0.00 0.00 0.00 2.73
3627 4810 9.694137 AAAACTCACTAACATTCTACAGTACTC 57.306 33.333 0.00 0.00 0.00 2.59
3628 4811 7.393841 ACTCACTAACATTCTACAGTACTCC 57.606 40.000 0.00 0.00 0.00 3.85
3629 4812 6.377712 ACTCACTAACATTCTACAGTACTCCC 59.622 42.308 0.00 0.00 0.00 4.30
3630 4813 6.491383 TCACTAACATTCTACAGTACTCCCT 58.509 40.000 0.00 0.00 0.00 4.20
3631 4814 6.602406 TCACTAACATTCTACAGTACTCCCTC 59.398 42.308 0.00 0.00 0.00 4.30
3632 4815 5.892686 ACTAACATTCTACAGTACTCCCTCC 59.107 44.000 0.00 0.00 0.00 4.30
3633 4816 3.288964 ACATTCTACAGTACTCCCTCCG 58.711 50.000 0.00 0.00 0.00 4.63
3634 4817 3.288964 CATTCTACAGTACTCCCTCCGT 58.711 50.000 0.00 0.00 0.00 4.69
3635 4818 2.706339 TCTACAGTACTCCCTCCGTC 57.294 55.000 0.00 0.00 0.00 4.79
3636 4819 1.211457 TCTACAGTACTCCCTCCGTCC 59.789 57.143 0.00 0.00 0.00 4.79
3637 4820 0.257039 TACAGTACTCCCTCCGTCCC 59.743 60.000 0.00 0.00 0.00 4.46
3638 4821 1.000019 CAGTACTCCCTCCGTCCCA 60.000 63.158 0.00 0.00 0.00 4.37
3639 4822 0.397254 CAGTACTCCCTCCGTCCCAT 60.397 60.000 0.00 0.00 0.00 4.00
3640 4823 1.133575 CAGTACTCCCTCCGTCCCATA 60.134 57.143 0.00 0.00 0.00 2.74
3641 4824 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3642 4825 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3643 4826 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3644 4827 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3645 4828 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3646 4829 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3647 4830 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
3648 4831 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
3649 4832 3.006967 CCCTCCGTCCCATAATGTAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
3650 4833 3.555168 CCTCCGTCCCATAATGTAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
3651 4834 2.035449 TCCGTCCCATAATGTAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
3652 4835 2.223971 CCGTCCCATAATGTAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
3653 4836 3.454375 CGTCCCATAATGTAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
3654 4837 3.869246 CGTCCCATAATGTAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
3655 4838 4.331717 CGTCCCATAATGTAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
3656 4839 5.163794 CGTCCCATAATGTAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
3657 4840 6.027749 GTCCCATAATGTAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
3658 4841 5.941058 TCCCATAATGTAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
3659 4842 6.027749 CCCATAATGTAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
3660 4843 6.348950 CCCATAATGTAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
3661 4844 6.523201 CCATAATGTAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
3662 4845 5.751243 AATGTAAGAGCGTTTTTGACACT 57.249 34.783 0.00 0.00 0.00 3.55
3663 4846 6.854496 AATGTAAGAGCGTTTTTGACACTA 57.146 33.333 0.00 0.00 0.00 2.74
3664 4847 5.646467 TGTAAGAGCGTTTTTGACACTAC 57.354 39.130 0.00 0.00 0.00 2.73
3665 4848 5.353938 TGTAAGAGCGTTTTTGACACTACT 58.646 37.500 0.00 0.00 0.00 2.57
3666 4849 6.506147 TGTAAGAGCGTTTTTGACACTACTA 58.494 36.000 0.00 0.00 0.00 1.82
3667 4850 6.639686 TGTAAGAGCGTTTTTGACACTACTAG 59.360 38.462 0.00 0.00 0.00 2.57
3668 4851 5.197682 AGAGCGTTTTTGACACTACTAGT 57.802 39.130 0.00 0.00 0.00 2.57
3669 4852 6.323203 AGAGCGTTTTTGACACTACTAGTA 57.677 37.500 1.89 1.89 0.00 1.82
3676 4859 9.925268 CGTTTTTGACACTACTAGTATTTTGTT 57.075 29.630 2.33 0.00 0.00 2.83
3699 4882 7.012327 TGTTCAAATAACTCTGACTGTTCCTTG 59.988 37.037 0.00 0.00 0.00 3.61
3712 4895 1.480545 GTTCCTTGTGCCCTTGTTGTT 59.519 47.619 0.00 0.00 0.00 2.83
3718 4901 4.298332 CTTGTGCCCTTGTTGTTAATGTC 58.702 43.478 0.00 0.00 0.00 3.06
3833 5022 8.519492 ACATGGACTTGATTTAATTCGTTTTG 57.481 30.769 0.00 0.00 0.00 2.44
3837 5026 6.128929 GGACTTGATTTAATTCGTTTTGTGCC 60.129 38.462 0.00 0.00 0.00 5.01
3961 5158 3.629398 GGGTCTCAACTTCATTATGCCAG 59.371 47.826 0.00 0.00 0.00 4.85
4216 5426 4.202441 CCATGTCTAATCCCTCCAAACTG 58.798 47.826 0.00 0.00 0.00 3.16
4217 5427 4.080356 CCATGTCTAATCCCTCCAAACTGA 60.080 45.833 0.00 0.00 0.00 3.41
4235 5445 2.491693 CTGAACAATTTATGGGCGTGGT 59.508 45.455 0.00 0.00 0.00 4.16
4284 5494 5.104982 TGCTGAATTTTCCTGTTTGTTTCCT 60.105 36.000 0.00 0.00 0.00 3.36
4285 5495 6.097554 TGCTGAATTTTCCTGTTTGTTTCCTA 59.902 34.615 0.00 0.00 0.00 2.94
4286 5496 7.154656 GCTGAATTTTCCTGTTTGTTTCCTAT 58.845 34.615 0.00 0.00 0.00 2.57
4287 5497 8.303876 GCTGAATTTTCCTGTTTGTTTCCTATA 58.696 33.333 0.00 0.00 0.00 1.31
4313 5523 4.771127 GGAGAAGTTCCACGTGCA 57.229 55.556 10.91 0.00 46.01 4.57
4317 5527 1.464997 GAGAAGTTCCACGTGCATTCC 59.535 52.381 10.91 0.00 0.00 3.01
4347 5557 1.959042 ACAAGGATGCGATGATGTCC 58.041 50.000 0.37 0.00 0.00 4.02
4487 5697 3.642503 CGTAAGCCCACCCCACCA 61.643 66.667 0.00 0.00 0.00 4.17
4513 5723 1.133513 TCCCTGCAACAATGGAGTGTT 60.134 47.619 0.00 0.00 42.97 3.32
4515 5725 2.102925 CCCTGCAACAATGGAGTGTTTT 59.897 45.455 0.00 0.00 42.97 2.43
4527 5737 3.003275 TGGAGTGTTTTCGTTTCATCTGC 59.997 43.478 0.00 0.00 0.00 4.26
4760 5973 3.369471 CGAGAACAAGGTACACCATGGAT 60.369 47.826 21.47 8.74 38.92 3.41
4761 5974 4.589908 GAGAACAAGGTACACCATGGATT 58.410 43.478 21.47 6.94 38.92 3.01
4762 5975 4.335416 AGAACAAGGTACACCATGGATTG 58.665 43.478 21.47 10.08 38.92 2.67
4763 5976 3.806949 ACAAGGTACACCATGGATTGT 57.193 42.857 21.47 16.05 38.92 2.71
4764 5977 4.919774 ACAAGGTACACCATGGATTGTA 57.080 40.909 21.47 14.92 38.92 2.41
4778 5999 6.206243 CCATGGATTGTAATGATCTCAAGGTC 59.794 42.308 5.56 0.00 0.00 3.85
4782 6003 6.293845 GGATTGTAATGATCTCAAGGTCATGC 60.294 42.308 6.54 4.35 35.38 4.06
4784 6005 4.877823 TGTAATGATCTCAAGGTCATGCAC 59.122 41.667 6.54 8.42 35.38 4.57
4809 6030 0.838987 TTTCTTAGGTGACCCCGGCT 60.839 55.000 0.00 0.00 38.74 5.52
4816 6037 1.029947 GGTGACCCCGGCTTAACATG 61.030 60.000 0.00 0.00 0.00 3.21
4817 6038 0.322187 GTGACCCCGGCTTAACATGT 60.322 55.000 0.00 0.00 0.00 3.21
4818 6039 0.322098 TGACCCCGGCTTAACATGTG 60.322 55.000 0.00 0.00 0.00 3.21
4819 6040 0.322187 GACCCCGGCTTAACATGTGT 60.322 55.000 0.00 0.00 0.00 3.72
4820 6041 0.608035 ACCCCGGCTTAACATGTGTG 60.608 55.000 0.00 0.00 0.00 3.82
4822 6043 0.608035 CCCGGCTTAACATGTGTGGT 60.608 55.000 0.00 0.00 0.00 4.16
4823 6044 0.521291 CCGGCTTAACATGTGTGGTG 59.479 55.000 0.00 0.00 0.00 4.17
4824 6045 1.518325 CGGCTTAACATGTGTGGTGA 58.482 50.000 0.00 0.00 0.00 4.02
5043 6264 2.659016 CTCAGCACGCTCAAGGGA 59.341 61.111 0.59 0.00 0.00 4.20
5055 6276 0.193574 TCAAGGGAAGGGTGGAGTCT 59.806 55.000 0.00 0.00 0.00 3.24
5131 6354 1.352083 ATGATGGATCGAACCGGGAT 58.648 50.000 6.32 0.00 0.00 3.85
5232 6455 1.269174 TCGTTTTGGTCGTCGGATACA 59.731 47.619 0.00 0.00 0.00 2.29
5233 6456 2.094597 TCGTTTTGGTCGTCGGATACAT 60.095 45.455 0.00 0.00 0.00 2.29
5368 6591 5.065988 CGCTATAAACTTGGCTGTGGTTTAT 59.934 40.000 12.66 12.66 43.75 1.40
5393 6616 0.609662 CAACCCTGGCATGGAAAAGG 59.390 55.000 16.19 0.00 0.00 3.11
5519 6747 4.948341 ATTCATACATGTGCCCGTACTA 57.052 40.909 9.11 0.00 0.00 1.82
5539 6767 3.065019 ACTCGCATTTGTTTGTGTGAC 57.935 42.857 0.00 0.00 32.07 3.67
5615 6843 9.577110 TTTGCAAAATTATCTGATTGAGCTAAG 57.423 29.630 10.02 0.00 0.00 2.18
5616 6844 7.198390 TGCAAAATTATCTGATTGAGCTAAGC 58.802 34.615 0.00 0.00 0.00 3.09
5618 6846 7.866393 GCAAAATTATCTGATTGAGCTAAGCAT 59.134 33.333 0.00 0.00 33.62 3.79
5619 6847 9.181805 CAAAATTATCTGATTGAGCTAAGCATG 57.818 33.333 0.00 0.00 33.62 4.06
5640 6868 1.849039 CTCCATCTGGTTCCCCTTCAT 59.151 52.381 0.00 0.00 36.34 2.57
5642 6870 2.654385 TCCATCTGGTTCCCCTTCATTT 59.346 45.455 0.00 0.00 36.34 2.32
5656 6884 5.045140 CCCCTTCATTTCTTTACTCCTGGTA 60.045 44.000 0.00 0.00 0.00 3.25
5672 6900 8.240267 ACTCCTGGTATTAAGACAGTAATCTC 57.760 38.462 2.17 0.00 0.00 2.75
5702 6930 0.251564 TGTTGATTGGCGGGTTGGAT 60.252 50.000 0.00 0.00 0.00 3.41
5703 6931 0.455815 GTTGATTGGCGGGTTGGATC 59.544 55.000 0.00 0.00 0.00 3.36
5704 6932 1.029408 TTGATTGGCGGGTTGGATCG 61.029 55.000 0.00 0.00 0.00 3.69
5712 6940 0.944386 CGGGTTGGATCGCTTATTGG 59.056 55.000 0.00 0.00 0.00 3.16
5713 6941 0.668535 GGGTTGGATCGCTTATTGGC 59.331 55.000 0.00 0.00 0.00 4.52
5714 6942 0.668535 GGTTGGATCGCTTATTGGCC 59.331 55.000 0.00 0.00 0.00 5.36
5715 6943 1.680338 GTTGGATCGCTTATTGGCCT 58.320 50.000 3.32 0.00 0.00 5.19
5716 6944 1.604278 GTTGGATCGCTTATTGGCCTC 59.396 52.381 3.32 0.00 0.00 4.70
5717 6945 0.249868 TGGATCGCTTATTGGCCTCG 60.250 55.000 3.32 0.00 0.00 4.63
5718 6946 0.249911 GGATCGCTTATTGGCCTCGT 60.250 55.000 3.32 0.00 0.00 4.18
5719 6947 1.583054 GATCGCTTATTGGCCTCGTT 58.417 50.000 3.32 0.00 0.00 3.85
5720 6948 1.940613 GATCGCTTATTGGCCTCGTTT 59.059 47.619 3.32 0.00 0.00 3.60
5721 6949 2.676632 TCGCTTATTGGCCTCGTTTA 57.323 45.000 3.32 0.00 0.00 2.01
5722 6950 3.188159 TCGCTTATTGGCCTCGTTTAT 57.812 42.857 3.32 0.00 0.00 1.40
5723 6951 2.869801 TCGCTTATTGGCCTCGTTTATG 59.130 45.455 3.32 0.00 0.00 1.90
5724 6952 2.869801 CGCTTATTGGCCTCGTTTATGA 59.130 45.455 3.32 0.00 0.00 2.15
5725 6953 3.303132 CGCTTATTGGCCTCGTTTATGAC 60.303 47.826 3.32 0.00 0.00 3.06
5726 6954 3.625764 GCTTATTGGCCTCGTTTATGACA 59.374 43.478 3.32 0.00 0.00 3.58
5727 6955 4.260784 GCTTATTGGCCTCGTTTATGACAG 60.261 45.833 3.32 0.00 0.00 3.51
5728 6956 2.851263 TTGGCCTCGTTTATGACAGT 57.149 45.000 3.32 0.00 0.00 3.55
5729 6957 2.851263 TGGCCTCGTTTATGACAGTT 57.149 45.000 3.32 0.00 0.00 3.16
5730 6958 3.134574 TGGCCTCGTTTATGACAGTTT 57.865 42.857 3.32 0.00 0.00 2.66
5731 6959 3.071479 TGGCCTCGTTTATGACAGTTTC 58.929 45.455 3.32 0.00 0.00 2.78
5732 6960 3.244422 TGGCCTCGTTTATGACAGTTTCT 60.244 43.478 3.32 0.00 0.00 2.52
5733 6961 3.125316 GGCCTCGTTTATGACAGTTTCTG 59.875 47.826 0.00 0.00 37.52 3.02
5747 6975 6.518208 ACAGTTTCTGTCTCTGATAGTACC 57.482 41.667 0.00 0.00 41.21 3.34
5748 6976 6.010850 ACAGTTTCTGTCTCTGATAGTACCA 58.989 40.000 0.00 0.00 41.21 3.25
5749 6977 6.151985 ACAGTTTCTGTCTCTGATAGTACCAG 59.848 42.308 0.00 0.00 41.21 4.00
5916 7148 4.153958 TGACGCATATGGTCAAACAAAC 57.846 40.909 18.83 0.00 41.17 2.93
5920 7152 5.352284 ACGCATATGGTCAAACAAACAAAA 58.648 33.333 4.56 0.00 0.00 2.44
5921 7153 5.812642 ACGCATATGGTCAAACAAACAAAAA 59.187 32.000 4.56 0.00 0.00 1.94
5939 7171 2.481289 AAAGACCAGCCAGAACTAGC 57.519 50.000 0.00 0.00 0.00 3.42
5940 7172 0.615850 AAGACCAGCCAGAACTAGCC 59.384 55.000 0.00 0.00 0.00 3.93
5941 7173 1.222113 GACCAGCCAGAACTAGCCC 59.778 63.158 0.00 0.00 0.00 5.19
5942 7174 1.229658 ACCAGCCAGAACTAGCCCT 60.230 57.895 0.00 0.00 0.00 5.19
5943 7175 0.842467 ACCAGCCAGAACTAGCCCTT 60.842 55.000 0.00 0.00 0.00 3.95
5944 7176 1.204146 CCAGCCAGAACTAGCCCTTA 58.796 55.000 0.00 0.00 0.00 2.69
5945 7177 1.139853 CCAGCCAGAACTAGCCCTTAG 59.860 57.143 0.00 0.00 35.39 2.18
5946 7178 1.834263 CAGCCAGAACTAGCCCTTAGT 59.166 52.381 0.00 0.00 44.55 2.24
5947 7179 1.834263 AGCCAGAACTAGCCCTTAGTG 59.166 52.381 0.00 0.00 41.80 2.74
5948 7180 1.134371 GCCAGAACTAGCCCTTAGTGG 60.134 57.143 0.00 0.00 41.80 4.00
5949 7181 2.188817 CCAGAACTAGCCCTTAGTGGT 58.811 52.381 0.00 0.00 41.80 4.16
5950 7182 2.093447 CCAGAACTAGCCCTTAGTGGTG 60.093 54.545 0.00 0.00 41.80 4.17
5951 7183 2.093447 CAGAACTAGCCCTTAGTGGTGG 60.093 54.545 0.00 0.00 41.80 4.61
5952 7184 0.618981 AACTAGCCCTTAGTGGTGGC 59.381 55.000 0.00 0.00 41.80 5.01
5971 7203 5.476945 GGTGGCATATTTTTAGGGATAGGTG 59.523 44.000 0.00 0.00 0.00 4.00
5976 7208 3.662759 TTTTTAGGGATAGGTGGCCAG 57.337 47.619 5.11 0.00 0.00 4.85
6085 7317 0.949397 CTTGATCCGATGCCATGTGG 59.051 55.000 0.00 0.00 38.53 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 365 1.745087 CATCCCACCAATGAAGAACGG 59.255 52.381 0.00 0.00 0.00 4.44
122 401 2.435372 TACCGACCATACTAACCCGT 57.565 50.000 0.00 0.00 0.00 5.28
132 411 8.458843 CACAGATAAAAGAAAAATACCGACCAT 58.541 33.333 0.00 0.00 0.00 3.55
147 426 3.895041 ACCCAACCCAACACAGATAAAAG 59.105 43.478 0.00 0.00 0.00 2.27
163 448 7.662897 TGGTCAGAACATAAATTAAACCCAAC 58.337 34.615 0.00 0.00 0.00 3.77
202 487 4.501559 AACAACGGTTCATCACGATATACG 59.498 41.667 0.00 0.00 39.56 3.06
203 488 5.961395 AACAACGGTTCATCACGATATAC 57.039 39.130 0.00 0.00 29.00 1.47
206 491 5.124297 TCTCTAACAACGGTTCATCACGATA 59.876 40.000 0.00 0.00 38.45 2.92
207 492 4.082408 TCTCTAACAACGGTTCATCACGAT 60.082 41.667 0.00 0.00 38.45 3.73
219 504 8.708742 TCAGAACAAACAATATCTCTAACAACG 58.291 33.333 0.00 0.00 0.00 4.10
255 542 2.905075 TCACACATCATCCGATTCCAC 58.095 47.619 0.00 0.00 0.00 4.02
262 549 4.183865 ACACTACAATCACACATCATCCG 58.816 43.478 0.00 0.00 0.00 4.18
275 997 5.451908 CGAAACATGCAAAGACACTACAAT 58.548 37.500 0.00 0.00 0.00 2.71
286 1008 0.033228 CCAAGGCCGAAACATGCAAA 59.967 50.000 0.00 0.00 0.00 3.68
289 1011 1.080569 CACCAAGGCCGAAACATGC 60.081 57.895 0.00 0.00 0.00 4.06
309 1031 0.238289 CACACAACAACCATCGGCTC 59.762 55.000 0.00 0.00 0.00 4.70
338 1066 6.379417 CCCAAGATGATCTAGAAAAAGGCTTT 59.621 38.462 6.68 6.68 0.00 3.51
349 1077 6.795144 ATATGAGCTCCCAAGATGATCTAG 57.205 41.667 12.15 0.00 0.00 2.43
357 1085 2.103094 CGTGGAATATGAGCTCCCAAGA 59.897 50.000 12.15 0.00 0.00 3.02
389 1117 6.982141 CCATGTGAACATAATAGCAGCAATTT 59.018 34.615 0.00 0.00 34.26 1.82
402 1131 2.509131 TGGGCTGATCCATGTGAACATA 59.491 45.455 0.00 0.00 34.26 2.29
434 1163 2.731027 GCGAAAATAAAACCTGGGCGAG 60.731 50.000 0.00 0.00 0.00 5.03
435 1164 1.200484 GCGAAAATAAAACCTGGGCGA 59.800 47.619 0.00 0.00 0.00 5.54
436 1165 1.201414 AGCGAAAATAAAACCTGGGCG 59.799 47.619 0.00 0.00 0.00 6.13
437 1166 2.230266 TGAGCGAAAATAAAACCTGGGC 59.770 45.455 0.00 0.00 0.00 5.36
438 1167 3.506067 AGTGAGCGAAAATAAAACCTGGG 59.494 43.478 0.00 0.00 0.00 4.45
452 1184 1.938657 GCTAGCAGTGGAGTGAGCGA 61.939 60.000 10.63 0.00 0.00 4.93
587 1321 9.356929 CAAATTCGCAAACTTTTTGAAATCTAC 57.643 29.630 2.80 0.00 30.69 2.59
600 1334 9.353999 GATACCTTTATTTCAAATTCGCAAACT 57.646 29.630 0.00 0.00 0.00 2.66
601 1335 9.134734 TGATACCTTTATTTCAAATTCGCAAAC 57.865 29.630 0.00 0.00 0.00 2.93
678 1413 6.252599 AGTAAGCCATGATGTCAATTCCTA 57.747 37.500 0.00 0.00 0.00 2.94
740 1475 6.201044 TCTCTTCTTCTGCTTTTACTTTGTCG 59.799 38.462 0.00 0.00 0.00 4.35
867 1729 2.494888 TAGCTGGATGGATGGAAGGA 57.505 50.000 0.00 0.00 0.00 3.36
1137 2002 8.551205 CGATGCATAGAACATGTAACAACTTAT 58.449 33.333 0.00 0.00 0.00 1.73
1217 2090 9.391006 ACGCTTACATCTTCTCCATTTTAATTA 57.609 29.630 0.00 0.00 0.00 1.40
1218 2091 8.281212 ACGCTTACATCTTCTCCATTTTAATT 57.719 30.769 0.00 0.00 0.00 1.40
1219 2092 7.865706 ACGCTTACATCTTCTCCATTTTAAT 57.134 32.000 0.00 0.00 0.00 1.40
1220 2093 8.255206 TCTACGCTTACATCTTCTCCATTTTAA 58.745 33.333 0.00 0.00 0.00 1.52
1221 2094 7.778083 TCTACGCTTACATCTTCTCCATTTTA 58.222 34.615 0.00 0.00 0.00 1.52
1222 2095 6.640518 TCTACGCTTACATCTTCTCCATTTT 58.359 36.000 0.00 0.00 0.00 1.82
1223 2096 6.222038 TCTACGCTTACATCTTCTCCATTT 57.778 37.500 0.00 0.00 0.00 2.32
1315 2202 4.367450 GTGAAGCCAACAATAAAAGCACA 58.633 39.130 0.00 0.00 0.00 4.57
1317 2204 3.551863 CCGTGAAGCCAACAATAAAAGCA 60.552 43.478 0.00 0.00 0.00 3.91
1357 2244 3.057734 GAGAAACAAAGACGATCGGTGT 58.942 45.455 20.98 14.21 0.00 4.16
1451 2346 4.082733 TCGGATAGAGACGGCTAATCAATG 60.083 45.833 13.58 4.77 0.00 2.82
1508 2427 3.492313 GCACAGATTAGCCAAGAAAACG 58.508 45.455 0.00 0.00 0.00 3.60
1717 2640 8.856490 ATGGTATAAATTTCAGCAACGAAATC 57.144 30.769 8.62 0.00 43.21 2.17
1739 2662 9.015367 TCTATCTAGAAATCCTAACGAAGATGG 57.985 37.037 0.00 0.00 0.00 3.51
1769 2692 1.136721 CCGTTAGAAACTTGCACGACG 60.137 52.381 0.00 0.00 32.51 5.12
1770 2693 1.398071 GCCGTTAGAAACTTGCACGAC 60.398 52.381 0.00 0.00 32.51 4.34
1771 2694 0.863144 GCCGTTAGAAACTTGCACGA 59.137 50.000 0.00 0.00 32.51 4.35
1772 2695 0.584396 TGCCGTTAGAAACTTGCACG 59.416 50.000 0.00 0.00 33.69 5.34
1773 2696 2.766970 TTGCCGTTAGAAACTTGCAC 57.233 45.000 0.00 0.00 36.82 4.57
1774 2697 2.030363 CCATTGCCGTTAGAAACTTGCA 60.030 45.455 0.00 0.00 35.80 4.08
1775 2698 2.595386 CCATTGCCGTTAGAAACTTGC 58.405 47.619 0.00 0.00 0.00 4.01
1776 2699 2.595386 GCCATTGCCGTTAGAAACTTG 58.405 47.619 0.00 0.00 0.00 3.16
1777 2700 1.199097 CGCCATTGCCGTTAGAAACTT 59.801 47.619 0.00 0.00 0.00 2.66
1912 2989 2.526873 AAGTCCTGCCAGTCCGGT 60.527 61.111 0.00 0.00 36.97 5.28
1963 3040 4.537751 TCTCCTCGATGTAAGAGATGGTT 58.462 43.478 0.00 0.00 37.93 3.67
2476 3659 2.775856 GCCGATGAGGAGCACGAGA 61.776 63.158 0.00 0.00 45.00 4.04
2578 3761 1.887242 GATGGCCGTCATGCGCTTA 60.887 57.895 20.55 0.00 39.71 3.09
2746 3929 0.842030 TGGCATCCTGGTTCTCCACT 60.842 55.000 0.00 0.00 39.03 4.00
2823 4006 2.300996 GGGAGGAAGTGCATCTCCA 58.699 57.895 21.48 0.00 46.55 3.86
2863 4046 2.781595 CTTGGTAGGTGAGCGCGGTT 62.782 60.000 14.00 0.00 0.00 4.44
3340 4523 0.320073 CGTACTTGTGCTCGGGGAAA 60.320 55.000 0.00 0.00 0.00 3.13
3603 4786 7.093858 GGGAGTACTGTAGAATGTTAGTGAGTT 60.094 40.741 0.00 0.00 0.00 3.01
3609 4792 5.008811 CGGAGGGAGTACTGTAGAATGTTAG 59.991 48.000 0.00 0.00 0.00 2.34
3611 4794 3.700038 CGGAGGGAGTACTGTAGAATGTT 59.300 47.826 0.00 0.00 0.00 2.71
3620 4803 0.397254 ATGGGACGGAGGGAGTACTG 60.397 60.000 0.00 0.00 0.00 2.74
3621 4804 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
3622 4805 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3623 4806 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3626 4809 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3627 4810 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
3628 4811 3.555168 GCTCTTACATTATGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
3629 4812 3.654414 GCTCTTACATTATGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
3630 4813 2.035449 CGCTCTTACATTATGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
3631 4814 2.223971 ACGCTCTTACATTATGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
3632 4815 3.093717 ACGCTCTTACATTATGGGACG 57.906 47.619 0.00 2.61 0.00 4.79
3633 4816 5.813080 AAAACGCTCTTACATTATGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
3634 4817 5.941058 TCAAAAACGCTCTTACATTATGGGA 59.059 36.000 0.00 0.00 0.00 4.37
3635 4818 6.027749 GTCAAAAACGCTCTTACATTATGGG 58.972 40.000 0.00 0.00 0.00 4.00
3636 4819 6.523201 GTGTCAAAAACGCTCTTACATTATGG 59.477 38.462 0.00 0.00 35.42 2.74
3637 4820 7.298122 AGTGTCAAAAACGCTCTTACATTATG 58.702 34.615 0.00 0.00 45.69 1.90
3638 4821 7.435068 AGTGTCAAAAACGCTCTTACATTAT 57.565 32.000 0.00 0.00 45.69 1.28
3639 4822 6.854496 AGTGTCAAAAACGCTCTTACATTA 57.146 33.333 0.00 0.00 45.69 1.90
3640 4823 5.751243 AGTGTCAAAAACGCTCTTACATT 57.249 34.783 0.00 0.00 45.69 2.71
3641 4824 5.989777 AGTAGTGTCAAAAACGCTCTTACAT 59.010 36.000 0.00 0.00 45.69 2.29
3642 4825 5.353938 AGTAGTGTCAAAAACGCTCTTACA 58.646 37.500 0.00 0.00 45.69 2.41
3643 4826 5.902051 AGTAGTGTCAAAAACGCTCTTAC 57.098 39.130 0.00 0.00 45.69 2.34
3644 4827 6.742109 ACTAGTAGTGTCAAAAACGCTCTTA 58.258 36.000 0.85 0.00 45.69 2.10
3645 4828 5.598769 ACTAGTAGTGTCAAAAACGCTCTT 58.401 37.500 0.85 0.00 45.69 2.85
3646 4829 5.197682 ACTAGTAGTGTCAAAAACGCTCT 57.802 39.130 0.85 0.00 45.69 4.09
3647 4830 7.578169 AATACTAGTAGTGTCAAAAACGCTC 57.422 36.000 13.29 0.00 45.69 5.03
3649 4832 8.066000 ACAAAATACTAGTAGTGTCAAAAACGC 58.934 33.333 13.29 0.00 38.74 4.84
3650 4833 9.925268 AACAAAATACTAGTAGTGTCAAAAACG 57.075 29.630 13.29 0.00 0.00 3.60
3669 4852 9.736023 GAACAGTCAGAGTTATTTGAACAAAAT 57.264 29.630 4.12 0.00 41.47 1.82
3676 4859 6.483307 CACAAGGAACAGTCAGAGTTATTTGA 59.517 38.462 0.00 0.00 31.89 2.69
3692 4875 1.111277 ACAACAAGGGCACAAGGAAC 58.889 50.000 0.00 0.00 0.00 3.62
3693 4876 1.859302 AACAACAAGGGCACAAGGAA 58.141 45.000 0.00 0.00 0.00 3.36
3699 4882 2.890945 AGGACATTAACAACAAGGGCAC 59.109 45.455 0.00 0.00 0.00 5.01
3712 4895 4.098349 ACACCGCGTAAATCTAGGACATTA 59.902 41.667 4.92 0.00 0.00 1.90
3718 4901 1.135527 TGGACACCGCGTAAATCTAGG 59.864 52.381 4.92 0.00 0.00 3.02
3743 4926 9.706691 ATAATTTGACTTACCACTATACGGATG 57.293 33.333 0.00 0.00 0.00 3.51
3776 4960 8.362639 CCTACCAGTATAAGAGCGGTTAATAAA 58.637 37.037 0.00 0.00 0.00 1.40
3786 4970 7.756395 TGTACATACCTACCAGTATAAGAGC 57.244 40.000 0.00 0.00 31.66 4.09
3833 5022 1.941812 CAGTTCAGTTCCACGGCAC 59.058 57.895 0.00 0.00 0.00 5.01
3837 5026 0.882042 AGCTGCAGTTCAGTTCCACG 60.882 55.000 16.64 0.00 44.66 4.94
4216 5426 3.057174 TGAACCACGCCCATAAATTGTTC 60.057 43.478 0.00 0.00 33.32 3.18
4217 5427 2.894126 TGAACCACGCCCATAAATTGTT 59.106 40.909 0.00 0.00 0.00 2.83
4284 5494 6.929049 CGTGGAACTTCTCCTGCAATTATATA 59.071 38.462 0.00 0.00 45.64 0.86
4285 5495 5.760253 CGTGGAACTTCTCCTGCAATTATAT 59.240 40.000 0.00 0.00 45.64 0.86
4286 5496 5.116180 CGTGGAACTTCTCCTGCAATTATA 58.884 41.667 0.00 0.00 45.64 0.98
4287 5497 3.941483 CGTGGAACTTCTCCTGCAATTAT 59.059 43.478 0.00 0.00 45.64 1.28
4288 5498 3.244422 ACGTGGAACTTCTCCTGCAATTA 60.244 43.478 0.00 0.00 45.64 1.40
4317 5527 1.767759 CATCCTTGTTGCCCCTTAGG 58.232 55.000 0.00 0.00 39.47 2.69
4347 5557 0.895530 TCACTTGAAGGTAGAGGGCG 59.104 55.000 0.00 0.00 0.00 6.13
4487 5697 3.210012 ATTGTTGCAGGGAGGCCGT 62.210 57.895 0.00 0.00 0.00 5.68
4495 5705 3.383761 GAAAACACTCCATTGTTGCAGG 58.616 45.455 0.00 0.00 39.70 4.85
4513 5723 2.998772 GCAGTTGCAGATGAAACGAAA 58.001 42.857 4.54 0.00 38.61 3.46
4760 5973 5.355071 GTGCATGACCTTGAGATCATTACAA 59.645 40.000 0.00 0.00 33.18 2.41
4761 5974 4.877823 GTGCATGACCTTGAGATCATTACA 59.122 41.667 0.00 0.00 33.18 2.41
4762 5975 4.274459 GGTGCATGACCTTGAGATCATTAC 59.726 45.833 0.00 0.00 42.25 1.89
4763 5976 4.080413 TGGTGCATGACCTTGAGATCATTA 60.080 41.667 13.32 0.00 46.32 1.90
4764 5977 3.285484 GGTGCATGACCTTGAGATCATT 58.715 45.455 0.00 0.00 42.25 2.57
4778 5999 2.552315 ACCTAAGAAACGTTGGTGCATG 59.448 45.455 0.00 0.00 0.00 4.06
4782 6003 2.546789 GGTCACCTAAGAAACGTTGGTG 59.453 50.000 22.38 22.38 46.71 4.17
4784 6005 2.148768 GGGTCACCTAAGAAACGTTGG 58.851 52.381 0.00 0.00 0.00 3.77
4788 6009 0.390735 CCGGGGTCACCTAAGAAACG 60.391 60.000 0.00 0.00 36.97 3.60
4802 6023 1.312371 CCACACATGTTAAGCCGGGG 61.312 60.000 2.18 0.00 0.00 5.73
4809 6030 6.025749 TGTTTGTTTCACCACACATGTTAA 57.974 33.333 0.00 0.00 0.00 2.01
4816 6037 3.617669 CGATCTGTTTGTTTCACCACAC 58.382 45.455 0.00 0.00 0.00 3.82
4817 6038 2.032799 GCGATCTGTTTGTTTCACCACA 59.967 45.455 0.00 0.00 0.00 4.17
4818 6039 2.604614 GGCGATCTGTTTGTTTCACCAC 60.605 50.000 0.00 0.00 0.00 4.16
4819 6040 1.606668 GGCGATCTGTTTGTTTCACCA 59.393 47.619 0.00 0.00 0.00 4.17
4820 6041 1.880027 AGGCGATCTGTTTGTTTCACC 59.120 47.619 0.00 0.00 0.00 4.02
4822 6043 3.003275 GTGAAGGCGATCTGTTTGTTTCA 59.997 43.478 0.00 0.00 0.00 2.69
4823 6044 3.555518 GTGAAGGCGATCTGTTTGTTTC 58.444 45.455 0.00 0.00 0.00 2.78
4824 6045 2.032030 CGTGAAGGCGATCTGTTTGTTT 60.032 45.455 0.00 0.00 0.00 2.83
5043 6264 2.526873 ACCGCAGACTCCACCCTT 60.527 61.111 0.00 0.00 0.00 3.95
5055 6276 4.020617 CCCTTGAGCCTCACCGCA 62.021 66.667 0.00 0.00 0.00 5.69
5154 6377 5.163754 GCTCCTAAAAATGTGCAACGAGTAT 60.164 40.000 0.00 0.00 42.39 2.12
5266 6489 4.391216 CGTCTCTGAACAATTGAAGAGCAT 59.609 41.667 22.01 0.00 36.84 3.79
5268 6491 3.124297 CCGTCTCTGAACAATTGAAGAGC 59.876 47.826 22.01 17.81 36.84 4.09
5272 6495 3.804036 ACACCGTCTCTGAACAATTGAA 58.196 40.909 13.59 0.00 0.00 2.69
5380 6603 1.714541 TTTCTGCCTTTTCCATGCCA 58.285 45.000 0.00 0.00 0.00 4.92
5381 6604 2.837532 TTTTCTGCCTTTTCCATGCC 57.162 45.000 0.00 0.00 0.00 4.40
5382 6605 4.317488 TGATTTTTCTGCCTTTTCCATGC 58.683 39.130 0.00 0.00 0.00 4.06
5393 6616 6.389091 TGATTGGTGTACATGATTTTTCTGC 58.611 36.000 0.00 0.00 0.00 4.26
5519 6747 2.538737 CGTCACACAAACAAATGCGAGT 60.539 45.455 0.00 0.00 0.00 4.18
5539 6767 4.228912 AGTTCAAACTGAAAAGCCATCG 57.771 40.909 0.00 0.00 38.22 3.84
5614 6842 0.106819 GGAACCAGATGGAGCATGCT 60.107 55.000 22.92 22.92 38.94 3.79
5615 6843 2.412605 GGAACCAGATGGAGCATGC 58.587 57.895 10.51 10.51 38.94 4.06
5640 6868 8.877195 ACTGTCTTAATACCAGGAGTAAAGAAA 58.123 33.333 0.00 0.00 32.26 2.52
5642 6870 9.537852 TTACTGTCTTAATACCAGGAGTAAAGA 57.462 33.333 0.00 0.00 33.70 2.52
5661 6889 7.813852 ACACATTAAAGACGAGATTACTGTC 57.186 36.000 0.00 0.00 0.00 3.51
5672 6900 3.845775 CGCCAATCAACACATTAAAGACG 59.154 43.478 0.00 0.00 0.00 4.18
5677 6905 2.520069 ACCCGCCAATCAACACATTAA 58.480 42.857 0.00 0.00 0.00 1.40
5680 6908 0.602562 CAACCCGCCAATCAACACAT 59.397 50.000 0.00 0.00 0.00 3.21
5702 6930 2.676632 TAAACGAGGCCAATAAGCGA 57.323 45.000 5.01 0.00 0.00 4.93
5703 6931 2.869801 TCATAAACGAGGCCAATAAGCG 59.130 45.455 5.01 0.70 0.00 4.68
5704 6932 3.625764 TGTCATAAACGAGGCCAATAAGC 59.374 43.478 5.01 0.00 0.00 3.09
5705 6933 4.876107 ACTGTCATAAACGAGGCCAATAAG 59.124 41.667 5.01 0.00 0.00 1.73
5706 6934 4.839121 ACTGTCATAAACGAGGCCAATAA 58.161 39.130 5.01 0.00 0.00 1.40
5707 6935 4.481368 ACTGTCATAAACGAGGCCAATA 57.519 40.909 5.01 0.00 0.00 1.90
5708 6936 3.350219 ACTGTCATAAACGAGGCCAAT 57.650 42.857 5.01 0.00 0.00 3.16
5709 6937 2.851263 ACTGTCATAAACGAGGCCAA 57.149 45.000 5.01 0.00 0.00 4.52
5710 6938 2.851263 AACTGTCATAAACGAGGCCA 57.149 45.000 5.01 0.00 0.00 5.36
5711 6939 3.125316 CAGAAACTGTCATAAACGAGGCC 59.875 47.826 0.00 0.00 0.00 5.19
5712 6940 3.746492 ACAGAAACTGTCATAAACGAGGC 59.254 43.478 0.00 0.00 41.21 4.70
5724 6952 6.151985 CTGGTACTATCAGAGACAGAAACTGT 59.848 42.308 4.01 4.01 39.74 3.55
5725 6953 6.516739 TGGTACTATCAGAGACAGAAACTG 57.483 41.667 0.00 0.00 37.52 3.16
5726 6954 5.126384 GCTGGTACTATCAGAGACAGAAACT 59.874 44.000 0.02 0.00 34.36 2.66
5727 6955 5.126384 AGCTGGTACTATCAGAGACAGAAAC 59.874 44.000 0.02 0.00 34.36 2.78
5728 6956 5.265191 AGCTGGTACTATCAGAGACAGAAA 58.735 41.667 0.02 0.00 34.36 2.52
5729 6957 4.861196 AGCTGGTACTATCAGAGACAGAA 58.139 43.478 0.02 0.00 34.36 3.02
5730 6958 4.456535 GAGCTGGTACTATCAGAGACAGA 58.543 47.826 0.02 0.00 34.36 3.41
5731 6959 3.568007 GGAGCTGGTACTATCAGAGACAG 59.432 52.174 0.02 0.00 34.36 3.51
5732 6960 3.203263 AGGAGCTGGTACTATCAGAGACA 59.797 47.826 0.02 0.00 34.36 3.41
5733 6961 3.818773 GAGGAGCTGGTACTATCAGAGAC 59.181 52.174 0.02 0.00 34.36 3.36
5734 6962 3.719479 AGAGGAGCTGGTACTATCAGAGA 59.281 47.826 0.02 0.00 34.36 3.10
5735 6963 3.820467 CAGAGGAGCTGGTACTATCAGAG 59.180 52.174 0.02 0.00 41.07 3.35
5736 6964 3.826524 CAGAGGAGCTGGTACTATCAGA 58.173 50.000 0.02 0.00 41.07 3.27
5737 6965 2.295909 GCAGAGGAGCTGGTACTATCAG 59.704 54.545 0.00 0.00 45.03 2.90
5738 6966 2.311463 GCAGAGGAGCTGGTACTATCA 58.689 52.381 0.00 0.00 45.03 2.15
5746 6974 3.073735 ACGGAGCAGAGGAGCTGG 61.074 66.667 0.00 0.00 46.75 4.85
5747 6975 2.493973 GACGGAGCAGAGGAGCTG 59.506 66.667 0.00 0.00 46.75 4.24
5749 6977 3.844090 GGGACGGAGCAGAGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
5812 7044 5.516339 CCTCAACTGTTGTTCAACAATTCAC 59.484 40.000 19.12 0.00 40.59 3.18
5835 7067 1.280421 AGCCAGAAAGAGTGTCCATCC 59.720 52.381 0.00 0.00 0.00 3.51
5920 7152 1.003696 GGCTAGTTCTGGCTGGTCTTT 59.996 52.381 7.97 0.00 0.00 2.52
5921 7153 0.615850 GGCTAGTTCTGGCTGGTCTT 59.384 55.000 7.97 0.00 0.00 3.01
5924 7156 0.842467 AAGGGCTAGTTCTGGCTGGT 60.842 55.000 7.97 0.00 0.00 4.00
5925 7157 1.139853 CTAAGGGCTAGTTCTGGCTGG 59.860 57.143 7.97 0.00 0.00 4.85
5926 7158 1.834263 ACTAAGGGCTAGTTCTGGCTG 59.166 52.381 7.97 0.00 37.61 4.85
5927 7159 1.834263 CACTAAGGGCTAGTTCTGGCT 59.166 52.381 7.97 0.00 38.92 4.75
5928 7160 1.134371 CCACTAAGGGCTAGTTCTGGC 60.134 57.143 0.00 0.00 38.92 4.85
5929 7161 2.093447 CACCACTAAGGGCTAGTTCTGG 60.093 54.545 0.00 0.00 38.92 3.86
5930 7162 2.093447 CCACCACTAAGGGCTAGTTCTG 60.093 54.545 0.00 0.00 38.92 3.02
5931 7163 2.188817 CCACCACTAAGGGCTAGTTCT 58.811 52.381 0.00 0.00 38.92 3.01
5932 7164 1.407025 GCCACCACTAAGGGCTAGTTC 60.407 57.143 0.00 0.00 44.32 3.01
5933 7165 0.618981 GCCACCACTAAGGGCTAGTT 59.381 55.000 0.00 0.00 44.32 2.24
5934 7166 2.297937 GCCACCACTAAGGGCTAGT 58.702 57.895 0.00 0.00 44.32 2.57
5939 7171 5.301805 CCTAAAAATATGCCACCACTAAGGG 59.698 44.000 0.00 0.00 43.89 3.95
5940 7172 5.301805 CCCTAAAAATATGCCACCACTAAGG 59.698 44.000 0.00 0.00 45.67 2.69
5941 7173 6.126409 TCCCTAAAAATATGCCACCACTAAG 58.874 40.000 0.00 0.00 0.00 2.18
5942 7174 6.080969 TCCCTAAAAATATGCCACCACTAA 57.919 37.500 0.00 0.00 0.00 2.24
5943 7175 5.718801 TCCCTAAAAATATGCCACCACTA 57.281 39.130 0.00 0.00 0.00 2.74
5944 7176 4.601406 TCCCTAAAAATATGCCACCACT 57.399 40.909 0.00 0.00 0.00 4.00
5945 7177 5.476945 CCTATCCCTAAAAATATGCCACCAC 59.523 44.000 0.00 0.00 0.00 4.16
5946 7178 5.135362 ACCTATCCCTAAAAATATGCCACCA 59.865 40.000 0.00 0.00 0.00 4.17
5947 7179 5.476945 CACCTATCCCTAAAAATATGCCACC 59.523 44.000 0.00 0.00 0.00 4.61
5948 7180 5.476945 CCACCTATCCCTAAAAATATGCCAC 59.523 44.000 0.00 0.00 0.00 5.01
5949 7181 5.640147 CCACCTATCCCTAAAAATATGCCA 58.360 41.667 0.00 0.00 0.00 4.92
5950 7182 4.462834 GCCACCTATCCCTAAAAATATGCC 59.537 45.833 0.00 0.00 0.00 4.40
5951 7183 4.462834 GGCCACCTATCCCTAAAAATATGC 59.537 45.833 0.00 0.00 0.00 3.14
5952 7184 5.640147 TGGCCACCTATCCCTAAAAATATG 58.360 41.667 0.00 0.00 0.00 1.78
5953 7185 5.615261 TCTGGCCACCTATCCCTAAAAATAT 59.385 40.000 0.00 0.00 0.00 1.28
5954 7186 4.979039 TCTGGCCACCTATCCCTAAAAATA 59.021 41.667 0.00 0.00 0.00 1.40
5955 7187 3.791545 TCTGGCCACCTATCCCTAAAAAT 59.208 43.478 0.00 0.00 0.00 1.82
5971 7203 2.352805 CTGGACCTTGGTCTGGCC 59.647 66.667 17.99 0.00 37.90 5.36
5976 7208 1.209747 GATGGTACCTGGACCTTGGTC 59.790 57.143 14.36 11.13 40.46 4.02
6085 7317 2.213499 CCGCAATCATGGAGGAAGTAC 58.787 52.381 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.