Multiple sequence alignment - TraesCS1A01G065300

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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 TraesCS1A01G065300 chr1A 100.000 8788 0 0 1 8788 47579617 47588404 0.000000e+00 16229.0
1 TraesCS1A01G065300 chr1A 95.000 40 2 0 3372 3411 15192549 15192588 7.370000e-06 63.9
2 TraesCS1A01G065300 chr1D 95.269 3995 117 26 2716 6683 47710959 47714908 0.000000e+00 6264.0
3 TraesCS1A01G065300 chr1D 92.790 2247 81 20 524 2744 47708705 47710896 0.000000e+00 3177.0
4 TraesCS1A01G065300 chr1D 96.818 880 26 2 7218 8097 47715620 47716497 0.000000e+00 1469.0
5 TraesCS1A01G065300 chr1D 96.565 524 15 2 6681 7203 47715044 47715565 0.000000e+00 865.0
6 TraesCS1A01G065300 chr1D 86.464 724 52 16 8091 8788 47721987 47722690 0.000000e+00 752.0
7 TraesCS1A01G065300 chr1D 94.421 484 24 3 2 483 47708221 47708703 0.000000e+00 741.0
8 TraesCS1A01G065300 chr1D 87.000 100 6 6 476 573 216848253 216848347 1.210000e-18 106.0
9 TraesCS1A01G065300 chr1D 86.000 100 7 6 476 573 207834849 207834943 5.610000e-17 100.0
10 TraesCS1A01G065300 chr1D 92.982 57 3 1 6618 6673 48391408 48391464 2.030000e-11 82.4
11 TraesCS1A01G065300 chr1B 94.564 3753 128 31 3 3711 67441974 67445694 0.000000e+00 5731.0
12 TraesCS1A01G065300 chr1B 95.098 2856 97 22 3694 6529 67445817 67448649 0.000000e+00 4458.0
13 TraesCS1A01G065300 chr1B 95.033 1047 34 3 7211 8257 67449056 67450084 0.000000e+00 1629.0
14 TraesCS1A01G065300 chr1B 97.814 366 7 1 6841 7205 67448645 67449010 1.610000e-176 630.0
15 TraesCS1A01G065300 chr1B 85.992 257 18 6 8541 8788 67450551 67450798 8.750000e-65 259.0
16 TraesCS1A01G065300 chr1B 88.439 173 15 2 8271 8438 67450270 67450442 4.160000e-48 204.0
17 TraesCS1A01G065300 chr1B 93.617 94 5 1 8419 8511 67450457 67450550 1.190000e-28 139.0
18 TraesCS1A01G065300 chr5A 90.538 1226 66 17 3699 4895 169808410 169809614 0.000000e+00 1576.0
19 TraesCS1A01G065300 chr5A 93.299 985 57 5 3699 4680 598959986 598960964 0.000000e+00 1445.0
20 TraesCS1A01G065300 chr5A 90.435 230 11 5 4666 4895 598960978 598961196 8.630000e-75 292.0
21 TraesCS1A01G065300 chr2B 89.951 1224 65 21 3699 4895 789678311 789679503 0.000000e+00 1526.0
22 TraesCS1A01G065300 chr2D 93.535 990 49 7 3699 4680 484800054 484799072 0.000000e+00 1459.0
23 TraesCS1A01G065300 chr2D 93.496 246 15 1 4666 4911 478676233 478675989 1.800000e-96 364.0
24 TraesCS1A01G065300 chr2D 92.683 246 16 2 4666 4911 484799058 484798815 3.900000e-93 353.0
25 TraesCS1A01G065300 chr2D 83.582 67 8 3 2562 2626 535105558 535105623 9.530000e-05 60.2
26 TraesCS1A01G065300 chr6B 93.401 985 56 5 3699 4680 720468797 720467819 0.000000e+00 1450.0
27 TraesCS1A01G065300 chr6B 93.198 985 58 5 3699 4680 705172627 705171649 0.000000e+00 1439.0
28 TraesCS1A01G065300 chr6B 93.096 985 59 5 3699 4680 653299685 653298707 0.000000e+00 1434.0
29 TraesCS1A01G065300 chr6B 89.700 233 13 5 4666 4898 653298693 653298472 4.010000e-73 287.0
30 TraesCS1A01G065300 chr6B 89.700 233 13 5 4666 4898 705171635 705171414 4.010000e-73 287.0
31 TraesCS1A01G065300 chr5B 93.198 985 58 5 3699 4680 461870784 461869806 0.000000e+00 1439.0
32 TraesCS1A01G065300 chr5B 89.700 233 13 5 4666 4898 461869792 461869571 4.010000e-73 287.0
33 TraesCS1A01G065300 chr3A 93.089 246 15 2 4666 4911 452367896 452368139 8.390000e-95 359.0
34 TraesCS1A01G065300 chr3A 82.036 167 18 6 1868 2028 426862712 426862872 1.990000e-26 132.0
35 TraesCS1A01G065300 chr3A 93.220 59 3 1 6618 6675 34532504 34532446 1.570000e-12 86.1
36 TraesCS1A01G065300 chr4B 91.870 246 18 2 4666 4911 549922985 549923228 8.450000e-90 342.0
37 TraesCS1A01G065300 chr3B 88.024 167 13 1 737 903 168938024 168938183 3.240000e-44 191.0
38 TraesCS1A01G065300 chr3B 78.313 166 15 10 1869 2028 414018446 414018596 4.370000e-13 87.9
39 TraesCS1A01G065300 chr3B 93.220 59 3 1 6618 6675 42630873 42630815 1.570000e-12 86.1
40 TraesCS1A01G065300 chr3B 92.982 57 3 1 6618 6673 556089701 556089757 2.030000e-11 82.4
41 TraesCS1A01G065300 chr6D 91.358 81 5 2 474 553 336354132 336354211 9.330000e-20 110.0
42 TraesCS1A01G065300 chr6D 85.859 99 8 5 476 573 163255405 163255498 5.610000e-17 100.0
43 TraesCS1A01G065300 chr4A 86.869 99 7 5 476 573 182478729 182478636 1.210000e-18 106.0
44 TraesCS1A01G065300 chr4A 91.803 61 4 1 6618 6677 71997827 71997887 5.650000e-12 84.2
45 TraesCS1A01G065300 chr3D 87.500 96 6 5 479 573 124764702 124764792 1.210000e-18 106.0
46 TraesCS1A01G065300 chr3D 92.982 57 3 1 6618 6673 426451914 426451858 2.030000e-11 82.4
47 TraesCS1A01G065300 chr3D 89.231 65 6 1 2573 2636 558222107 558222043 7.310000e-11 80.5
48 TraesCS1A01G065300 chr3D 85.938 64 6 3 2567 2628 406158324 406158386 2.050000e-06 65.8
49 TraesCS1A01G065300 chr7A 86.139 101 8 5 474 573 464911313 464911408 4.340000e-18 104.0
50 TraesCS1A01G065300 chr7A 89.655 58 5 1 2574 2630 290618252 290618195 1.220000e-08 73.1
51 TraesCS1A01G065300 chr7A 80.000 85 13 4 2545 2626 60731045 60731128 9.530000e-05 60.2
52 TraesCS1A01G065300 chr7B 92.982 57 2 2 6618 6673 568676561 568676616 2.030000e-11 82.4
53 TraesCS1A01G065300 chr5D 89.552 67 4 3 2572 2636 439641842 439641777 2.030000e-11 82.4
54 TraesCS1A01G065300 chr5D 86.111 72 8 2 6618 6688 464070504 464070574 9.460000e-10 76.8
55 TraesCS1A01G065300 chr7D 82.353 85 11 4 2545 2626 56946617 56946700 4.400000e-08 71.3
56 TraesCS1A01G065300 chr4D 97.436 39 1 0 3373 3411 179862498 179862536 5.690000e-07 67.6
57 TraesCS1A01G065300 chr2A 100.000 34 0 0 3372 3405 174427276 174427243 7.370000e-06 63.9


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 TraesCS1A01G065300 chr1A 47579617 47588404 8787 False 16229.000000 16229 100.000000 1 8788 1 chr1A.!!$F2 8787
1 TraesCS1A01G065300 chr1D 47708221 47716497 8276 False 2503.200000 6264 95.172600 2 8097 5 chr1D.!!$F5 8095
2 TraesCS1A01G065300 chr1D 47721987 47722690 703 False 752.000000 752 86.464000 8091 8788 1 chr1D.!!$F1 697
3 TraesCS1A01G065300 chr1B 67441974 67450798 8824 False 1864.285714 5731 92.936714 3 8788 7 chr1B.!!$F1 8785
4 TraesCS1A01G065300 chr5A 169808410 169809614 1204 False 1576.000000 1576 90.538000 3699 4895 1 chr5A.!!$F1 1196
5 TraesCS1A01G065300 chr5A 598959986 598961196 1210 False 868.500000 1445 91.867000 3699 4895 2 chr5A.!!$F2 1196
6 TraesCS1A01G065300 chr2B 789678311 789679503 1192 False 1526.000000 1526 89.951000 3699 4895 1 chr2B.!!$F1 1196
7 TraesCS1A01G065300 chr2D 484798815 484800054 1239 True 906.000000 1459 93.109000 3699 4911 2 chr2D.!!$R2 1212
8 TraesCS1A01G065300 chr6B 720467819 720468797 978 True 1450.000000 1450 93.401000 3699 4680 1 chr6B.!!$R1 981
9 TraesCS1A01G065300 chr6B 705171414 705172627 1213 True 863.000000 1439 91.449000 3699 4898 2 chr6B.!!$R3 1199
10 TraesCS1A01G065300 chr6B 653298472 653299685 1213 True 860.500000 1434 91.398000 3699 4898 2 chr6B.!!$R2 1199
11 TraesCS1A01G065300 chr5B 461869571 461870784 1213 True 863.000000 1439 91.449000 3699 4898 2 chr5B.!!$R1 1199

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
513 551 0.806102 GCCACGAGTGTGCGTATCAT 60.806 55.000 2.36 0.0 45.04 2.45 F
1486 1533 0.188587 TCAGGGAGGCCGTATCAGAT 59.811 55.000 0.00 0.0 0.00 2.90 F
1749 1796 0.796312 CGCACTGTCCGTTTTATGCT 59.204 50.000 0.00 0.0 0.00 3.79 F
1979 2030 2.887790 AGTCCGCATAGCTGACTCA 58.112 52.632 9.77 0.0 46.95 3.41 F
2637 2730 2.921121 TGTACTAAAGCTGCGACAATCG 59.079 45.455 0.00 0.0 43.89 3.34 F
3624 3832 0.912486 CCTCCCCGTCAGGAAATTCT 59.088 55.000 0.00 0.0 41.02 2.40 F
4685 5075 1.484038 AGGTGTTTGGCTTTCTGCAA 58.516 45.000 0.00 0.0 45.15 4.08 F
4833 5233 0.250295 GCAGCTGTGTTGGTAGTCCA 60.250 55.000 16.64 0.0 42.66 4.02 F
6659 7075 0.610174 TGTGGGAGCTTCTAGCACTG 59.390 55.000 1.09 0.0 45.56 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2024 1.300620 CTCACCCGCGTTTGAGTCA 60.301 57.895 20.59 0.00 35.48 3.41 R
3322 3523 0.530744 TACTAACGCAGCTCTGTGGG 59.469 55.000 14.09 6.97 44.78 4.61 R
3325 3526 1.835494 TCCTACTAACGCAGCTCTGT 58.165 50.000 0.00 0.00 0.00 3.41 R
3611 3819 1.927895 AGCGCTAGAATTTCCTGACG 58.072 50.000 8.99 0.00 0.00 4.35 R
4422 4784 2.813754 TGCTTGCTGTGGTTCATTACTC 59.186 45.455 0.00 0.00 0.00 2.59 R
4833 5233 0.106519 ACAAACTTCCAGCCTGCACT 60.107 50.000 0.00 0.00 0.00 4.40 R
6635 7051 0.539051 CTAGAAGCTCCCACACCAGG 59.461 60.000 0.00 0.00 0.00 4.45 R
6725 7279 1.390565 CCACTCCTCCTACTACCACG 58.609 60.000 0.00 0.00 0.00 4.94 R
8654 9482 0.460987 CGAACATGACTGCTCTCCCC 60.461 60.000 0.00 0.00 0.00 4.81 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
127 128 3.496870 CCTCAGTTTTGGCCTAGTCTTGT 60.497 47.826 3.32 0.00 0.00 3.16
130 131 1.953686 GTTTTGGCCTAGTCTTGTGCA 59.046 47.619 3.32 0.00 0.00 4.57
138 139 3.648009 CCTAGTCTTGTGCATAGCTAGC 58.352 50.000 6.62 6.62 0.00 3.42
184 185 2.650322 TCCACTTTCTTGGCGTTTTCT 58.350 42.857 0.00 0.00 36.48 2.52
198 200 5.589452 TGGCGTTTTCTTCCTAGTACAAAAA 59.411 36.000 0.00 0.00 0.00 1.94
217 219 7.577979 ACAAAAATGACACATTTTGATGCATC 58.422 30.769 24.33 20.14 45.09 3.91
388 392 6.919662 ACTGTTTCTCATTTGCTGTGTTATTG 59.080 34.615 0.00 0.00 0.00 1.90
445 449 5.582689 CACTTTATGCTCCCCCTTTAAAG 57.417 43.478 8.32 8.32 0.00 1.85
501 539 4.398549 TTTTTCTTGAATACGCCACGAG 57.601 40.909 0.00 0.00 0.00 4.18
502 540 2.736144 TTCTTGAATACGCCACGAGT 57.264 45.000 0.00 0.00 0.00 4.18
503 541 1.990799 TCTTGAATACGCCACGAGTG 58.009 50.000 0.00 0.00 0.00 3.51
504 542 1.271379 TCTTGAATACGCCACGAGTGT 59.729 47.619 2.36 0.00 43.23 3.55
505 543 1.390123 CTTGAATACGCCACGAGTGTG 59.610 52.381 2.36 0.00 46.00 3.82
506 544 1.011968 TGAATACGCCACGAGTGTGC 61.012 55.000 2.36 4.84 45.04 4.57
510 548 2.506217 CGCCACGAGTGTGCGTAT 60.506 61.111 21.84 0.00 45.04 3.06
511 549 2.505498 CGCCACGAGTGTGCGTATC 61.505 63.158 21.84 0.00 45.04 2.24
512 550 1.445410 GCCACGAGTGTGCGTATCA 60.445 57.895 2.36 0.00 45.04 2.15
513 551 0.806102 GCCACGAGTGTGCGTATCAT 60.806 55.000 2.36 0.00 45.04 2.45
514 552 1.640428 CCACGAGTGTGCGTATCATT 58.360 50.000 2.36 0.00 45.04 2.57
515 553 1.588404 CCACGAGTGTGCGTATCATTC 59.412 52.381 2.36 0.00 45.04 2.67
516 554 2.258755 CACGAGTGTGCGTATCATTCA 58.741 47.619 0.00 0.00 43.59 2.57
517 555 2.860136 CACGAGTGTGCGTATCATTCAT 59.140 45.455 0.00 0.00 43.59 2.57
518 556 3.306973 CACGAGTGTGCGTATCATTCATT 59.693 43.478 0.00 0.00 43.59 2.57
519 557 4.502645 CACGAGTGTGCGTATCATTCATTA 59.497 41.667 0.00 0.00 43.59 1.90
520 558 5.005299 CACGAGTGTGCGTATCATTCATTAA 59.995 40.000 0.00 0.00 43.59 1.40
521 559 5.579119 ACGAGTGTGCGTATCATTCATTAAA 59.421 36.000 0.00 0.00 43.61 1.52
522 560 6.122782 CGAGTGTGCGTATCATTCATTAAAG 58.877 40.000 0.00 0.00 0.00 1.85
587 626 3.104512 AGTTACACGGATTCCTCCATCA 58.895 45.455 0.30 0.00 42.19 3.07
616 663 6.839134 TCCACTCCACATCTAACACATACTAT 59.161 38.462 0.00 0.00 0.00 2.12
617 664 7.014326 TCCACTCCACATCTAACACATACTATC 59.986 40.741 0.00 0.00 0.00 2.08
702 749 3.756117 CTTGCCTCCAAACTCTACCTTT 58.244 45.455 0.00 0.00 0.00 3.11
718 765 3.944087 ACCTTTGCTGTCAATCCTCTAC 58.056 45.455 0.00 0.00 31.33 2.59
743 790 8.585881 ACAAAGCTCTACTGTTATCAACTTCTA 58.414 33.333 0.00 0.00 0.00 2.10
877 924 6.958255 TCACATACAGACTGTTTTTGTGATG 58.042 36.000 27.52 19.90 37.97 3.07
905 952 7.192913 TCAATTGCGTTATTTAAGCATAGGTG 58.807 34.615 0.00 0.00 40.83 4.00
968 1015 5.611796 TTGAGAAGTGATCAATGGTTTCG 57.388 39.130 0.00 0.00 31.86 3.46
1052 1099 2.746362 GACCATCTCAACAAGAGCAAGG 59.254 50.000 0.00 0.00 44.35 3.61
1215 1262 3.893326 TCAAGAGAATCCAATCGCTCA 57.107 42.857 0.00 0.00 33.66 4.26
1290 1337 2.436115 GTAAGAGGCCCGTGGTGC 60.436 66.667 0.00 0.00 0.00 5.01
1377 1424 3.875134 CTGGGTTTCGGGTATGTGATTAC 59.125 47.826 0.00 0.00 0.00 1.89
1436 1483 9.166126 GTTTATATATGTTTACCGCTTCTTTGC 57.834 33.333 0.00 0.00 0.00 3.68
1486 1533 0.188587 TCAGGGAGGCCGTATCAGAT 59.811 55.000 0.00 0.00 0.00 2.90
1605 1652 7.105241 ACAATACCTAGTAAACCTCTTACGG 57.895 40.000 0.00 0.00 0.00 4.02
1640 1687 4.152938 GGTTTCGTTGTAACCCTGTACATC 59.847 45.833 0.00 0.00 39.29 3.06
1683 1730 6.475727 GCTTCTGTTTAACTTGTTTTTCTCCC 59.524 38.462 0.00 0.00 0.00 4.30
1686 1733 4.098196 TGTTTAACTTGTTTTTCTCCCGGG 59.902 41.667 16.85 16.85 0.00 5.73
1742 1789 1.944032 ACTTTTACGCACTGTCCGTT 58.056 45.000 0.62 0.00 39.88 4.44
1749 1796 0.796312 CGCACTGTCCGTTTTATGCT 59.204 50.000 0.00 0.00 0.00 3.79
1784 1833 4.815533 AATACTCTGCAGTGTGTCAGAT 57.184 40.909 27.28 12.39 38.50 2.90
1821 1870 7.881142 TCGATGAATTTTACATCAAACTGGTT 58.119 30.769 0.00 0.00 42.68 3.67
1863 1914 9.918630 ATCTATTTTGTTCTTTGTTTCCTCATG 57.081 29.630 0.00 0.00 0.00 3.07
1979 2030 2.887790 AGTCCGCATAGCTGACTCA 58.112 52.632 9.77 0.00 46.95 3.41
2073 2154 9.927081 ATATCAAGAGATTGACCCTTTGTTTAT 57.073 29.630 0.00 0.00 35.67 1.40
2074 2155 8.655935 ATCAAGAGATTGACCCTTTGTTTATT 57.344 30.769 0.00 0.00 33.23 1.40
2075 2156 8.477419 TCAAGAGATTGACCCTTTGTTTATTT 57.523 30.769 0.00 0.00 0.00 1.40
2076 2157 8.359642 TCAAGAGATTGACCCTTTGTTTATTTG 58.640 33.333 0.00 0.00 0.00 2.32
2077 2158 7.839680 AGAGATTGACCCTTTGTTTATTTGT 57.160 32.000 0.00 0.00 0.00 2.83
2078 2159 8.250143 AGAGATTGACCCTTTGTTTATTTGTT 57.750 30.769 0.00 0.00 0.00 2.83
2079 2160 8.360390 AGAGATTGACCCTTTGTTTATTTGTTC 58.640 33.333 0.00 0.00 0.00 3.18
2080 2161 8.250143 AGATTGACCCTTTGTTTATTTGTTCT 57.750 30.769 0.00 0.00 0.00 3.01
2081 2162 8.360390 AGATTGACCCTTTGTTTATTTGTTCTC 58.640 33.333 0.00 0.00 0.00 2.87
2082 2163 7.654022 TTGACCCTTTGTTTATTTGTTCTCT 57.346 32.000 0.00 0.00 0.00 3.10
2083 2164 7.272037 TGACCCTTTGTTTATTTGTTCTCTC 57.728 36.000 0.00 0.00 0.00 3.20
2084 2165 6.831353 TGACCCTTTGTTTATTTGTTCTCTCA 59.169 34.615 0.00 0.00 0.00 3.27
2085 2166 7.340743 TGACCCTTTGTTTATTTGTTCTCTCAA 59.659 33.333 0.00 0.00 0.00 3.02
2086 2167 8.073467 ACCCTTTGTTTATTTGTTCTCTCAAA 57.927 30.769 0.00 0.00 40.74 2.69
2087 2168 8.704668 ACCCTTTGTTTATTTGTTCTCTCAAAT 58.295 29.630 9.12 9.12 45.83 2.32
2088 2169 9.546428 CCCTTTGTTTATTTGTTCTCTCAAATT 57.454 29.630 9.37 0.00 42.88 1.82
2093 2174 9.734620 TGTTTATTTGTTCTCTCAAATTCAGTG 57.265 29.630 9.37 0.00 42.88 3.66
2094 2175 9.736023 GTTTATTTGTTCTCTCAAATTCAGTGT 57.264 29.630 9.37 0.00 42.88 3.55
2098 2179 9.956720 ATTTGTTCTCTCAAATTCAGTGTTAAG 57.043 29.630 0.00 0.00 42.88 1.85
2099 2180 8.506168 TTGTTCTCTCAAATTCAGTGTTAAGT 57.494 30.769 0.00 0.00 0.00 2.24
2100 2181 8.506168 TGTTCTCTCAAATTCAGTGTTAAGTT 57.494 30.769 0.00 0.00 0.00 2.66
2101 2182 8.956426 TGTTCTCTCAAATTCAGTGTTAAGTTT 58.044 29.630 0.00 0.00 0.00 2.66
2555 2636 9.970395 TCACGTTCTGATAGTTAACTAAAAGAA 57.030 29.630 25.16 25.16 34.43 2.52
2602 2683 6.095440 CCTCCGATCCAAATTAATTGTCACTT 59.905 38.462 0.39 0.00 37.32 3.16
2636 2729 4.389077 AGTTGTACTAAAGCTGCGACAATC 59.611 41.667 0.00 0.00 0.00 2.67
2637 2730 2.921121 TGTACTAAAGCTGCGACAATCG 59.079 45.455 0.00 0.00 43.89 3.34
2688 2791 7.633621 TCATGTATTTCATCAGAGAAAATCGC 58.366 34.615 0.00 0.00 40.54 4.58
2886 3086 8.369424 CCATCCATCATTTCTGGCAAATAATTA 58.631 33.333 0.00 0.00 33.56 1.40
2993 3194 4.705991 TGATCTGTTTTGCAGGCATATTCA 59.294 37.500 0.00 0.00 45.08 2.57
3000 3201 3.632643 TGCAGGCATATTCAAGTCTGA 57.367 42.857 0.00 0.00 39.77 3.27
3120 3321 6.839454 AGTCTACCTCTAGATAACCGAATCA 58.161 40.000 0.00 0.00 31.39 2.57
3150 3351 9.167311 ACTGTTTGTTCTATGATAATTCCTGTC 57.833 33.333 0.00 0.00 0.00 3.51
3284 3485 3.071023 CCCTGAATCCGGAGCATAAGTTA 59.929 47.826 11.34 0.00 0.00 2.24
3335 3536 2.985512 GATAGCCCCACAGAGCTGCG 62.986 65.000 0.00 0.00 40.28 5.18
3471 3672 6.761714 GGCAGGCATTAATACGTTATATAGCT 59.238 38.462 0.00 0.00 0.00 3.32
3611 3819 3.721706 CTGCCACTGACCCTCCCC 61.722 72.222 0.00 0.00 0.00 4.81
3624 3832 0.912486 CCTCCCCGTCAGGAAATTCT 59.088 55.000 0.00 0.00 41.02 2.40
3635 3843 3.809832 TCAGGAAATTCTAGCGCTATTGC 59.190 43.478 19.19 14.31 0.00 3.56
3636 3844 3.058639 CAGGAAATTCTAGCGCTATTGCC 60.059 47.826 19.19 18.25 35.36 4.52
3637 3845 3.142174 GGAAATTCTAGCGCTATTGCCT 58.858 45.455 19.19 2.75 35.36 4.75
3638 3846 4.040461 AGGAAATTCTAGCGCTATTGCCTA 59.960 41.667 24.01 1.45 35.87 3.93
3639 3847 4.938226 GGAAATTCTAGCGCTATTGCCTAT 59.062 41.667 19.19 1.26 35.36 2.57
3640 3848 5.412904 GGAAATTCTAGCGCTATTGCCTATT 59.587 40.000 19.19 7.07 35.36 1.73
3641 3849 5.869753 AATTCTAGCGCTATTGCCTATTG 57.130 39.130 19.19 2.70 35.36 1.90
3642 3850 3.319137 TCTAGCGCTATTGCCTATTGG 57.681 47.619 19.19 1.90 35.36 3.16
3643 3851 2.632996 TCTAGCGCTATTGCCTATTGGT 59.367 45.455 19.19 0.00 35.36 3.67
3977 4331 7.504403 TCAATAAAGTTTTCAAAAGATGGCCA 58.496 30.769 8.56 8.56 0.00 5.36
4050 4404 1.746760 CAAACAAAGTGACAGAGCGC 58.253 50.000 0.00 0.00 0.00 5.92
4083 4437 4.782019 TGTGGTATGAAAGTCAAATGCC 57.218 40.909 0.00 0.00 0.00 4.40
4117 4471 4.262617 GTTCCTTCCATAACCTGTCCTTC 58.737 47.826 0.00 0.00 0.00 3.46
4124 4478 4.785914 TCCATAACCTGTCCTTCCAATGTA 59.214 41.667 0.00 0.00 0.00 2.29
4125 4479 4.881850 CCATAACCTGTCCTTCCAATGTAC 59.118 45.833 0.00 0.00 0.00 2.90
4126 4480 5.339200 CCATAACCTGTCCTTCCAATGTACT 60.339 44.000 0.00 0.00 0.00 2.73
4127 4481 3.703001 ACCTGTCCTTCCAATGTACTG 57.297 47.619 0.00 0.00 0.00 2.74
4128 4482 2.979678 ACCTGTCCTTCCAATGTACTGT 59.020 45.455 0.00 0.00 0.00 3.55
4174 4528 7.966812 ACACATATCTGCTTAGGTCATATTCA 58.033 34.615 0.00 0.00 0.00 2.57
4272 4630 8.008279 GGAGTTTGTTTGTACGATTTTAGTCTC 58.992 37.037 0.00 0.00 0.00 3.36
4277 4635 3.766151 TGTACGATTTTAGTCTCCTGCG 58.234 45.455 0.00 0.00 0.00 5.18
4369 4731 5.057149 GCATCCTCTAATGGTTCGTTATGT 58.943 41.667 0.00 0.00 0.00 2.29
4422 4784 3.609103 GCGTTAGGCATAACAGATTGG 57.391 47.619 20.13 4.88 41.22 3.16
4645 5007 7.065204 GCCAAAAGGAAAATGTCAAACAGTTTA 59.935 33.333 5.60 0.00 44.96 2.01
4685 5075 1.484038 AGGTGTTTGGCTTTCTGCAA 58.516 45.000 0.00 0.00 45.15 4.08
4833 5233 0.250295 GCAGCTGTGTTGGTAGTCCA 60.250 55.000 16.64 0.00 42.66 4.02
4849 5249 4.488790 CAGTGCAGGCTGGAAGTT 57.511 55.556 17.64 0.00 35.30 2.66
4962 5362 1.354101 TGGAACAGTGGTTACGGGAT 58.646 50.000 0.00 0.00 41.00 3.85
5332 5732 6.609212 TCAGTAGAGAAGAAGTTATCTGGCAT 59.391 38.462 0.00 0.00 38.79 4.40
5397 5797 4.923281 AGTTCAAAAACTTATCGGCAATGC 59.077 37.500 0.00 0.00 43.28 3.56
5399 5799 4.233789 TCAAAAACTTATCGGCAATGCAC 58.766 39.130 7.79 0.00 0.00 4.57
5400 5800 3.932545 AAAACTTATCGGCAATGCACA 57.067 38.095 7.79 0.00 0.00 4.57
5469 5880 6.038356 GCAAACTCCAACATGATTTATCTGG 58.962 40.000 0.00 0.00 0.00 3.86
5734 6145 2.479566 TCATCTCCAACTGCAAGGAC 57.520 50.000 0.00 0.00 39.30 3.85
5924 6335 4.699257 AGATGATCAACTCTGGCAAAAGTC 59.301 41.667 0.00 0.00 0.00 3.01
6001 6413 7.672983 TTCCTGTCTTCTATGAACATGTTTC 57.327 36.000 13.36 6.80 0.00 2.78
6047 6459 7.770897 CAGAGGAGCCATAATTAACTTTAGTGT 59.229 37.037 0.00 0.00 0.00 3.55
6049 6461 7.862675 AGGAGCCATAATTAACTTTAGTGTCT 58.137 34.615 0.00 0.00 0.00 3.41
6081 6493 9.420118 ACTGGGCTGTTGATAATATTAATTCAA 57.580 29.630 7.22 7.22 0.00 2.69
6207 6622 8.276325 GCTTTATGTTTATCCTATGTGAACTCG 58.724 37.037 0.00 0.00 0.00 4.18
6352 6767 3.259123 AGAAGCCCGATTTTTGAAGCATT 59.741 39.130 0.00 0.00 0.00 3.56
6453 6868 4.585879 ACAGGTTAGTTGTGAACTTGTGT 58.414 39.130 2.90 0.00 43.18 3.72
6526 6941 9.065871 GCATCACATAAATCTTTCTACAAACAC 57.934 33.333 0.00 0.00 0.00 3.32
6552 6967 0.835941 ATCCTTCCTGCTGTAGGCTG 59.164 55.000 6.95 2.28 46.87 4.85
6563 6978 3.009033 TGCTGTAGGCTGTCTAAATTGGT 59.991 43.478 0.00 0.00 42.39 3.67
6625 7040 7.559897 TCTTTCTACAAACACCTGAATCCTTTT 59.440 33.333 0.00 0.00 0.00 2.27
6635 7051 3.950395 CCTGAATCCTTTTCAGATCCCAC 59.050 47.826 15.12 0.00 46.57 4.61
6659 7075 0.610174 TGTGGGAGCTTCTAGCACTG 59.390 55.000 1.09 0.00 45.56 3.66
6672 7088 0.846693 AGCACTGGGTCTGTCCTTTT 59.153 50.000 0.00 0.00 36.25 2.27
6708 7262 3.534889 GCAAAATGCTGCTTTTCGTTTC 58.465 40.909 13.04 0.09 40.96 2.78
6713 7267 1.474478 TGCTGCTTTTCGTTTCCACAA 59.526 42.857 0.00 0.00 0.00 3.33
6725 7279 4.035909 TCGTTTCCACAAAGGTAAAAGCTC 59.964 41.667 0.00 0.00 39.02 4.09
6731 7285 3.810941 CACAAAGGTAAAAGCTCGTGGTA 59.189 43.478 0.00 0.00 0.00 3.25
6800 7354 2.924926 TGCAACGGTTTATACTGCTACG 59.075 45.455 0.00 0.00 33.73 3.51
6824 7378 9.026074 ACGAGTTATGGTTGTTTTGTTTTATTG 57.974 29.630 0.00 0.00 0.00 1.90
7420 8015 5.129320 GGCCCTGAAGGAACAAATTATGAAT 59.871 40.000 0.00 0.00 38.24 2.57
7695 8290 1.117150 GTGGGACGGCTATCTGGTAA 58.883 55.000 0.00 0.00 0.00 2.85
7715 8310 1.299976 GTGGGAAGCAACGGAGGAT 59.700 57.895 0.00 0.00 0.00 3.24
7730 8325 1.804326 GGATGACGACGACCCAACG 60.804 63.158 0.00 0.00 39.31 4.10
7961 8556 6.954232 TGAAGGATTAGTTTAGGTCCGAAAT 58.046 36.000 0.08 0.00 35.89 2.17
7979 8574 4.853196 CGAAATACTTGCACAAATCCACAG 59.147 41.667 0.00 0.00 0.00 3.66
7994 8589 2.762887 TCCACAGTAGAGCATCAAGGAG 59.237 50.000 0.00 0.00 37.82 3.69
8196 8791 9.282569 GAAAGAGTGGATAGAATGCTTATTGAT 57.717 33.333 0.00 0.00 0.00 2.57
8202 8797 9.252962 GTGGATAGAATGCTTATTGATTTTTGG 57.747 33.333 0.00 0.00 0.00 3.28
8301 9088 1.526917 AACGCCAGCAAGCAAGACT 60.527 52.632 0.00 0.00 0.00 3.24
8305 9092 1.404181 CGCCAGCAAGCAAGACTACTA 60.404 52.381 0.00 0.00 0.00 1.82
8308 9095 3.119101 GCCAGCAAGCAAGACTACTACTA 60.119 47.826 0.00 0.00 0.00 1.82
8309 9096 4.442192 GCCAGCAAGCAAGACTACTACTAT 60.442 45.833 0.00 0.00 0.00 2.12
8311 9103 6.683110 GCCAGCAAGCAAGACTACTACTATAA 60.683 42.308 0.00 0.00 0.00 0.98
8369 9161 7.664082 AGATTGAATAACCATGCTATCTTCG 57.336 36.000 0.00 0.00 30.57 3.79
8400 9193 2.945668 GTCATAGGGGACTTGCATGTTC 59.054 50.000 6.70 4.47 43.67 3.18
8461 9288 7.135591 TGACATCCTATTGTACATGATCCAA 57.864 36.000 0.00 0.00 0.00 3.53
8478 9306 7.395190 TGATCCAAGATTATTTTCACACTGG 57.605 36.000 0.00 0.00 0.00 4.00
8482 9310 7.230747 TCCAAGATTATTTTCACACTGGAAGA 58.769 34.615 0.00 0.00 37.43 2.87
8499 9327 5.445964 TGGAAGAAAACTTGCTAAAGGAGT 58.554 37.500 0.00 0.00 37.76 3.85
8570 9398 7.453393 TCTATGTATTTGCCCTGGATTTCTAG 58.547 38.462 0.00 0.00 0.00 2.43
8672 9504 0.615331 TGGGGAGAGCAGTCATGTTC 59.385 55.000 0.00 0.00 36.95 3.18
8696 9528 4.612264 AAATTTTCTTGCAGGCATGTCT 57.388 36.364 0.00 0.00 0.00 3.41
8697 9529 4.612264 AATTTTCTTGCAGGCATGTCTT 57.388 36.364 0.00 0.00 0.00 3.01
8698 9530 5.726980 AATTTTCTTGCAGGCATGTCTTA 57.273 34.783 0.00 0.00 0.00 2.10
8699 9531 5.726980 ATTTTCTTGCAGGCATGTCTTAA 57.273 34.783 0.00 0.00 0.00 1.85
8700 9532 4.771590 TTTCTTGCAGGCATGTCTTAAG 57.228 40.909 12.68 12.68 0.00 1.85
8701 9533 2.715046 TCTTGCAGGCATGTCTTAAGG 58.285 47.619 16.81 2.41 0.00 2.69
8702 9534 1.133790 CTTGCAGGCATGTCTTAAGGC 59.866 52.381 0.00 0.00 0.00 4.35
8703 9535 1.026182 TGCAGGCATGTCTTAAGGCG 61.026 55.000 0.00 0.00 0.00 5.52
8704 9536 1.718757 GCAGGCATGTCTTAAGGCGG 61.719 60.000 0.00 0.00 0.00 6.13
8711 9543 2.773993 TGTCTTAAGGCGGTTAAGGG 57.226 50.000 14.14 0.00 45.49 3.95
8715 9547 0.322726 TTAAGGCGGTTAAGGGGCAC 60.323 55.000 2.67 0.00 0.00 5.01
8731 9563 1.283793 CACAACGGCTCCAGCTTTG 59.716 57.895 10.27 10.27 41.70 2.77
8736 9568 2.694760 CGGCTCCAGCTTTGCCTTC 61.695 63.158 16.34 0.00 44.09 3.46
8744 9576 3.894427 TCCAGCTTTGCCTTCATGTAAAA 59.106 39.130 0.00 0.00 0.00 1.52
8745 9577 4.022068 TCCAGCTTTGCCTTCATGTAAAAG 60.022 41.667 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.270550 GGCCTGTGGAAGAAACATGTG 59.729 52.381 0.00 0.00 0.00 3.21
127 128 0.543277 AACAGCCAGCTAGCTATGCA 59.457 50.000 29.57 0.00 42.61 3.96
130 131 3.356529 AAACAACAGCCAGCTAGCTAT 57.643 42.857 18.86 3.46 42.61 2.97
138 139 2.290641 ACGAAGCTTAAACAACAGCCAG 59.709 45.455 0.00 0.00 36.62 4.85
184 185 9.743057 CAAAATGTGTCATTTTTGTACTAGGAA 57.257 29.630 14.96 0.00 37.80 3.36
198 200 5.124297 TCGAAGATGCATCAAAATGTGTCAT 59.876 36.000 27.81 0.00 35.18 3.06
255 258 4.098654 CGTCTCAACTGATGATAGAGGGTT 59.901 45.833 0.00 0.00 37.44 4.11
388 392 2.762745 AACACCTAACGTGGTCATGAC 58.237 47.619 17.91 17.91 38.28 3.06
483 521 2.288579 ACACTCGTGGCGTATTCAAGAA 60.289 45.455 1.77 0.00 34.19 2.52
484 522 1.271379 ACACTCGTGGCGTATTCAAGA 59.729 47.619 1.77 0.00 34.19 3.02
485 523 1.390123 CACACTCGTGGCGTATTCAAG 59.610 52.381 1.77 0.00 39.64 3.02
486 524 1.424403 CACACTCGTGGCGTATTCAA 58.576 50.000 1.77 0.00 39.64 2.69
487 525 1.011968 GCACACTCGTGGCGTATTCA 61.012 55.000 1.77 0.00 43.81 2.57
488 526 1.708027 GCACACTCGTGGCGTATTC 59.292 57.895 1.77 0.00 43.81 1.75
489 527 2.092291 CGCACACTCGTGGCGTATT 61.092 57.895 18.27 0.00 43.81 1.89
490 528 2.506217 CGCACACTCGTGGCGTAT 60.506 61.111 18.27 0.00 43.81 3.06
494 532 0.806102 ATGATACGCACACTCGTGGC 60.806 55.000 1.77 1.85 43.81 5.01
495 533 1.588404 GAATGATACGCACACTCGTGG 59.412 52.381 1.77 0.00 43.81 4.94
496 534 2.258755 TGAATGATACGCACACTCGTG 58.741 47.619 0.00 0.00 46.56 4.35
497 535 2.647529 TGAATGATACGCACACTCGT 57.352 45.000 0.00 0.00 45.49 4.18
498 536 5.635549 TTAATGAATGATACGCACACTCG 57.364 39.130 0.00 0.00 0.00 4.18
499 537 7.234187 TCTTTAATGAATGATACGCACACTC 57.766 36.000 0.00 0.00 0.00 3.51
500 538 7.201644 CCTTCTTTAATGAATGATACGCACACT 60.202 37.037 4.42 0.00 0.00 3.55
501 539 6.907212 CCTTCTTTAATGAATGATACGCACAC 59.093 38.462 4.42 0.00 0.00 3.82
502 540 6.821160 TCCTTCTTTAATGAATGATACGCACA 59.179 34.615 4.42 0.00 0.00 4.57
503 541 7.246674 TCCTTCTTTAATGAATGATACGCAC 57.753 36.000 4.42 0.00 0.00 5.34
504 542 6.483307 CCTCCTTCTTTAATGAATGATACGCA 59.517 38.462 4.42 0.00 0.00 5.24
505 543 6.073003 CCCTCCTTCTTTAATGAATGATACGC 60.073 42.308 4.42 0.00 0.00 4.42
506 544 6.428159 CCCCTCCTTCTTTAATGAATGATACG 59.572 42.308 4.42 0.00 0.00 3.06
507 545 7.518188 TCCCCTCCTTCTTTAATGAATGATAC 58.482 38.462 4.42 0.00 0.00 2.24
508 546 7.705912 TCCCCTCCTTCTTTAATGAATGATA 57.294 36.000 4.42 0.00 0.00 2.15
509 547 6.596869 TCCCCTCCTTCTTTAATGAATGAT 57.403 37.500 4.42 0.00 0.00 2.45
510 548 6.401537 TTCCCCTCCTTCTTTAATGAATGA 57.598 37.500 4.42 6.58 0.00 2.57
511 549 6.891908 TCTTTCCCCTCCTTCTTTAATGAATG 59.108 38.462 4.42 2.81 0.00 2.67
512 550 6.892456 GTCTTTCCCCTCCTTCTTTAATGAAT 59.108 38.462 4.42 0.00 0.00 2.57
513 551 6.183361 TGTCTTTCCCCTCCTTCTTTAATGAA 60.183 38.462 3.97 3.97 0.00 2.57
514 552 5.312178 TGTCTTTCCCCTCCTTCTTTAATGA 59.688 40.000 0.00 0.00 0.00 2.57
515 553 5.570320 TGTCTTTCCCCTCCTTCTTTAATG 58.430 41.667 0.00 0.00 0.00 1.90
516 554 5.860648 TGTCTTTCCCCTCCTTCTTTAAT 57.139 39.130 0.00 0.00 0.00 1.40
517 555 5.281037 GGATGTCTTTCCCCTCCTTCTTTAA 60.281 44.000 0.00 0.00 0.00 1.52
518 556 4.227527 GGATGTCTTTCCCCTCCTTCTTTA 59.772 45.833 0.00 0.00 0.00 1.85
519 557 3.010696 GGATGTCTTTCCCCTCCTTCTTT 59.989 47.826 0.00 0.00 0.00 2.52
520 558 2.578480 GGATGTCTTTCCCCTCCTTCTT 59.422 50.000 0.00 0.00 0.00 2.52
521 559 2.200955 GGATGTCTTTCCCCTCCTTCT 58.799 52.381 0.00 0.00 0.00 2.85
522 560 2.719531 GGATGTCTTTCCCCTCCTTC 57.280 55.000 0.00 0.00 0.00 3.46
587 626 4.041567 TGTGTTAGATGTGGAGTGGATGTT 59.958 41.667 0.00 0.00 0.00 2.71
616 663 1.954733 GCAATGTGGGTAGTGCATGGA 60.955 52.381 0.00 0.00 41.00 3.41
617 664 0.457035 GCAATGTGGGTAGTGCATGG 59.543 55.000 0.00 0.00 41.00 3.66
702 749 3.008375 AGCTTTGTAGAGGATTGACAGCA 59.992 43.478 0.00 0.00 0.00 4.41
718 765 7.897575 AGAAGTTGATAACAGTAGAGCTTTG 57.102 36.000 0.00 0.00 0.00 2.77
743 790 6.399639 AAATTCCAAAAAGGTGTCATACGT 57.600 33.333 0.00 0.00 39.02 3.57
877 924 9.329913 CCTATGCTTAAATAACGCAATTGATAC 57.670 33.333 10.34 0.00 37.20 2.24
905 952 5.858381 TCCATTGCTAGATATCCACAGAAC 58.142 41.667 0.00 0.00 0.00 3.01
968 1015 9.032420 GCCACTGACTTAGTCAATACTATTTAC 57.968 37.037 16.28 0.00 42.26 2.01
1063 1110 7.660112 TCAATGACAAACACTTCATTAGCAAT 58.340 30.769 0.00 0.00 39.86 3.56
1411 1458 9.116067 AGCAAAGAAGCGGTAAACATATATAAA 57.884 29.630 0.00 0.00 40.15 1.40
1436 1483 5.203358 TCGCATCGAAGATTGTTAAACAG 57.797 39.130 0.00 0.00 45.12 3.16
1529 1576 1.447317 CCACCGCAGACTTTTGCAGT 61.447 55.000 0.00 0.00 44.28 4.40
1605 1652 7.148869 GGTTACAACGAAACCAAATAAGCAATC 60.149 37.037 0.00 0.00 44.83 2.67
1686 1733 5.591099 CATGTAAACATGCTTATGGGTTCC 58.409 41.667 9.98 0.00 45.92 3.62
1749 1796 5.651576 TGCAGAGTATTTTGTATGGCAATGA 59.348 36.000 0.00 0.00 36.89 2.57
1821 1870 8.533657 ACAAAATAGATGCTGAAAAATCATCCA 58.466 29.630 0.00 0.00 37.82 3.41
1973 2024 1.300620 CTCACCCGCGTTTGAGTCA 60.301 57.895 20.59 0.00 35.48 3.41
2032 2083 7.128751 TCTCTTGATATGAGGAAGGAGAAAGA 58.871 38.462 0.00 0.00 32.78 2.52
2073 2154 8.956426 ACTTAACACTGAATTTGAGAGAACAAA 58.044 29.630 0.00 0.00 42.58 2.83
2074 2155 8.506168 ACTTAACACTGAATTTGAGAGAACAA 57.494 30.769 0.00 0.00 0.00 2.83
2075 2156 8.506168 AACTTAACACTGAATTTGAGAGAACA 57.494 30.769 0.00 0.00 0.00 3.18
2081 2162 9.774742 GGCTATAAACTTAACACTGAATTTGAG 57.225 33.333 0.00 0.00 0.00 3.02
2082 2163 9.290988 TGGCTATAAACTTAACACTGAATTTGA 57.709 29.630 0.00 0.00 0.00 2.69
2085 2166 8.612619 CGATGGCTATAAACTTAACACTGAATT 58.387 33.333 0.00 0.00 0.00 2.17
2086 2167 7.985184 TCGATGGCTATAAACTTAACACTGAAT 59.015 33.333 0.00 0.00 0.00 2.57
2087 2168 7.324935 TCGATGGCTATAAACTTAACACTGAA 58.675 34.615 0.00 0.00 0.00 3.02
2088 2169 6.869695 TCGATGGCTATAAACTTAACACTGA 58.130 36.000 0.00 0.00 0.00 3.41
2089 2170 7.534085 TTCGATGGCTATAAACTTAACACTG 57.466 36.000 0.00 0.00 0.00 3.66
2090 2171 9.477484 CTATTCGATGGCTATAAACTTAACACT 57.523 33.333 0.00 0.00 0.00 3.55
2091 2172 9.257651 ACTATTCGATGGCTATAAACTTAACAC 57.742 33.333 0.00 0.00 0.00 3.32
2092 2173 9.826574 AACTATTCGATGGCTATAAACTTAACA 57.173 29.630 0.00 0.00 0.00 2.41
2095 2176 9.826574 ACAAACTATTCGATGGCTATAAACTTA 57.173 29.630 0.00 0.00 0.00 2.24
2096 2177 8.732746 ACAAACTATTCGATGGCTATAAACTT 57.267 30.769 0.00 0.00 0.00 2.66
2097 2178 9.826574 TTACAAACTATTCGATGGCTATAAACT 57.173 29.630 0.00 0.00 0.00 2.66
2128 2209 6.620733 GCACTGAACATATGAAACACTACCAC 60.621 42.308 10.38 0.00 0.00 4.16
2182 2263 2.935201 CAAAGTGTAGCTCATGAGGCTC 59.065 50.000 23.89 7.79 40.74 4.70
2555 2636 5.197806 AGGGAGTACCAATTATTTCCCCATT 59.802 40.000 7.76 0.00 44.30 3.16
2636 2729 4.035675 GCAGGAAATAATCAACTCCCTTCG 59.964 45.833 0.00 0.00 0.00 3.79
2637 2730 4.339530 GGCAGGAAATAATCAACTCCCTTC 59.660 45.833 0.00 0.00 0.00 3.46
2850 3043 7.436080 CCAGAAATGATGGATGGAATTTTTACG 59.564 37.037 0.00 0.00 40.51 3.18
2895 3095 9.996554 TCAAGTCTAGTTCATAAAGTCAATGAA 57.003 29.630 0.00 0.00 40.21 2.57
2993 3194 2.633481 GTGAACAGTAGGGGTCAGACTT 59.367 50.000 0.00 0.00 0.00 3.01
3000 3201 6.214819 ACATTTACTATGTGAACAGTAGGGGT 59.785 38.462 0.00 0.00 0.00 4.95
3150 3351 4.182693 ACATGCTGATGACAATTGTTGG 57.817 40.909 13.36 3.12 33.36 3.77
3284 3485 0.952497 CCATCGAGCACAGCACAGTT 60.952 55.000 0.00 0.00 0.00 3.16
3322 3523 0.530744 TACTAACGCAGCTCTGTGGG 59.469 55.000 14.09 6.97 44.78 4.61
3325 3526 1.835494 TCCTACTAACGCAGCTCTGT 58.165 50.000 0.00 0.00 0.00 3.41
3335 3536 9.926158 GCCTATTCTTTTACCTATCCTACTAAC 57.074 37.037 0.00 0.00 0.00 2.34
3471 3672 8.749354 TGCTTCTATCTAGAGTTTTGTATGTGA 58.251 33.333 0.00 0.00 33.21 3.58
3575 3783 4.440802 GGCAGCATACTAGATAATCCTCCG 60.441 50.000 0.00 0.00 0.00 4.63
3611 3819 1.927895 AGCGCTAGAATTTCCTGACG 58.072 50.000 8.99 0.00 0.00 4.35
3624 3832 3.138304 CAACCAATAGGCAATAGCGCTA 58.862 45.455 21.30 21.30 43.41 4.26
3635 3843 9.319143 CTAAAAGATAGACAGACAACCAATAGG 57.681 37.037 0.00 0.00 42.21 2.57
3636 3844 9.877178 ACTAAAAGATAGACAGACAACCAATAG 57.123 33.333 0.00 0.00 0.00 1.73
3638 3846 9.220767 GAACTAAAAGATAGACAGACAACCAAT 57.779 33.333 0.00 0.00 0.00 3.16
3639 3847 8.429641 AGAACTAAAAGATAGACAGACAACCAA 58.570 33.333 0.00 0.00 0.00 3.67
3640 3848 7.963532 AGAACTAAAAGATAGACAGACAACCA 58.036 34.615 0.00 0.00 0.00 3.67
3641 3849 7.546316 GGAGAACTAAAAGATAGACAGACAACC 59.454 40.741 0.00 0.00 0.00 3.77
3642 3850 8.308207 AGGAGAACTAAAAGATAGACAGACAAC 58.692 37.037 0.00 0.00 0.00 3.32
3643 3851 8.423906 AGGAGAACTAAAAGATAGACAGACAA 57.576 34.615 0.00 0.00 0.00 3.18
3977 4331 4.081752 TGCTGTTTCCAACAACAAGTTCAT 60.082 37.500 0.00 0.00 41.61 2.57
4050 4404 5.761165 TTCATACCACATGAGCATGAATG 57.239 39.130 16.70 12.90 41.20 2.67
4083 4437 7.371159 GTTATGGAAGGAACAAAAGAAAGAGG 58.629 38.462 0.00 0.00 0.00 3.69
4117 4471 4.814234 ACAGTGTTGTGTACAGTACATTGG 59.186 41.667 24.29 14.96 41.34 3.16
4124 4478 3.438781 CACCAAACAGTGTTGTGTACAGT 59.561 43.478 9.79 1.66 41.14 3.55
4125 4479 3.687212 TCACCAAACAGTGTTGTGTACAG 59.313 43.478 20.04 6.89 37.45 2.74
4126 4480 3.676093 TCACCAAACAGTGTTGTGTACA 58.324 40.909 20.04 0.00 37.67 2.90
4127 4481 4.893424 ATCACCAAACAGTGTTGTGTAC 57.107 40.909 20.04 0.00 37.67 2.90
4128 4482 5.294799 GTGTATCACCAAACAGTGTTGTGTA 59.705 40.000 20.04 12.23 37.67 2.90
4272 4630 4.332543 TGTAAGTGCATTTCTATTCGCAGG 59.667 41.667 0.00 0.00 34.49 4.85
4369 4731 5.819379 GCTTCATGTGGATGATTACTTCAGA 59.181 40.000 0.00 0.00 38.43 3.27
4404 4766 7.715249 TCATTACTCCAATCTGTTATGCCTAAC 59.285 37.037 5.05 5.05 38.17 2.34
4414 4776 5.241403 TGTGGTTCATTACTCCAATCTGT 57.759 39.130 0.00 0.00 32.82 3.41
4422 4784 2.813754 TGCTTGCTGTGGTTCATTACTC 59.186 45.455 0.00 0.00 0.00 2.59
4685 5075 4.464008 CATATACCATCACCCTGCAGTTT 58.536 43.478 13.81 0.00 0.00 2.66
4833 5233 0.106519 ACAAACTTCCAGCCTGCACT 60.107 50.000 0.00 0.00 0.00 4.40
4962 5362 0.107410 GACCCAACCACTGTGTCACA 60.107 55.000 5.36 5.36 0.00 3.58
5332 5732 7.969004 TGTTGGTATAATTAGCCAGCTACATA 58.031 34.615 19.11 0.00 35.07 2.29
5397 5797 8.095937 AGATATCACATGCAGTAATCATTGTG 57.904 34.615 5.32 6.49 0.00 3.33
5495 5906 9.912634 GTTTTCATTGATTTCACATTTCCTAGA 57.087 29.630 0.00 0.00 0.00 2.43
5638 6049 1.223187 AAACACCTACTGGTTTCGCG 58.777 50.000 0.00 0.00 46.05 5.87
5924 6335 7.860613 TCAATACATATAATTCGGCACAGTTG 58.139 34.615 0.00 0.00 0.00 3.16
6001 6413 5.674525 TCTGCAAGTATTTCTGGTATGGAG 58.325 41.667 0.00 0.00 33.76 3.86
6047 6459 2.325484 TCAACAGCCCAGTAAGTGAGA 58.675 47.619 0.00 0.00 0.00 3.27
6049 6461 4.901197 TTATCAACAGCCCAGTAAGTGA 57.099 40.909 0.00 0.00 0.00 3.41
6055 6467 8.995027 TGAATTAATATTATCAACAGCCCAGT 57.005 30.769 0.00 0.00 0.00 4.00
6081 6493 8.568617 ACATAGTCCATAAACCCTAGAAATCT 57.431 34.615 0.00 0.00 0.00 2.40
6254 6669 6.687081 TGAGAAAACAGTTGTACGGAAAAT 57.313 33.333 0.00 0.00 0.00 1.82
6352 6767 4.021192 TGTGGCTAGCGATTGATCATATGA 60.021 41.667 8.10 8.10 0.00 2.15
6526 6941 2.800250 ACAGCAGGAAGGATTTTCAGG 58.200 47.619 0.00 0.00 0.00 3.86
6625 7040 2.376063 CACACCAGGTGGGATCTGA 58.624 57.895 24.13 0.00 39.67 3.27
6635 7051 0.539051 CTAGAAGCTCCCACACCAGG 59.461 60.000 0.00 0.00 0.00 4.45
6687 7103 3.534889 GAAACGAAAAGCAGCATTTTGC 58.465 40.909 9.82 0.00 45.46 3.68
6708 7262 2.031157 CCACGAGCTTTTACCTTTGTGG 60.031 50.000 0.00 0.00 39.58 4.17
6713 7267 4.081807 CCTACTACCACGAGCTTTTACCTT 60.082 45.833 0.00 0.00 0.00 3.50
6725 7279 1.390565 CCACTCCTCCTACTACCACG 58.609 60.000 0.00 0.00 0.00 4.94
6731 7285 5.340891 TCTATTATGCCACTCCTCCTACT 57.659 43.478 0.00 0.00 0.00 2.57
7460 8055 1.549203 ACCAAGGCATCGAAAAGCAT 58.451 45.000 9.57 0.26 0.00 3.79
7465 8060 2.846193 GGCTATACCAAGGCATCGAAA 58.154 47.619 0.00 0.00 41.51 3.46
7695 8290 2.750350 CTCCGTTGCTTCCCACCT 59.250 61.111 0.00 0.00 0.00 4.00
7715 8310 2.332514 GTCGTTGGGTCGTCGTCA 59.667 61.111 0.00 0.00 0.00 4.35
7961 8556 5.222079 TCTACTGTGGATTTGTGCAAGTA 57.778 39.130 0.00 0.00 0.00 2.24
7979 8574 3.681897 CACAACACTCCTTGATGCTCTAC 59.318 47.826 0.00 0.00 31.11 2.59
7994 8589 3.859411 AGCTCTAGTCTAGCACAACAC 57.141 47.619 1.60 0.00 42.62 3.32
8196 8791 6.231211 TGGCTAACACAAAAACTTCCAAAAA 58.769 32.000 0.00 0.00 0.00 1.94
8202 8797 8.642908 AAATAGTTGGCTAACACAAAAACTTC 57.357 30.769 15.86 0.00 39.30 3.01
8360 9152 4.491676 TGACCAAGTTACACGAAGATAGC 58.508 43.478 0.00 0.00 0.00 2.97
8369 9161 3.518303 AGTCCCCTATGACCAAGTTACAC 59.482 47.826 0.00 0.00 35.83 2.90
8400 9193 3.759581 CATAAGAACTGATGGGGGATGG 58.240 50.000 0.00 0.00 0.00 3.51
8461 9288 9.136323 AGTTTTCTTCCAGTGTGAAAATAATCT 57.864 29.630 14.56 7.90 40.34 2.40
8478 9306 6.619801 TCACTCCTTTAGCAAGTTTTCTTC 57.380 37.500 0.00 0.00 38.17 2.87
8482 9310 8.409358 ACATATTCACTCCTTTAGCAAGTTTT 57.591 30.769 0.00 0.00 0.00 2.43
8570 9398 7.224297 TGAATATCTTGCTATTTCCCACTACC 58.776 38.462 0.00 0.00 0.00 3.18
8641 9469 2.493675 GCTCTCCCCATTTCCAGTTTTC 59.506 50.000 0.00 0.00 0.00 2.29
8642 9470 2.158325 TGCTCTCCCCATTTCCAGTTTT 60.158 45.455 0.00 0.00 0.00 2.43
8643 9471 1.428912 TGCTCTCCCCATTTCCAGTTT 59.571 47.619 0.00 0.00 0.00 2.66
8644 9472 1.005215 CTGCTCTCCCCATTTCCAGTT 59.995 52.381 0.00 0.00 0.00 3.16
8645 9473 0.622665 CTGCTCTCCCCATTTCCAGT 59.377 55.000 0.00 0.00 0.00 4.00
8646 9474 0.622665 ACTGCTCTCCCCATTTCCAG 59.377 55.000 0.00 0.00 0.00 3.86
8647 9475 0.620556 GACTGCTCTCCCCATTTCCA 59.379 55.000 0.00 0.00 0.00 3.53
8648 9476 0.620556 TGACTGCTCTCCCCATTTCC 59.379 55.000 0.00 0.00 0.00 3.13
8649 9477 2.295885 CATGACTGCTCTCCCCATTTC 58.704 52.381 0.00 0.00 0.00 2.17
8651 9479 1.293062 ACATGACTGCTCTCCCCATT 58.707 50.000 0.00 0.00 0.00 3.16
8652 9480 1.211457 GAACATGACTGCTCTCCCCAT 59.789 52.381 0.00 0.00 0.00 4.00
8653 9481 0.615331 GAACATGACTGCTCTCCCCA 59.385 55.000 0.00 0.00 0.00 4.96
8654 9482 0.460987 CGAACATGACTGCTCTCCCC 60.461 60.000 0.00 0.00 0.00 4.81
8672 9504 3.742369 ACATGCCTGCAAGAAAATTTTCG 59.258 39.130 21.98 12.10 41.92 3.46
8696 9528 0.322726 GTGCCCCTTAACCGCCTTAA 60.323 55.000 0.00 0.00 0.00 1.85
8697 9529 1.300634 GTGCCCCTTAACCGCCTTA 59.699 57.895 0.00 0.00 0.00 2.69
8698 9530 2.035155 GTGCCCCTTAACCGCCTT 59.965 61.111 0.00 0.00 0.00 4.35
8699 9531 2.836187 TTGTGCCCCTTAACCGCCT 61.836 57.895 0.00 0.00 0.00 5.52
8700 9532 2.282603 TTGTGCCCCTTAACCGCC 60.283 61.111 0.00 0.00 0.00 6.13
8701 9533 2.959372 GTTGTGCCCCTTAACCGC 59.041 61.111 0.00 0.00 0.00 5.68
8702 9534 2.329614 CCGTTGTGCCCCTTAACCG 61.330 63.158 0.00 0.00 0.00 4.44
8703 9535 2.632544 GCCGTTGTGCCCCTTAACC 61.633 63.158 0.00 0.00 0.00 2.85
8704 9536 1.583495 GAGCCGTTGTGCCCCTTAAC 61.583 60.000 0.00 0.00 0.00 2.01
8715 9547 2.256461 GCAAAGCTGGAGCCGTTG 59.744 61.111 7.86 7.86 43.38 4.10
8724 9556 5.125100 TCTTTTACATGAAGGCAAAGCTG 57.875 39.130 0.00 0.00 0.00 4.24
8731 9563 3.126858 TGTGCGATCTTTTACATGAAGGC 59.873 43.478 0.00 0.00 0.00 4.35
8736 9568 5.034554 ACTGTTGTGCGATCTTTTACATG 57.965 39.130 0.00 0.00 0.00 3.21
8744 9576 3.059884 CTGTTGTACTGTTGTGCGATCT 58.940 45.455 0.00 0.00 0.00 2.75
8745 9577 3.057019 TCTGTTGTACTGTTGTGCGATC 58.943 45.455 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.