Multiple sequence alignment - TraesCS4B01G075600

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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 TraesCS4B01G075600 chr4B 100.000 5266 0 0 1 5266 71595513 71600778 0.000000e+00 9725.0
1 TraesCS4B01G075600 chr4B 98.089 157 3 0 5109 5265 389466946 389466790 1.870000e-69 274.0
2 TraesCS4B01G075600 chr4D 90.835 2804 150 45 665 3409 48714506 48717261 0.000000e+00 3655.0
3 TraesCS4B01G075600 chr4D 92.177 1240 60 17 3404 4616 48717302 48718531 0.000000e+00 1718.0
4 TraesCS4B01G075600 chr4D 89.044 502 34 15 4628 5113 48718966 48719462 2.100000e-168 603.0
5 TraesCS4B01G075600 chr4D 86.971 307 20 14 308 609 48714218 48714509 1.410000e-85 327.0
6 TraesCS4B01G075600 chr4D 92.424 66 3 2 24 89 3472952 3473015 5.620000e-15 93.5
7 TraesCS4B01G075600 chr4A 91.582 1770 89 28 697 2440 548527982 548526247 0.000000e+00 2388.0
8 TraesCS4B01G075600 chr4A 95.829 983 20 6 2435 3409 548520680 548519711 0.000000e+00 1568.0
9 TraesCS4B01G075600 chr4A 88.925 1228 79 26 3408 4615 548519667 548518477 0.000000e+00 1461.0
10 TraesCS4B01G075600 chr4A 86.706 504 55 10 85 582 548528713 548528216 2.770000e-152 549.0
11 TraesCS4B01G075600 chr4A 89.826 344 27 3 4778 5113 548515804 548515461 8.100000e-118 435.0
12 TraesCS4B01G075600 chr2D 98.750 160 2 0 5107 5266 426427970 426427811 8.630000e-73 285.0
13 TraesCS4B01G075600 chr2D 99.359 156 1 0 5111 5266 560959650 560959495 3.100000e-72 283.0
14 TraesCS4B01G075600 chr2D 99.355 155 1 0 5112 5266 161907016 161906862 1.120000e-71 281.0
15 TraesCS4B01G075600 chr2D 88.000 75 5 3 11 81 449523659 449523733 9.400000e-13 86.1
16 TraesCS4B01G075600 chr6D 99.359 156 1 0 5111 5266 206560273 206560428 3.100000e-72 283.0
17 TraesCS4B01G075600 chr6D 99.359 156 1 0 5111 5266 392896974 392897129 3.100000e-72 283.0
18 TraesCS4B01G075600 chr6D 93.651 63 3 1 24 85 144066097 144066035 5.620000e-15 93.5
19 TraesCS4B01G075600 chr1D 99.359 156 1 0 5111 5266 178466471 178466316 3.100000e-72 283.0
20 TraesCS4B01G075600 chr6B 98.148 162 1 2 5107 5266 240046887 240047048 1.120000e-71 281.0
21 TraesCS4B01G075600 chr6B 96.552 58 2 0 28 85 88890843 88890786 4.340000e-16 97.1
22 TraesCS4B01G075600 chr1B 93.889 180 6 3 5089 5266 221271030 221271206 3.130000e-67 267.0
23 TraesCS4B01G075600 chr5A 89.655 87 5 4 1 83 520586796 520586710 2.010000e-19 108.0
24 TraesCS4B01G075600 chr5A 93.548 62 4 0 24 85 232836544 232836605 5.620000e-15 93.5
25 TraesCS4B01G075600 chr5D 93.548 62 4 0 24 85 195652893 195652954 5.620000e-15 93.5
26 TraesCS4B01G075600 chr2B 87.654 81 3 5 11 85 11819212 11819291 2.610000e-13 87.9
27 TraesCS4B01G075600 chr2B 83.871 93 8 5 1 86 383374057 383373965 1.220000e-11 82.4
28 TraesCS4B01G075600 chr3B 88.060 67 6 2 499 564 325803505 325803570 1.570000e-10 78.7


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 TraesCS4B01G075600 chr4B 71595513 71600778 5265 False 9725.000000 9725 100.000000 1 5266 1 chr4B.!!$F1 5265
1 TraesCS4B01G075600 chr4D 48714218 48719462 5244 False 1575.750000 3655 89.756750 308 5113 4 chr4D.!!$F2 4805
2 TraesCS4B01G075600 chr4A 548526247 548528713 2466 True 1468.500000 2388 89.144000 85 2440 2 chr4A.!!$R2 2355
3 TraesCS4B01G075600 chr4A 548515461 548520680 5219 True 1154.666667 1568 91.526667 2435 5113 3 chr4A.!!$R1 2678

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
650 804 0.239082 GTAAACGAAAACCCGGCCAG 59.761 55.000 2.24 0.0 0.00 4.85 F
955 1144 0.248702 CTAGGAAACTCGCGGCTCTC 60.249 60.000 6.13 0.0 43.67 3.20 F
1242 1441 0.875059 GCTCCCCTTTCACTTTCACG 59.125 55.000 0.00 0.0 0.00 4.35 F
2298 2517 1.645919 ACCCTTGGTGCCTATCCAAAT 59.354 47.619 0.00 0.0 43.16 2.32 F
3451 3732 4.982295 GCATTAAGATTATGCCGGGTTTTC 59.018 41.667 2.18 0.0 35.44 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1945 0.036875 AACAGTGCTCTTGTAGGGGC 59.963 55.000 0.00 0.0 0.00 5.80 R
2151 2370 2.034179 TGAATACCGGCGATCACAGTAG 59.966 50.000 9.30 0.0 0.00 2.57 R
2673 2896 4.452455 AGGCTATCTCAAACTTGTGTTTCG 59.548 41.667 0.00 0.0 43.75 3.46 R
3478 3759 0.036294 GGCCGGTGCTCTTAAGAACT 60.036 55.000 6.63 0.0 37.74 3.01 R
4465 4765 0.108774 TGGGTGCACACAAATACGGA 59.891 50.000 22.04 0.0 0.00 4.69 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
59 60 8.094548 TGTTATATTCATATAGAGGTGTGTGGC 58.905 37.037 0.00 0.00 0.00 5.01
60 61 6.686484 ATATTCATATAGAGGTGTGTGGCA 57.314 37.500 0.00 0.00 0.00 4.92
61 62 3.819564 TCATATAGAGGTGTGTGGCAC 57.180 47.619 11.55 11.55 46.97 5.01
68 69 2.357517 GTGTGTGGCACCCGAGAG 60.358 66.667 16.26 0.00 42.10 3.20
69 70 4.314440 TGTGTGGCACCCGAGAGC 62.314 66.667 16.26 0.00 32.73 4.09
75 76 2.281484 GCACCCGAGAGCCACAAA 60.281 61.111 0.00 0.00 0.00 2.83
76 77 1.675641 GCACCCGAGAGCCACAAAT 60.676 57.895 0.00 0.00 0.00 2.32
77 78 1.648467 GCACCCGAGAGCCACAAATC 61.648 60.000 0.00 0.00 0.00 2.17
78 79 1.026718 CACCCGAGAGCCACAAATCC 61.027 60.000 0.00 0.00 0.00 3.01
79 80 1.201429 ACCCGAGAGCCACAAATCCT 61.201 55.000 0.00 0.00 0.00 3.24
80 81 0.462759 CCCGAGAGCCACAAATCCTC 60.463 60.000 0.00 0.00 0.00 3.71
81 82 0.539051 CCGAGAGCCACAAATCCTCT 59.461 55.000 0.00 0.00 38.58 3.69
82 83 1.065854 CCGAGAGCCACAAATCCTCTT 60.066 52.381 0.00 0.00 36.16 2.85
83 84 2.275318 CGAGAGCCACAAATCCTCTTC 58.725 52.381 0.00 0.00 36.16 2.87
84 85 2.637947 GAGAGCCACAAATCCTCTTCC 58.362 52.381 0.00 0.00 36.16 3.46
85 86 1.988107 AGAGCCACAAATCCTCTTCCA 59.012 47.619 0.00 0.00 32.27 3.53
86 87 2.026449 AGAGCCACAAATCCTCTTCCAG 60.026 50.000 0.00 0.00 32.27 3.86
87 88 1.707427 AGCCACAAATCCTCTTCCAGT 59.293 47.619 0.00 0.00 0.00 4.00
88 89 2.108952 AGCCACAAATCCTCTTCCAGTT 59.891 45.455 0.00 0.00 0.00 3.16
89 90 2.489722 GCCACAAATCCTCTTCCAGTTC 59.510 50.000 0.00 0.00 0.00 3.01
93 94 5.048434 CCACAAATCCTCTTCCAGTTCTTTC 60.048 44.000 0.00 0.00 0.00 2.62
121 122 9.961264 GGCTTATTTAGGCCTATAGAAATAAGT 57.039 33.333 33.80 15.99 45.34 2.24
153 154 8.304596 AGTAGGCTTCTAAAATTTTAAGTTGGC 58.695 33.333 11.62 12.75 0.00 4.52
156 157 8.210946 AGGCTTCTAAAATTTTAAGTTGGCTTT 58.789 29.630 11.62 3.79 36.22 3.51
195 196 3.492337 GGGACAACCTATTTCCACAACA 58.508 45.455 0.00 0.00 35.85 3.33
198 199 3.886505 GACAACCTATTTCCACAACACCA 59.113 43.478 0.00 0.00 0.00 4.17
259 260 9.229784 CGACTCAATTAAAACGCTAGATAACTA 57.770 33.333 0.00 0.00 0.00 2.24
267 268 9.880157 TTAAAACGCTAGATAACTAGGTTGATT 57.120 29.630 8.91 6.44 44.33 2.57
269 270 6.466885 ACGCTAGATAACTAGGTTGATTGT 57.533 37.500 8.91 0.00 44.33 2.71
274 275 8.144478 GCTAGATAACTAGGTTGATTGTGATGA 58.856 37.037 8.91 0.00 44.33 2.92
277 278 9.988815 AGATAACTAGGTTGATTGTGATGATAC 57.011 33.333 0.00 0.00 0.00 2.24
299 300 9.628500 GATACCTTAACTTGGTCAAAATCCTAT 57.372 33.333 0.00 0.00 38.88 2.57
301 302 6.663523 ACCTTAACTTGGTCAAAATCCTATGG 59.336 38.462 0.00 0.00 31.03 2.74
338 339 9.511144 GTACATTAGAAATTATTTTTCCACCGG 57.489 33.333 0.00 0.00 0.00 5.28
346 347 2.517650 TTTTTCCACCGGTGAAATGC 57.482 45.000 36.07 0.00 0.00 3.56
347 348 1.403814 TTTTCCACCGGTGAAATGCA 58.596 45.000 36.07 15.20 0.00 3.96
448 450 6.211184 TGTTGCAAGAGTAAATTTCCATGGAT 59.789 34.615 17.06 2.53 0.00 3.41
505 512 4.568152 TCTTAAACAGCTCTTTTGGCAC 57.432 40.909 0.00 0.00 0.00 5.01
572 579 3.632145 ACACCAACACATTTCAGAAGTCC 59.368 43.478 0.00 0.00 0.00 3.85
576 583 5.067805 ACCAACACATTTCAGAAGTCCTTTC 59.932 40.000 0.00 0.00 35.97 2.62
582 589 6.920210 CACATTTCAGAAGTCCTTTCCTTTTC 59.080 38.462 0.00 0.00 36.40 2.29
583 590 6.836007 ACATTTCAGAAGTCCTTTCCTTTTCT 59.164 34.615 0.00 0.00 36.40 2.52
584 591 6.944234 TTTCAGAAGTCCTTTCCTTTTCTC 57.056 37.500 0.00 0.00 36.40 2.87
585 592 4.974399 TCAGAAGTCCTTTCCTTTTCTCC 58.026 43.478 0.00 0.00 36.40 3.71
586 593 4.660771 TCAGAAGTCCTTTCCTTTTCTCCT 59.339 41.667 0.00 0.00 36.40 3.69
587 594 5.132816 TCAGAAGTCCTTTCCTTTTCTCCTT 59.867 40.000 0.00 0.00 36.40 3.36
629 745 1.048601 TCCAGAAGTCTGAAACGGCT 58.951 50.000 9.95 0.00 46.59 5.52
650 804 0.239082 GTAAACGAAAACCCGGCCAG 59.761 55.000 2.24 0.00 0.00 4.85
675 829 1.064060 CCGTCATTCTCCAAATTCGCC 59.936 52.381 0.00 0.00 0.00 5.54
676 830 2.009774 CGTCATTCTCCAAATTCGCCT 58.990 47.619 0.00 0.00 0.00 5.52
679 833 1.106285 ATTCTCCAAATTCGCCTGCC 58.894 50.000 0.00 0.00 0.00 4.85
680 834 0.965363 TTCTCCAAATTCGCCTGCCC 60.965 55.000 0.00 0.00 0.00 5.36
681 835 2.362375 TCCAAATTCGCCTGCCCC 60.362 61.111 0.00 0.00 0.00 5.80
682 836 3.825611 CCAAATTCGCCTGCCCCG 61.826 66.667 0.00 0.00 0.00 5.73
868 1054 2.506438 GCGCCTACACCGTCTGTC 60.506 66.667 0.00 0.00 33.91 3.51
878 1064 2.126307 CGTCTGTCTCCGGCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
943 1132 3.375647 GGTGGCATAAACCCTAGGAAA 57.624 47.619 11.48 0.00 0.00 3.13
955 1144 0.248702 CTAGGAAACTCGCGGCTCTC 60.249 60.000 6.13 0.00 43.67 3.20
1237 1436 1.003233 CCGTAAGCTCCCCTTTCACTT 59.997 52.381 0.00 0.00 34.95 3.16
1242 1441 0.875059 GCTCCCCTTTCACTTTCACG 59.125 55.000 0.00 0.00 0.00 4.35
1247 1446 2.572290 CCCTTTCACTTTCACGACCTT 58.428 47.619 0.00 0.00 0.00 3.50
1249 1448 4.131596 CCCTTTCACTTTCACGACCTTTA 58.868 43.478 0.00 0.00 0.00 1.85
1251 1450 5.935789 CCCTTTCACTTTCACGACCTTTATA 59.064 40.000 0.00 0.00 0.00 0.98
1267 1466 2.335316 TATACGGTTCCCATTGCCAC 57.665 50.000 0.00 0.00 0.00 5.01
1304 1503 1.880027 ACCTGTTTGACGAAATGCCTC 59.120 47.619 0.00 0.00 0.00 4.70
1340 1539 2.161486 GCTCGCGTCGATCAAGCTT 61.161 57.895 5.77 0.00 34.61 3.74
1452 1654 5.031066 AGTTCTGTACAGTTTGGCTAACA 57.969 39.130 21.99 0.00 39.30 2.41
1453 1655 4.814771 AGTTCTGTACAGTTTGGCTAACAC 59.185 41.667 21.99 4.50 39.30 3.32
1454 1656 4.682778 TCTGTACAGTTTGGCTAACACT 57.317 40.909 21.99 1.20 39.30 3.55
1455 1657 5.031066 TCTGTACAGTTTGGCTAACACTT 57.969 39.130 21.99 0.65 39.30 3.16
1620 1826 3.871594 GCGTATCTTTACCTTGCTGACAT 59.128 43.478 0.00 0.00 0.00 3.06
1654 1861 8.798859 AATGTATTACTGTGATTCTGCTTTCT 57.201 30.769 0.00 0.00 0.00 2.52
1672 1879 4.418013 TTCTGCAATTCGTTATGGTGTG 57.582 40.909 0.00 0.00 0.00 3.82
1693 1901 7.256691 GGTGTGGTTTAGATAGTGGGATATGAT 60.257 40.741 0.00 0.00 0.00 2.45
1694 1902 8.157476 GTGTGGTTTAGATAGTGGGATATGATT 58.843 37.037 0.00 0.00 0.00 2.57
1695 1903 8.723365 TGTGGTTTAGATAGTGGGATATGATTT 58.277 33.333 0.00 0.00 0.00 2.17
1816 2026 9.268268 TGTAAATGGGTCGTTTCAGATATATTC 57.732 33.333 0.00 0.00 0.00 1.75
1959 2178 2.444421 CTTGCTGCTCTGGGAGATTTT 58.556 47.619 0.00 0.00 32.36 1.82
2151 2370 7.151976 ACCTGGTAATACAACTTTGATTTTGC 58.848 34.615 0.00 0.00 0.00 3.68
2298 2517 1.645919 ACCCTTGGTGCCTATCCAAAT 59.354 47.619 0.00 0.00 43.16 2.32
2541 2764 7.484993 TTTTAGCACCTACCTCTACATTACA 57.515 36.000 0.00 0.00 0.00 2.41
2575 2798 5.068329 TGTGTAATTTTGTGTTCATGCCTCA 59.932 36.000 0.00 0.00 0.00 3.86
2673 2896 6.320494 TGTACATTGTACAAACCCAATGAC 57.680 37.500 23.82 11.36 46.93 3.06
2902 3125 6.884836 ACCTTCCACTATTTGTTTGACCTATC 59.115 38.462 0.00 0.00 0.00 2.08
2903 3126 7.112779 CCTTCCACTATTTGTTTGACCTATCT 58.887 38.462 0.00 0.00 0.00 1.98
2904 3127 7.611855 CCTTCCACTATTTGTTTGACCTATCTT 59.388 37.037 0.00 0.00 0.00 2.40
3042 3271 7.554835 TGAGGAAGTTTGTTTACATGTTACAGT 59.445 33.333 2.30 0.00 0.00 3.55
3194 3428 7.507304 CGTTAAATCATATTATGTGTCCCGAC 58.493 38.462 3.67 0.00 0.00 4.79
3299 3534 9.370930 TCTAAATAACCTCCTCATACGGAATAA 57.629 33.333 0.00 0.00 31.44 1.40
3316 3551 7.317390 ACGGAATAATGTGGTGGTTTTATTTC 58.683 34.615 0.00 0.00 0.00 2.17
3359 3594 5.617528 TTTGCTCCTTGGTTCGGTATATA 57.382 39.130 0.00 0.00 0.00 0.86
3406 3687 8.553459 AAACGTGAATGATCTCTTAACTTGAT 57.447 30.769 0.00 0.00 0.00 2.57
3436 3717 9.679661 TGATAATTGGTTTCTACTGCATTAAGA 57.320 29.630 0.00 0.00 0.00 2.10
3451 3732 4.982295 GCATTAAGATTATGCCGGGTTTTC 59.018 41.667 2.18 0.00 35.44 2.29
3453 3734 5.828299 TTAAGATTATGCCGGGTTTTCAG 57.172 39.130 2.18 0.00 0.00 3.02
3552 3833 3.864789 ACCTGTCAGAGGAAACAATGT 57.135 42.857 0.00 0.00 46.33 2.71
3563 3844 8.783093 TCAGAGGAAACAATGTTGTATTACTTG 58.217 33.333 0.00 4.79 41.31 3.16
3597 3878 5.828299 TCAAAGGACTTGTTGTTAACTGG 57.172 39.130 7.22 0.00 36.34 4.00
3752 4033 1.619827 TGGAGGCAATGAAGGCAAAAG 59.380 47.619 0.00 0.00 36.37 2.27
3885 4166 8.698854 GCTGAAGAAGAATCAATAATAGAGACG 58.301 37.037 0.00 0.00 0.00 4.18
3986 4267 7.351981 GCAACAATTAAGGTTTGATTTCCAAC 58.648 34.615 0.00 0.00 33.85 3.77
4009 4290 9.255029 CAACCCCTTTCCCCATATATATAAAAG 57.745 37.037 0.00 2.36 0.00 2.27
4129 4414 6.073765 CGATAACTTAATGGATGGAAGGTTCG 60.074 42.308 0.00 0.00 0.00 3.95
4155 4440 6.769822 CAGTGGATGTAATGGAAGAGCTAATT 59.230 38.462 0.00 0.00 0.00 1.40
4290 4575 6.092259 AGTCCGTGCAAATAGTTCTAATTCAC 59.908 38.462 0.00 0.00 0.00 3.18
4357 4653 8.836268 TGTGGTATTTTTCTAGTGATTAACGT 57.164 30.769 0.00 0.00 0.00 3.99
4380 4676 8.044908 ACGTGAAGATATAACAATTTGTACCCT 58.955 33.333 1.76 0.00 0.00 4.34
4393 4689 6.699575 ATTTGTACCCTTGCATATGACTTC 57.300 37.500 6.97 0.00 0.00 3.01
4395 4691 5.435686 TGTACCCTTGCATATGACTTCTT 57.564 39.130 6.97 0.00 0.00 2.52
4403 4699 6.595326 CCTTGCATATGACTTCTTGTTAGTGA 59.405 38.462 6.97 0.00 0.00 3.41
4430 4726 8.643752 CGCCATAATTTTTATTTGAGAACGTTT 58.356 29.630 0.46 0.00 0.00 3.60
4557 4867 6.067263 TGGTGGTCTAATTTTGTTTTCTCG 57.933 37.500 0.00 0.00 0.00 4.04
4565 4875 7.271438 GTCTAATTTTGTTTTCTCGAGGAATGC 59.729 37.037 13.56 7.07 33.53 3.56
4584 4894 4.970662 TGCCAATCTACTTCATTTCAGC 57.029 40.909 0.00 0.00 0.00 4.26
4595 4905 4.278170 ACTTCATTTCAGCGAAAACATGGA 59.722 37.500 0.00 0.00 35.11 3.41
4616 4926 7.969536 TGGAGAAAATGTTTAGAGTCAGAAG 57.030 36.000 0.00 0.00 0.00 2.85
4617 4927 6.428159 TGGAGAAAATGTTTAGAGTCAGAAGC 59.572 38.462 0.00 0.00 0.00 3.86
4618 4928 6.428159 GGAGAAAATGTTTAGAGTCAGAAGCA 59.572 38.462 0.00 0.00 0.00 3.91
4620 4930 8.401490 AGAAAATGTTTAGAGTCAGAAGCATT 57.599 30.769 11.59 11.59 37.88 3.56
4621 4931 9.507329 AGAAAATGTTTAGAGTCAGAAGCATTA 57.493 29.630 15.46 0.00 36.02 1.90
4625 4935 7.834068 TGTTTAGAGTCAGAAGCATTATGTC 57.166 36.000 0.00 0.00 38.69 3.06
4626 4936 7.386059 TGTTTAGAGTCAGAAGCATTATGTCA 58.614 34.615 0.00 0.00 38.69 3.58
4679 7576 2.760650 TGAGTGCCGACTACATTGATCT 59.239 45.455 0.00 0.00 30.16 2.75
4684 7581 5.050490 GTGCCGACTACATTGATCTAACAT 58.950 41.667 0.00 0.00 0.00 2.71
4752 7667 9.467258 CCAATGTTTATTCTTGCGATCAATAAT 57.533 29.630 0.00 0.00 34.62 1.28
4759 7674 9.944663 TTATTCTTGCGATCAATAATTACCAAC 57.055 29.630 0.00 0.00 33.09 3.77
4761 7676 6.781138 TCTTGCGATCAATAATTACCAACAC 58.219 36.000 0.00 0.00 0.00 3.32
4762 7677 5.150342 TGCGATCAATAATTACCAACACG 57.850 39.130 0.00 0.00 0.00 4.49
4763 7678 3.966218 GCGATCAATAATTACCAACACGC 59.034 43.478 0.00 0.00 35.06 5.34
4764 7679 4.495019 GCGATCAATAATTACCAACACGCA 60.495 41.667 0.00 0.00 40.63 5.24
4765 7680 5.564768 CGATCAATAATTACCAACACGCAA 58.435 37.500 0.00 0.00 0.00 4.85
4766 7681 6.024664 CGATCAATAATTACCAACACGCAAA 58.975 36.000 0.00 0.00 0.00 3.68
4767 7682 6.690957 CGATCAATAATTACCAACACGCAAAT 59.309 34.615 0.00 0.00 0.00 2.32
4769 7684 8.850454 ATCAATAATTACCAACACGCAAATAC 57.150 30.769 0.00 0.00 0.00 1.89
4770 7685 7.251994 TCAATAATTACCAACACGCAAATACC 58.748 34.615 0.00 0.00 0.00 2.73
4771 7686 4.443913 AATTACCAACACGCAAATACCC 57.556 40.909 0.00 0.00 0.00 3.69
4772 7687 1.440708 TACCAACACGCAAATACCCG 58.559 50.000 0.00 0.00 0.00 5.28
4774 7689 1.582610 CCAACACGCAAATACCCGCT 61.583 55.000 0.00 0.00 0.00 5.52
4775 7690 0.239879 CAACACGCAAATACCCGCTT 59.760 50.000 0.00 0.00 0.00 4.68
4776 7691 0.239879 AACACGCAAATACCCGCTTG 59.760 50.000 0.00 0.00 33.90 4.01
4783 7716 2.731027 GCAAATACCCGCTTGTAAGTGC 60.731 50.000 0.00 5.58 35.25 4.40
4811 7744 5.486526 AGAAAGCCTTAGATCACAAGTGAG 58.513 41.667 8.99 0.00 43.61 3.51
4829 7767 7.392673 ACAAGTGAGCTCAATGAAATACAATCT 59.607 33.333 28.26 11.97 0.00 2.40
4901 7842 4.440829 GGGGGAGCCGCCAAATCA 62.441 66.667 16.91 0.00 46.73 2.57
4909 7850 1.141591 GCCGCCAAATCAATCAAGCG 61.142 55.000 0.00 0.00 42.99 4.68
4932 7873 4.216472 GGCCTTCTTTTTCTTCGACTTCAT 59.784 41.667 0.00 0.00 0.00 2.57
4969 7910 8.080417 CCGATGAATATACTTAGGAACGAAAGA 58.920 37.037 0.00 0.00 32.06 2.52
4975 7916 4.338379 ACTTAGGAACGAAAGAAGCACT 57.662 40.909 0.00 0.00 32.06 4.40
5041 7982 7.175990 GGTAGAAAGTATTGGTGGACAAAATGA 59.824 37.037 0.00 0.00 43.46 2.57
5072 8013 3.582164 ACAAATGGCTAGGTGGGAAAAA 58.418 40.909 0.00 0.00 0.00 1.94
5117 8058 9.561069 AATACATAATCACAGAAACATACTCCC 57.439 33.333 0.00 0.00 0.00 4.30
5118 8059 7.200434 ACATAATCACAGAAACATACTCCCT 57.800 36.000 0.00 0.00 0.00 4.20
5119 8060 7.275920 ACATAATCACAGAAACATACTCCCTC 58.724 38.462 0.00 0.00 0.00 4.30
5120 8061 4.762289 ATCACAGAAACATACTCCCTCC 57.238 45.455 0.00 0.00 0.00 4.30
5121 8062 2.496070 TCACAGAAACATACTCCCTCCG 59.504 50.000 0.00 0.00 0.00 4.63
5122 8063 2.233922 CACAGAAACATACTCCCTCCGT 59.766 50.000 0.00 0.00 0.00 4.69
5123 8064 2.904434 ACAGAAACATACTCCCTCCGTT 59.096 45.455 0.00 0.00 0.00 4.44
5124 8065 3.056035 ACAGAAACATACTCCCTCCGTTC 60.056 47.826 0.00 0.00 0.00 3.95
5125 8066 2.500504 AGAAACATACTCCCTCCGTTCC 59.499 50.000 0.00 0.00 0.00 3.62
5126 8067 2.249309 AACATACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
5127 8068 3.393426 AACATACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
5128 8069 3.393426 ACATACTCCCTCCGTTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
5129 8070 3.716431 ACATACTCCCTCCGTTCCTAAA 58.284 45.455 0.00 0.00 0.00 1.85
5130 8071 4.296056 ACATACTCCCTCCGTTCCTAAAT 58.704 43.478 0.00 0.00 0.00 1.40
5131 8072 5.461327 ACATACTCCCTCCGTTCCTAAATA 58.539 41.667 0.00 0.00 0.00 1.40
5132 8073 6.082707 ACATACTCCCTCCGTTCCTAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
5133 8074 6.557633 ACATACTCCCTCCGTTCCTAAATATT 59.442 38.462 0.00 0.00 0.00 1.28
5134 8075 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5135 8076 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5136 8077 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5137 8078 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5138 8079 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5139 8080 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5140 8081 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5141 8082 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
5142 8083 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
5143 8084 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
5144 8085 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
5145 8086 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
5160 8101 9.559732 TGTCTTTCTAGAGATTTCAACAAATGA 57.440 29.630 0.00 0.00 31.94 2.57
5161 8102 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
5162 8103 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
5165 8106 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
5169 8110 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
5170 8111 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
5171 8112 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
5172 8113 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
5173 8114 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
5174 8115 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
5175 8116 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
5176 8117 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
5177 8118 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
5178 8119 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
5179 8120 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
5180 8121 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
5181 8122 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
5182 8123 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
5183 8124 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
5184 8125 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
5185 8126 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
5186 8127 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
5187 8128 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
5188 8129 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
5189 8130 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
5190 8131 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
5191 8132 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
5192 8133 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
5225 8166 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
5227 8168 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
5228 8169 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
5229 8170 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
5230 8171 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
5231 8172 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
5232 8173 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
5233 8174 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
5234 8175 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
5235 8176 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
5236 8177 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
5237 8178 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
5238 8179 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
5239 8180 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
5240 8181 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
5241 8182 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
5242 8183 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
5243 8184 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
5244 8185 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
5245 8186 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
5246 8187 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
5247 8188 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
5248 8189 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
5252 8193 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
5253 8194 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.094548 GCCACACACCTCTATATGAATATAACA 58.905 37.037 0.00 0.00 0.00 2.41
34 35 8.094548 TGCCACACACCTCTATATGAATATAAC 58.905 37.037 0.00 0.00 0.00 1.89
35 36 8.094548 GTGCCACACACCTCTATATGAATATAA 58.905 37.037 0.00 0.00 44.02 0.98
36 37 7.611770 GTGCCACACACCTCTATATGAATATA 58.388 38.462 0.00 0.00 44.02 0.86
37 38 6.467677 GTGCCACACACCTCTATATGAATAT 58.532 40.000 0.00 0.00 44.02 1.28
38 39 5.853936 GTGCCACACACCTCTATATGAATA 58.146 41.667 0.00 0.00 44.02 1.75
39 40 4.708177 GTGCCACACACCTCTATATGAAT 58.292 43.478 0.00 0.00 44.02 2.57
40 41 4.137116 GTGCCACACACCTCTATATGAA 57.863 45.455 0.00 0.00 44.02 2.57
41 42 3.819564 GTGCCACACACCTCTATATGA 57.180 47.619 0.00 0.00 44.02 2.15
52 53 4.314440 GCTCTCGGGTGCCACACA 62.314 66.667 0.00 0.00 35.86 3.72
58 59 1.648467 GATTTGTGGCTCTCGGGTGC 61.648 60.000 0.00 0.00 0.00 5.01
59 60 1.026718 GGATTTGTGGCTCTCGGGTG 61.027 60.000 0.00 0.00 0.00 4.61
60 61 1.201429 AGGATTTGTGGCTCTCGGGT 61.201 55.000 0.00 0.00 0.00 5.28
61 62 0.462759 GAGGATTTGTGGCTCTCGGG 60.463 60.000 0.00 0.00 0.00 5.14
62 63 0.539051 AGAGGATTTGTGGCTCTCGG 59.461 55.000 0.00 0.00 0.00 4.63
63 64 2.275318 GAAGAGGATTTGTGGCTCTCG 58.725 52.381 0.00 0.00 0.00 4.04
64 65 2.026822 TGGAAGAGGATTTGTGGCTCTC 60.027 50.000 0.00 0.00 0.00 3.20
65 66 1.988107 TGGAAGAGGATTTGTGGCTCT 59.012 47.619 0.00 0.00 0.00 4.09
66 67 2.290577 ACTGGAAGAGGATTTGTGGCTC 60.291 50.000 0.00 0.00 37.43 4.70
67 68 1.707427 ACTGGAAGAGGATTTGTGGCT 59.293 47.619 0.00 0.00 37.43 4.75
68 69 2.206576 ACTGGAAGAGGATTTGTGGC 57.793 50.000 0.00 0.00 37.43 5.01
69 70 4.026356 AGAACTGGAAGAGGATTTGTGG 57.974 45.455 0.00 0.00 37.43 4.17
70 71 5.334414 CGAAAGAACTGGAAGAGGATTTGTG 60.334 44.000 0.00 0.00 37.43 3.33
71 72 4.757149 CGAAAGAACTGGAAGAGGATTTGT 59.243 41.667 0.00 0.00 37.43 2.83
72 73 4.154918 CCGAAAGAACTGGAAGAGGATTTG 59.845 45.833 0.00 0.00 37.43 2.32
73 74 4.327680 CCGAAAGAACTGGAAGAGGATTT 58.672 43.478 0.00 0.00 37.43 2.17
74 75 3.307762 CCCGAAAGAACTGGAAGAGGATT 60.308 47.826 0.00 0.00 37.43 3.01
75 76 2.237392 CCCGAAAGAACTGGAAGAGGAT 59.763 50.000 0.00 0.00 37.43 3.24
76 77 1.623811 CCCGAAAGAACTGGAAGAGGA 59.376 52.381 0.00 0.00 37.43 3.71
77 78 1.946283 GCCCGAAAGAACTGGAAGAGG 60.946 57.143 0.00 0.00 37.43 3.69
78 79 1.002544 AGCCCGAAAGAACTGGAAGAG 59.997 52.381 0.00 0.00 37.43 2.85
79 80 1.056660 AGCCCGAAAGAACTGGAAGA 58.943 50.000 0.00 0.00 37.43 2.87
80 81 1.897560 AAGCCCGAAAGAACTGGAAG 58.102 50.000 0.00 0.00 42.29 3.46
81 82 3.713826 ATAAGCCCGAAAGAACTGGAA 57.286 42.857 0.00 0.00 0.00 3.53
82 83 3.713826 AATAAGCCCGAAAGAACTGGA 57.286 42.857 0.00 0.00 0.00 3.86
83 84 4.335594 CCTAAATAAGCCCGAAAGAACTGG 59.664 45.833 0.00 0.00 0.00 4.00
84 85 4.201920 GCCTAAATAAGCCCGAAAGAACTG 60.202 45.833 0.00 0.00 0.00 3.16
85 86 3.945921 GCCTAAATAAGCCCGAAAGAACT 59.054 43.478 0.00 0.00 0.00 3.01
86 87 3.066342 GGCCTAAATAAGCCCGAAAGAAC 59.934 47.826 0.00 0.00 43.76 3.01
87 88 3.284617 GGCCTAAATAAGCCCGAAAGAA 58.715 45.455 0.00 0.00 43.76 2.52
88 89 2.927028 GGCCTAAATAAGCCCGAAAGA 58.073 47.619 0.00 0.00 43.76 2.52
147 148 5.182487 CCCAACTTGTTTTAAAAGCCAACT 58.818 37.500 0.00 0.00 0.00 3.16
153 154 6.982141 GTCCCTTACCCAACTTGTTTTAAAAG 59.018 38.462 0.00 0.00 0.00 2.27
156 157 5.516984 TGTCCCTTACCCAACTTGTTTTAA 58.483 37.500 0.00 0.00 0.00 1.52
166 167 4.264038 GGAAATAGGTTGTCCCTTACCCAA 60.264 45.833 0.00 0.00 42.73 4.12
214 215 4.537135 TCGAAAGACTTCTACAGCCAAT 57.463 40.909 0.00 0.00 33.31 3.16
233 234 8.116624 AGTTATCTAGCGTTTTAATTGAGTCG 57.883 34.615 0.00 0.00 0.00 4.18
244 245 7.277981 CACAATCAACCTAGTTATCTAGCGTTT 59.722 37.037 2.71 0.00 41.49 3.60
259 260 7.633789 AGTTAAGGTATCATCACAATCAACCT 58.366 34.615 0.00 0.00 37.47 3.50
267 268 6.367374 TGACCAAGTTAAGGTATCATCACA 57.633 37.500 0.00 0.00 40.09 3.58
269 270 8.877864 ATTTTGACCAAGTTAAGGTATCATCA 57.122 30.769 0.00 0.00 40.09 3.07
274 275 9.408648 CATAGGATTTTGACCAAGTTAAGGTAT 57.591 33.333 0.00 0.00 40.09 2.73
276 277 6.663523 CCATAGGATTTTGACCAAGTTAAGGT 59.336 38.462 0.00 0.00 43.46 3.50
277 278 6.096846 CCCATAGGATTTTGACCAAGTTAAGG 59.903 42.308 0.00 0.00 33.47 2.69
313 314 9.245481 ACCGGTGGAAAAATAATTTCTAATGTA 57.755 29.630 6.12 0.00 0.00 2.29
327 328 1.757118 TGCATTTCACCGGTGGAAAAA 59.243 42.857 31.54 24.51 37.74 1.94
333 334 2.083774 AGTATGTGCATTTCACCGGTG 58.916 47.619 29.26 29.26 45.03 4.94
424 426 6.024552 TCCATGGAAATTTACTCTTGCAAC 57.975 37.500 13.46 0.00 0.00 4.17
425 427 6.855763 ATCCATGGAAATTTACTCTTGCAA 57.144 33.333 20.67 0.00 0.00 4.08
505 512 3.440173 CGAATTCCGATCCAAATATGGGG 59.560 47.826 0.00 0.00 43.53 4.96
546 553 2.158885 TCTGAAATGTGTTGGTGTCGGA 60.159 45.455 0.00 0.00 0.00 4.55
599 606 6.373005 TCAGACTTCTGGAATGGAATTGTA 57.627 37.500 6.40 0.00 43.91 2.41
601 608 6.385033 GTTTCAGACTTCTGGAATGGAATTG 58.615 40.000 3.23 0.00 42.89 2.32
602 609 5.182001 CGTTTCAGACTTCTGGAATGGAATT 59.818 40.000 10.60 0.00 42.89 2.17
603 610 4.697352 CGTTTCAGACTTCTGGAATGGAAT 59.303 41.667 10.60 0.00 42.89 3.01
604 611 4.065088 CGTTTCAGACTTCTGGAATGGAA 58.935 43.478 10.60 0.00 42.89 3.53
605 612 3.664107 CGTTTCAGACTTCTGGAATGGA 58.336 45.455 10.60 0.00 42.89 3.41
607 614 2.160417 GCCGTTTCAGACTTCTGGAATG 59.840 50.000 11.30 11.30 42.89 2.67
629 745 1.171549 GGCCGGGTTTTCGTTTACCA 61.172 55.000 2.18 0.00 36.10 3.25
650 804 0.881118 TTTGGAGAATGACGGCTTGC 59.119 50.000 0.00 0.00 0.00 4.01
680 834 2.918230 AAATTAGAGCGTCGGGGCGG 62.918 60.000 0.00 0.00 38.18 6.13
681 835 1.520787 AAATTAGAGCGTCGGGGCG 60.521 57.895 0.00 0.00 38.18 6.13
682 836 1.436983 CCAAATTAGAGCGTCGGGGC 61.437 60.000 0.00 0.00 0.00 5.80
695 849 2.903784 GGTTTAGGGTTCCTGCCAAATT 59.096 45.455 0.00 0.00 34.61 1.82
748 905 2.035783 GAGCTTGGTGGGTTCCCC 59.964 66.667 5.34 0.00 45.71 4.81
855 1041 1.801332 CCGGAGACAGACGGTGTAG 59.199 63.158 0.00 0.00 44.85 2.74
856 1042 3.991999 CCGGAGACAGACGGTGTA 58.008 61.111 0.00 0.00 44.85 2.90
861 1047 2.126307 CACAGCCGGAGACAGACG 60.126 66.667 5.05 0.00 0.00 4.18
862 1048 2.433318 GCACAGCCGGAGACAGAC 60.433 66.667 5.05 0.00 0.00 3.51
864 1050 2.433838 CTGCACAGCCGGAGACAG 60.434 66.667 5.05 6.68 0.00 3.51
878 1064 4.043200 GCGGTCTTGTTGGGCTGC 62.043 66.667 0.00 0.00 0.00 5.25
955 1144 2.037367 TCTGTCGGGTGAGAGGGG 59.963 66.667 0.00 0.00 36.21 4.79
1237 1436 3.368323 GGGAACCGTATAAAGGTCGTGAA 60.368 47.826 2.04 0.00 41.95 3.18
1340 1539 3.399181 GGGGGCGACATCACCTCA 61.399 66.667 0.00 0.00 0.00 3.86
1358 1557 3.220999 TTGGTCTGGTGTCTCGGCG 62.221 63.158 0.00 0.00 0.00 6.46
1367 1566 0.898320 CGACTGATCCTTGGTCTGGT 59.102 55.000 0.00 0.00 0.00 4.00
1370 1569 1.550976 GAACCGACTGATCCTTGGTCT 59.449 52.381 0.77 0.00 31.17 3.85
1537 1742 1.143813 CCAGGGCCTTGGATATGACT 58.856 55.000 29.70 0.00 40.87 3.41
1543 1748 2.003548 GTCCTCCAGGGCCTTGGAT 61.004 63.158 34.68 0.00 45.80 3.41
1620 1826 9.778741 GAATCACAGTAATACATTCATCCCTTA 57.221 33.333 0.00 0.00 0.00 2.69
1654 1861 2.509569 ACCACACCATAACGAATTGCA 58.490 42.857 0.00 0.00 0.00 4.08
1659 1866 6.814644 CACTATCTAAACCACACCATAACGAA 59.185 38.462 0.00 0.00 0.00 3.85
1693 1901 8.696374 TGGACAAATGAACCAACATAAGTAAAA 58.304 29.630 0.00 0.00 0.00 1.52
1694 1902 8.138712 GTGGACAAATGAACCAACATAAGTAAA 58.861 33.333 0.00 0.00 35.40 2.01
1695 1903 7.285629 TGTGGACAAATGAACCAACATAAGTAA 59.714 33.333 0.00 0.00 35.40 2.24
1737 1945 0.036875 AACAGTGCTCTTGTAGGGGC 59.963 55.000 0.00 0.00 0.00 5.80
1739 1947 3.126001 TCAAACAGTGCTCTTGTAGGG 57.874 47.619 0.00 0.00 0.00 3.53
1787 1997 3.930229 TCTGAAACGACCCATTTACATCG 59.070 43.478 0.00 0.00 40.39 3.84
1831 2047 3.331889 ACCCCTGAGACTTCAATTGACAT 59.668 43.478 7.89 0.00 31.69 3.06
1835 2051 2.816087 CACACCCCTGAGACTTCAATTG 59.184 50.000 0.00 0.00 31.69 2.32
1843 2059 4.015872 TGTAAAATCACACCCCTGAGAC 57.984 45.455 0.00 0.00 0.00 3.36
1898 2114 7.014134 TCCTAGAACTTGCATTTGAAACAATCA 59.986 33.333 0.00 0.00 35.85 2.57
1899 2115 7.370383 TCCTAGAACTTGCATTTGAAACAATC 58.630 34.615 0.00 0.00 0.00 2.67
1900 2116 7.288810 TCCTAGAACTTGCATTTGAAACAAT 57.711 32.000 0.00 0.00 0.00 2.71
1919 2138 9.096160 CAGCAAGCACAATAATATCTATCCTAG 57.904 37.037 0.00 0.00 0.00 3.02
1959 2178 7.619965 TGTGTGATCATCTATCAACCAAACTA 58.380 34.615 0.00 0.00 46.17 2.24
2046 2265 7.509546 TCCCAGAGCTACAAAATAGGATAAAG 58.490 38.462 0.00 0.00 0.00 1.85
2048 2267 7.072454 ACATCCCAGAGCTACAAAATAGGATAA 59.928 37.037 0.00 0.00 30.56 1.75
2151 2370 2.034179 TGAATACCGGCGATCACAGTAG 59.966 50.000 9.30 0.00 0.00 2.57
2541 2764 8.491331 AACACAAAATTACACAAGCAATTCTT 57.509 26.923 0.00 0.00 34.78 2.52
2673 2896 4.452455 AGGCTATCTCAAACTTGTGTTTCG 59.548 41.667 0.00 0.00 43.75 3.46
2902 3125 7.378181 ACCAGTGCTAATGTTTCCAATTAAAG 58.622 34.615 0.00 0.00 0.00 1.85
2903 3126 7.296628 ACCAGTGCTAATGTTTCCAATTAAA 57.703 32.000 0.00 0.00 0.00 1.52
2904 3127 6.909550 ACCAGTGCTAATGTTTCCAATTAA 57.090 33.333 0.00 0.00 0.00 1.40
3194 3428 6.390987 AACTTACTCGCATTAGAACGAAAG 57.609 37.500 0.00 0.00 37.94 2.62
3299 3534 6.709846 CCAAACATGAAATAAAACCACCACAT 59.290 34.615 0.00 0.00 0.00 3.21
3316 3551 9.643693 AGCAAAAAGATACTTATTCCAAACATG 57.356 29.630 0.00 0.00 0.00 3.21
3436 3717 4.787551 TCATACTGAAAACCCGGCATAAT 58.212 39.130 0.00 0.00 0.00 1.28
3471 3752 5.292101 CCGGTGCTCTTAAGAACTGAAATAG 59.708 44.000 15.03 0.00 39.57 1.73
3472 3753 5.175859 CCGGTGCTCTTAAGAACTGAAATA 58.824 41.667 15.03 0.00 39.57 1.40
3473 3754 4.003648 CCGGTGCTCTTAAGAACTGAAAT 58.996 43.478 15.03 0.00 39.57 2.17
3474 3755 3.399330 CCGGTGCTCTTAAGAACTGAAA 58.601 45.455 15.03 0.00 39.57 2.69
3475 3756 2.870435 GCCGGTGCTCTTAAGAACTGAA 60.870 50.000 15.03 0.00 39.57 3.02
3476 3757 1.337823 GCCGGTGCTCTTAAGAACTGA 60.338 52.381 15.03 0.00 39.57 3.41
3477 3758 1.079503 GCCGGTGCTCTTAAGAACTG 58.920 55.000 6.63 7.78 37.20 3.16
3478 3759 0.036294 GGCCGGTGCTCTTAAGAACT 60.036 55.000 6.63 0.00 37.74 3.01
3479 3760 0.036294 AGGCCGGTGCTCTTAAGAAC 60.036 55.000 6.63 2.49 37.74 3.01
3485 3766 0.400594 AACTTTAGGCCGGTGCTCTT 59.599 50.000 1.90 0.00 37.74 2.85
3517 3798 7.201947 CCTCTGACAGGTTCATCTGTATCATAA 60.202 40.741 1.81 0.00 46.76 1.90
3527 3808 4.008074 TGTTTCCTCTGACAGGTTCATC 57.992 45.455 1.81 0.00 43.95 2.92
3552 3833 9.629878 TTGAAGGAAAGTAACCAAGTAATACAA 57.370 29.630 0.00 0.00 0.00 2.41
3653 3934 9.549078 TGAACGCAACATAGTATTAATAATGGA 57.451 29.630 5.70 0.00 0.00 3.41
3654 3935 9.594038 GTGAACGCAACATAGTATTAATAATGG 57.406 33.333 5.70 1.12 0.00 3.16
3752 4033 9.638239 TTTCTCTGTTTACCAATTCATATTTGC 57.362 29.630 0.00 0.00 0.00 3.68
3885 4166 6.451393 AGAATCTAGAACAACTGTCACAGAC 58.549 40.000 13.14 0.00 35.18 3.51
3986 4267 7.839200 CCACTTTTATATATATGGGGAAAGGGG 59.161 40.741 15.80 15.80 39.12 4.79
4129 4414 2.615912 GCTCTTCCATTACATCCACTGC 59.384 50.000 0.00 0.00 0.00 4.40
4155 4440 1.131504 CGCCTGCGCAAATAAAAGGTA 59.868 47.619 13.05 0.00 34.03 3.08
4290 4575 4.537135 ATGTCACTACCAGTACAACCAG 57.463 45.455 0.00 0.00 0.00 4.00
4357 4653 8.682710 GCAAGGGTACAAATTGTTATATCTTCA 58.317 33.333 3.17 0.00 0.00 3.02
4372 4668 5.435686 AGAAGTCATATGCAAGGGTACAA 57.564 39.130 0.00 0.00 0.00 2.41
4380 4676 6.090763 CGTCACTAACAAGAAGTCATATGCAA 59.909 38.462 0.00 0.00 0.00 4.08
4393 4689 9.567848 AATAAAAATTATGGCGTCACTAACAAG 57.432 29.630 0.00 0.00 0.00 3.16
4395 4691 9.347934 CAAATAAAAATTATGGCGTCACTAACA 57.652 29.630 0.00 0.00 0.00 2.41
4403 4699 7.309920 ACGTTCTCAAATAAAAATTATGGCGT 58.690 30.769 0.00 0.00 0.00 5.68
4430 4726 5.568620 AGAGCTACTGGGAAAGAAAAGAA 57.431 39.130 0.00 0.00 0.00 2.52
4432 4728 5.555966 AGAAGAGCTACTGGGAAAGAAAAG 58.444 41.667 0.00 0.00 0.00 2.27
4458 4758 4.979197 GTGCACACAAATACGGAAAATGAA 59.021 37.500 13.17 0.00 0.00 2.57
4459 4759 4.541779 GTGCACACAAATACGGAAAATGA 58.458 39.130 13.17 0.00 0.00 2.57
4460 4760 3.672867 GGTGCACACAAATACGGAAAATG 59.327 43.478 20.43 0.00 0.00 2.32
4461 4761 3.305744 GGGTGCACACAAATACGGAAAAT 60.306 43.478 20.43 0.00 0.00 1.82
4465 4765 0.108774 TGGGTGCACACAAATACGGA 59.891 50.000 22.04 0.00 0.00 4.69
4466 4766 1.173043 ATGGGTGCACACAAATACGG 58.827 50.000 28.30 0.00 30.29 4.02
4467 4767 2.030363 ACAATGGGTGCACACAAATACG 60.030 45.455 28.30 14.73 30.29 3.06
4538 4848 6.796705 TCCTCGAGAAAACAAAATTAGACC 57.203 37.500 15.71 0.00 0.00 3.85
4557 4867 6.319658 TGAAATGAAGTAGATTGGCATTCCTC 59.680 38.462 5.80 0.60 0.00 3.71
4565 4875 5.801350 TTCGCTGAAATGAAGTAGATTGG 57.199 39.130 0.00 0.00 0.00 3.16
4595 4905 7.992754 ATGCTTCTGACTCTAAACATTTTCT 57.007 32.000 0.00 0.00 0.00 2.52
4609 4919 7.095229 TGTGTAGTTTGACATAATGCTTCTGAC 60.095 37.037 0.00 0.00 0.00 3.51
4616 4926 6.024049 GCTTCTGTGTAGTTTGACATAATGC 58.976 40.000 0.00 0.00 0.00 3.56
4617 4927 7.118245 TCTGCTTCTGTGTAGTTTGACATAATG 59.882 37.037 0.00 0.00 0.00 1.90
4618 4928 7.161404 TCTGCTTCTGTGTAGTTTGACATAAT 58.839 34.615 0.00 0.00 0.00 1.28
4620 4930 6.096673 TCTGCTTCTGTGTAGTTTGACATA 57.903 37.500 0.00 0.00 0.00 2.29
4621 4931 4.960938 TCTGCTTCTGTGTAGTTTGACAT 58.039 39.130 0.00 0.00 0.00 3.06
4623 4933 4.319118 GCTTCTGCTTCTGTGTAGTTTGAC 60.319 45.833 0.00 0.00 36.03 3.18
4625 4935 3.561310 TGCTTCTGCTTCTGTGTAGTTTG 59.439 43.478 0.00 0.00 40.48 2.93
4626 4936 3.808728 TGCTTCTGCTTCTGTGTAGTTT 58.191 40.909 0.00 0.00 40.48 2.66
4679 7576 9.736023 CATCGATAATTCTCGGATGATATGTTA 57.264 33.333 12.61 0.00 39.13 2.41
4684 7581 8.736244 TGTTACATCGATAATTCTCGGATGATA 58.264 33.333 21.09 12.66 39.13 2.15
4752 7667 1.805345 CGGGTATTTGCGTGTTGGTAA 59.195 47.619 0.00 0.00 0.00 2.85
4759 7674 1.080298 TACAAGCGGGTATTTGCGTG 58.920 50.000 0.00 0.00 44.49 5.34
4761 7676 1.735571 ACTTACAAGCGGGTATTTGCG 59.264 47.619 0.00 0.00 35.87 4.85
4762 7677 2.731027 GCACTTACAAGCGGGTATTTGC 60.731 50.000 7.76 7.76 0.00 3.68
4763 7678 2.159435 GGCACTTACAAGCGGGTATTTG 60.159 50.000 0.00 0.00 0.00 2.32
4764 7679 2.089201 GGCACTTACAAGCGGGTATTT 58.911 47.619 0.00 0.00 0.00 1.40
4765 7680 1.003812 TGGCACTTACAAGCGGGTATT 59.996 47.619 0.00 0.00 0.00 1.89
4766 7681 0.616371 TGGCACTTACAAGCGGGTAT 59.384 50.000 0.00 0.00 0.00 2.73
4767 7682 0.320946 GTGGCACTTACAAGCGGGTA 60.321 55.000 11.13 0.00 0.00 3.69
4769 7684 2.677003 CGTGGCACTTACAAGCGGG 61.677 63.158 16.72 0.00 0.00 6.13
4770 7685 1.626654 CTCGTGGCACTTACAAGCGG 61.627 60.000 16.72 0.00 0.00 5.52
4771 7686 0.666274 TCTCGTGGCACTTACAAGCG 60.666 55.000 16.72 0.00 0.00 4.68
4772 7687 1.508632 TTCTCGTGGCACTTACAAGC 58.491 50.000 16.72 0.00 0.00 4.01
4774 7689 1.871039 GCTTTCTCGTGGCACTTACAA 59.129 47.619 16.72 2.78 0.00 2.41
4775 7690 1.508632 GCTTTCTCGTGGCACTTACA 58.491 50.000 16.72 0.00 0.00 2.41
4776 7691 0.796927 GGCTTTCTCGTGGCACTTAC 59.203 55.000 16.72 0.00 0.00 2.34
4783 7716 3.190874 GTGATCTAAGGCTTTCTCGTGG 58.809 50.000 4.45 0.00 0.00 4.94
4811 7744 5.967674 CGTGGAAGATTGTATTTCATTGAGC 59.032 40.000 0.00 0.00 0.00 4.26
4829 7767 3.508793 CCTAGTAGACAGGTTTCGTGGAA 59.491 47.826 0.00 0.00 0.00 3.53
4891 7832 2.948093 CGCTTGATTGATTTGGCGG 58.052 52.632 0.00 0.00 39.12 6.13
4901 7842 2.893489 AGAAAAAGAAGGCCGCTTGATT 59.107 40.909 13.61 11.78 0.00 2.57
4909 7850 3.564225 TGAAGTCGAAGAAAAAGAAGGCC 59.436 43.478 0.00 0.00 39.69 5.19
4932 7873 7.290110 AGTATATTCATCGGTCTTGTGATGA 57.710 36.000 1.02 1.02 46.79 2.92
4969 7910 0.464735 TGTTTGCCGGTGTAGTGCTT 60.465 50.000 1.90 0.00 0.00 3.91
4975 7916 1.228003 CCCTGTGTTTGCCGGTGTA 60.228 57.895 1.90 0.00 0.00 2.90
5041 7982 3.879295 CCTAGCCATTTGTTGACGATGAT 59.121 43.478 0.00 0.00 0.00 2.45
5091 8032 9.561069 GGGAGTATGTTTCTGTGATTATGTATT 57.439 33.333 0.00 0.00 0.00 1.89
5098 8039 4.383118 CGGAGGGAGTATGTTTCTGTGATT 60.383 45.833 0.00 0.00 0.00 2.57
5100 8041 2.496070 CGGAGGGAGTATGTTTCTGTGA 59.504 50.000 0.00 0.00 0.00 3.58
5113 8054 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5114 8055 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5115 8056 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5116 8057 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
5117 8058 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
5118 8059 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
5119 8060 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
5134 8075 9.559732 TCATTTGTTGAAATCTCTAGAAAGACA 57.440 29.630 0.00 0.00 28.65 3.41
5135 8076 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
5136 8077 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
5139 8080 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
5143 8084 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
5144 8085 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
5145 8086 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
5146 8087 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
5147 8088 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
5148 8089 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
5149 8090 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
5150 8091 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
5151 8092 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
5152 8093 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
5153 8094 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
5154 8095 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
5155 8096 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
5156 8097 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
5157 8098 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
5158 8099 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
5159 8100 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
5160 8101 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
5161 8102 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
5162 8103 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
5163 8104 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
5164 8105 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
5165 8106 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
5166 8107 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
5167 8108 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
5168 8109 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
5169 8110 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
5170 8111 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
5199 8140 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
5201 8142 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
5202 8143 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
5203 8144 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
5204 8145 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
5205 8146 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
5206 8147 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
5207 8148 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
5208 8149 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
5209 8150 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
5210 8151 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
5226 8167 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
5227 8168 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.