Multiple sequence alignment - TraesCS4D01G299400

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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 TraesCS4D01G299400 chr4D 100.000 3061 0 0 3247 6307 468420381 468423441 0.000000e+00 5653.0
1 TraesCS4D01G299400 chr4D 100.000 2976 0 0 1 2976 468417135 468420110 0.000000e+00 5496.0
2 TraesCS4D01G299400 chr4B 93.503 1647 54 20 3254 4882 586932875 586934486 0.000000e+00 2399.0
3 TraesCS4D01G299400 chr4B 93.488 1290 60 9 1564 2839 586931128 586932407 0.000000e+00 1895.0
4 TraesCS4D01G299400 chr4B 91.407 1187 74 17 313 1477 586929651 586930831 0.000000e+00 1602.0
5 TraesCS4D01G299400 chr4B 92.192 999 30 18 3865 4843 587161966 587162936 0.000000e+00 1369.0
6 TraesCS4D01G299400 chr4B 86.580 842 76 19 2154 2974 587160163 587160988 0.000000e+00 894.0
7 TraesCS4D01G299400 chr4B 94.526 548 17 5 4937 5484 586934944 586935478 0.000000e+00 833.0
8 TraesCS4D01G299400 chr4B 88.277 563 46 9 5747 6307 586938169 586938713 0.000000e+00 656.0
9 TraesCS4D01G299400 chr4B 89.462 465 27 9 4937 5401 587162986 587163428 9.180000e-158 568.0
10 TraesCS4D01G299400 chr4B 88.698 407 31 7 1546 1937 587159604 587160010 3.420000e-132 483.0
11 TraesCS4D01G299400 chr4B 98.561 139 2 0 2838 2976 586932521 586932659 4.880000e-61 246.0
12 TraesCS4D01G299400 chr4B 88.535 157 13 3 3519 3675 587161604 587161755 1.080000e-42 185.0
13 TraesCS4D01G299400 chr4B 98.000 50 1 0 5516 5565 586937215 586937264 3.130000e-13 87.9
14 TraesCS4D01G299400 chr4B 92.982 57 3 1 2102 2158 587160021 587160076 1.460000e-11 82.4
15 TraesCS4D01G299400 chr4A 91.418 1573 71 30 3247 4792 3065079 3063544 0.000000e+00 2098.0
16 TraesCS4D01G299400 chr4A 91.717 1002 47 15 973 1943 3066975 3065979 0.000000e+00 1358.0
17 TraesCS4D01G299400 chr4A 91.093 842 55 11 2147 2976 3065935 3065102 0.000000e+00 1122.0
18 TraesCS4D01G299400 chr4A 89.474 646 36 17 314 948 3067588 3066964 0.000000e+00 787.0
19 TraesCS4D01G299400 chr4A 92.489 466 23 7 4937 5401 3063188 3062734 0.000000e+00 656.0
20 TraesCS4D01G299400 chr4A 93.229 192 10 3 5558 5748 579437664 579437853 4.810000e-71 279.0
21 TraesCS4D01G299400 chr4A 80.380 316 32 18 1 312 614007891 614008180 4.950000e-51 213.0
22 TraesCS4D01G299400 chr7D 99.361 313 1 1 1 312 602283985 602283673 3.300000e-157 566.0
23 TraesCS4D01G299400 chr7D 98.738 317 2 2 1 315 48276449 48276765 4.270000e-156 562.0
24 TraesCS4D01G299400 chr7D 98.433 319 4 1 1 318 602279714 602279396 1.540000e-155 560.0
25 TraesCS4D01G299400 chr7D 93.158 190 10 3 5563 5752 270730294 270730480 6.230000e-70 276.0
26 TraesCS4D01G299400 chr7D 79.474 190 39 0 4983 5172 413692761 413692950 1.100000e-27 135.0
27 TraesCS4D01G299400 chr1D 99.038 312 2 1 1 312 438586414 438586724 5.520000e-155 558.0
28 TraesCS4D01G299400 chr1D 91.960 199 11 5 5554 5750 465526822 465527017 2.240000e-69 274.0
29 TraesCS4D01G299400 chr5D 94.704 321 13 4 1 319 473047992 473047674 4.390000e-136 496.0
30 TraesCS4D01G299400 chr5D 96.414 251 9 0 1 251 510490260 510490510 1.270000e-111 414.0
31 TraesCS4D01G299400 chr7A 94.271 192 8 3 5559 5748 610448564 610448754 2.220000e-74 291.0
32 TraesCS4D01G299400 chr7A 84.227 317 22 10 1 309 712973987 712974283 3.720000e-72 283.0
33 TraesCS4D01G299400 chr2D 95.531 179 8 0 5563 5741 573905273 573905451 2.880000e-73 287.0
34 TraesCS4D01G299400 chr3A 93.684 190 11 1 5555 5743 28129021 28129210 3.720000e-72 283.0
35 TraesCS4D01G299400 chr3A 91.089 202 16 2 5563 5764 171039965 171039766 8.060000e-69 272.0
36 TraesCS4D01G299400 chr1A 92.857 196 11 3 5556 5749 133163747 133163553 1.340000e-71 281.0
37 TraesCS4D01G299400 chr7B 92.746 193 14 0 5558 5750 741291893 741292085 4.810000e-71 279.0
38 TraesCS4D01G299400 chr7B 78.261 184 40 0 4983 5166 428095519 428095702 1.110000e-22 119.0
39 TraesCS4D01G299400 chr2A 87.124 233 9 10 1 233 109602086 109602297 1.760000e-60 244.0
40 TraesCS4D01G299400 chr2A 80.317 315 31 18 2 312 705760999 705760712 6.410000e-50 209.0


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 TraesCS4D01G299400 chr4D 468417135 468423441 6306 False 5574.5 5653 100.0000 1 6307 2 chr4D.!!$F1 6306
1 TraesCS4D01G299400 chr4B 586929651 586938713 9062 False 1102.7 2399 93.9660 313 6307 7 chr4B.!!$F1 5994
2 TraesCS4D01G299400 chr4B 587159604 587163428 3824 False 596.9 1369 89.7415 1546 5401 6 chr4B.!!$F2 3855
3 TraesCS4D01G299400 chr4A 3062734 3067588 4854 True 1204.2 2098 91.2382 314 5401 5 chr4A.!!$R1 5087
4 TraesCS4D01G299400 chr7D 602279396 602283985 4589 True 563.0 566 98.8970 1 318 2 chr7D.!!$R1 317

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
380 382 1.045407 AGTTAGAACCAGTCGTGCCA 58.955 50.000 0.00 0.00 0.00 4.92 F
1720 3083 0.108662 TCATACAGTCACTGGCAGCG 60.109 55.000 15.89 5.01 35.51 5.18 F
2077 4271 0.179089 AGCTCACTGATAGCAAGCGG 60.179 55.000 8.30 0.00 42.62 5.52 F
2085 4279 0.320421 GATAGCAAGCGGCCGGAATA 60.320 55.000 29.38 7.44 46.50 1.75 F
3575 6299 0.687354 ACGTGCTGGGAAGATCAAGT 59.313 50.000 0.00 0.00 0.00 3.16 F
4523 7325 1.196354 ACACGTACGAGTAGAGTGTGC 59.804 52.381 24.41 0.00 43.39 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 3210 0.598419 CGCTCTTGCATATCTCGGCA 60.598 55.000 0.00 0.00 39.64 5.69 R
3575 6299 0.037139 CCACCCCGTACACGATTGAA 60.037 55.000 2.76 0.00 43.02 2.69 R
4006 6781 0.968393 AGAGAGAAGGTGAGGTCGCC 60.968 60.000 0.95 0.95 46.57 5.54 R
4069 6846 4.435436 CTAGTGCAGCCGCCGTCA 62.435 66.667 0.00 0.00 37.32 4.35 R
4927 7871 0.106894 GCGATAAACAGGAGGAGGGG 59.893 60.000 0.00 0.00 0.00 4.79 R
5656 10590 0.036765 GGATACAACCCACGTCAGCA 60.037 55.000 0.00 0.00 0.00 4.41 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
380 382 1.045407 AGTTAGAACCAGTCGTGCCA 58.955 50.000 0.00 0.00 0.00 4.92
431 433 6.592607 TGAGACGTCCTAATTAACAAATGGTC 59.407 38.462 13.01 0.00 0.00 4.02
541 772 1.069500 CAGTAAACAAAGAACCGCCCG 60.069 52.381 0.00 0.00 0.00 6.13
715 951 2.354729 CACCATCCGGGGCTTCAA 59.645 61.111 0.00 0.00 42.91 2.69
774 1010 5.997384 AAAGGAAGACGTGGTAAGACTAT 57.003 39.130 0.00 0.00 0.00 2.12
775 1011 7.472334 AAAAGGAAGACGTGGTAAGACTATA 57.528 36.000 0.00 0.00 0.00 1.31
777 1013 5.503927 AGGAAGACGTGGTAAGACTATACA 58.496 41.667 0.00 0.00 0.00 2.29
779 1015 5.356470 GGAAGACGTGGTAAGACTATACACT 59.644 44.000 0.00 0.00 0.00 3.55
781 1017 5.743117 AGACGTGGTAAGACTATACACTCT 58.257 41.667 0.00 0.00 0.00 3.24
782 1018 5.585445 AGACGTGGTAAGACTATACACTCTG 59.415 44.000 0.00 0.00 0.00 3.35
783 1019 4.639310 ACGTGGTAAGACTATACACTCTGG 59.361 45.833 0.00 0.00 0.00 3.86
786 1022 4.645136 TGGTAAGACTATACACTCTGGCAG 59.355 45.833 8.58 8.58 0.00 4.85
941 1269 1.075601 ATCTTCTCCAACCCTTGCCA 58.924 50.000 0.00 0.00 0.00 4.92
1083 1669 3.674997 TGTGCAGGATGGTAAGAAGTTC 58.325 45.455 0.00 0.00 35.86 3.01
1115 1701 0.520827 GAGACGCTCGTCAAGGTACG 60.521 60.000 22.18 0.00 46.76 3.67
1121 1707 0.456312 CTCGTCAAGGTACGGTGCTC 60.456 60.000 0.00 0.00 43.05 4.26
1123 1709 0.456312 CGTCAAGGTACGGTGCTCTC 60.456 60.000 0.00 0.00 39.19 3.20
1124 1710 0.108756 GTCAAGGTACGGTGCTCTCC 60.109 60.000 0.00 0.00 0.00 3.71
1125 1711 1.218316 CAAGGTACGGTGCTCTCCC 59.782 63.158 0.00 0.00 0.00 4.30
1148 1734 2.635714 TGCTCCTCTTGTGCATATGTG 58.364 47.619 4.29 0.00 38.48 3.21
1223 1814 8.758633 AGATCGGTTAAATTTACGATATCTGG 57.241 34.615 18.34 0.00 44.99 3.86
1310 2225 2.843113 GGCCTATCTAGATCCTGGCAAT 59.157 50.000 29.34 4.77 41.86 3.56
1382 2526 1.100510 CTCGGGTCACGGTTCTCATA 58.899 55.000 0.00 0.00 44.45 2.15
1459 2610 6.886459 ACAGATATGAGGTAGTGCACATTTTT 59.114 34.615 21.04 0.00 0.00 1.94
1460 2611 7.148188 ACAGATATGAGGTAGTGCACATTTTTG 60.148 37.037 21.04 5.98 0.00 2.44
1604 2965 2.632512 TCATCCCAAAACCAAAAGGAGC 59.367 45.455 0.00 0.00 0.00 4.70
1641 3004 3.381590 ACTTCTGTCTTTTGCTTTGTCCC 59.618 43.478 0.00 0.00 0.00 4.46
1642 3005 3.011566 TCTGTCTTTTGCTTTGTCCCA 57.988 42.857 0.00 0.00 0.00 4.37
1714 3077 1.857217 GCGCTGATCATACAGTCACTG 59.143 52.381 2.22 2.22 39.73 3.66
1720 3083 0.108662 TCATACAGTCACTGGCAGCG 60.109 55.000 15.89 5.01 35.51 5.18
1750 3113 6.050432 TGGCGTGGTTACAGGTATATTAAAG 58.950 40.000 0.00 0.00 35.03 1.85
1764 3129 5.968528 ATATTAAAGTCCACAACGCCAAA 57.031 34.783 0.00 0.00 0.00 3.28
1794 3159 8.038492 ACATACAAAACAAAATGCAACTTGTT 57.962 26.923 18.74 18.74 45.35 2.83
1990 4184 2.362077 GCGGGGAAAATCAATATGCTGT 59.638 45.455 0.00 0.00 0.00 4.40
2002 4196 7.997773 ATCAATATGCTGTCAATAATGCTCT 57.002 32.000 0.00 0.00 0.00 4.09
2030 4224 2.497675 AGTTGGCGTCTCAGTGACATAT 59.502 45.455 3.60 0.00 45.60 1.78
2031 4225 3.699538 AGTTGGCGTCTCAGTGACATATA 59.300 43.478 3.60 0.00 45.60 0.86
2072 4266 4.100498 TCATGATCAAGCTCACTGATAGCA 59.900 41.667 0.00 0.00 42.62 3.49
2076 4270 1.326852 CAAGCTCACTGATAGCAAGCG 59.673 52.381 8.30 0.00 42.62 4.68
2077 4271 0.179089 AGCTCACTGATAGCAAGCGG 60.179 55.000 8.30 0.00 42.62 5.52
2085 4279 0.320421 GATAGCAAGCGGCCGGAATA 60.320 55.000 29.38 7.44 46.50 1.75
2103 4462 6.978659 CCGGAATAACACGACAGCATATATAT 59.021 38.462 0.00 0.00 0.00 0.86
2104 4463 8.132995 CCGGAATAACACGACAGCATATATATA 58.867 37.037 0.00 0.00 0.00 0.86
2105 4464 9.511144 CGGAATAACACGACAGCATATATATAA 57.489 33.333 0.00 0.00 0.00 0.98
2282 4731 0.877071 GTGCACATGGTGGAGTCAAG 59.123 55.000 13.17 0.00 33.95 3.02
2347 4796 6.183347 ACCTGCTCTATTGACTTTTGCTAAT 58.817 36.000 0.00 0.00 0.00 1.73
2378 4827 1.257155 AGCGACGACGAAAACAAGTTC 59.743 47.619 12.29 0.00 42.66 3.01
2417 4877 2.484264 GACGGCAGCAGTTGAAAATAGT 59.516 45.455 0.00 0.00 0.00 2.12
2418 4878 2.226437 ACGGCAGCAGTTGAAAATAGTG 59.774 45.455 0.00 0.00 0.00 2.74
2478 4938 9.877178 ATGTCATCTAAGTTTCTTACGAAATCT 57.123 29.630 0.00 0.00 40.91 2.40
2596 5056 2.757917 AGCACGCTCCTCCTCCTC 60.758 66.667 0.00 0.00 0.00 3.71
2602 5062 2.042435 CTCCTCCTCCTCGGCCTT 60.042 66.667 0.00 0.00 0.00 4.35
2650 5110 2.941720 GTTTCTCATCTCCATGCTGGTC 59.058 50.000 2.68 0.00 39.03 4.02
2825 5294 8.177119 AGTGTGGATTGCTAAAAACTATCAAA 57.823 30.769 0.00 0.00 0.00 2.69
3279 5998 5.641636 TGCCTACTAAACATATGTGTGTGTG 59.358 40.000 9.63 5.93 38.92 3.82
3468 6187 6.769822 CCTCATTTCTGCTCAAGGTACATAAT 59.230 38.462 0.00 0.00 0.00 1.28
3476 6195 6.578944 TGCTCAAGGTACATAATAACACGAT 58.421 36.000 0.00 0.00 0.00 3.73
3477 6196 6.700081 TGCTCAAGGTACATAATAACACGATC 59.300 38.462 0.00 0.00 0.00 3.69
3478 6197 6.129168 GCTCAAGGTACATAATAACACGATCG 60.129 42.308 14.88 14.88 0.00 3.69
3479 6198 7.030075 TCAAGGTACATAATAACACGATCGA 57.970 36.000 24.34 0.00 0.00 3.59
3489 6208 9.661187 CATAATAACACGATCGACTAGTTAGTT 57.339 33.333 24.34 18.11 36.50 2.24
3498 6217 8.121708 ACGATCGACTAGTTAGTTCAAAGTATC 58.878 37.037 24.34 0.00 36.50 2.24
3566 6290 1.375908 GCATCAGAACGTGCTGGGA 60.376 57.895 23.51 5.47 38.30 4.37
3572 6296 0.976641 AGAACGTGCTGGGAAGATCA 59.023 50.000 0.00 0.00 0.00 2.92
3575 6299 0.687354 ACGTGCTGGGAAGATCAAGT 59.313 50.000 0.00 0.00 0.00 3.16
3578 6302 2.783135 GTGCTGGGAAGATCAAGTTCA 58.217 47.619 0.00 0.00 0.00 3.18
3680 6404 5.582665 GCAGGTACTTTCCAGCTATATATGC 59.417 44.000 0.00 0.00 34.60 3.14
3794 6562 1.518367 TCTGTGGGTTTCTTGGTCCT 58.482 50.000 0.00 0.00 0.00 3.85
4069 6846 8.047310 ACTGTCAATATTAGGGAGAACGAAAAT 58.953 33.333 0.00 0.00 0.00 1.82
4152 6936 5.729510 ACACACACACACATATATAGTGCA 58.270 37.500 14.25 0.00 40.59 4.57
4199 6988 6.183360 ACGACTTAACTACGACTTACTAGCAG 60.183 42.308 0.00 0.00 0.00 4.24
4200 6989 5.878133 ACTTAACTACGACTTACTAGCAGC 58.122 41.667 0.00 0.00 0.00 5.25
4201 6990 3.779271 AACTACGACTTACTAGCAGCC 57.221 47.619 0.00 0.00 0.00 4.85
4202 6991 2.719739 ACTACGACTTACTAGCAGCCA 58.280 47.619 0.00 0.00 0.00 4.75
4309 7098 8.202461 ACGGAATGATTGGGTTCTATCTTATA 57.798 34.615 0.00 0.00 0.00 0.98
4310 7099 8.826765 ACGGAATGATTGGGTTCTATCTTATAT 58.173 33.333 0.00 0.00 0.00 0.86
4513 7315 3.843510 GCTTGTTTTTGGACACGTACGAG 60.844 47.826 24.41 17.53 0.00 4.18
4515 7317 4.039151 TGTTTTTGGACACGTACGAGTA 57.961 40.909 24.41 2.89 0.00 2.59
4516 7318 4.043750 TGTTTTTGGACACGTACGAGTAG 58.956 43.478 24.41 10.93 0.00 2.57
4518 7320 3.818961 TTTGGACACGTACGAGTAGAG 57.181 47.619 24.41 6.65 0.00 2.43
4519 7321 2.462456 TGGACACGTACGAGTAGAGT 57.538 50.000 24.41 9.81 0.00 3.24
4520 7322 2.071540 TGGACACGTACGAGTAGAGTG 58.928 52.381 24.41 10.30 38.63 3.51
4523 7325 1.196354 ACACGTACGAGTAGAGTGTGC 59.804 52.381 24.41 0.00 43.39 4.57
4524 7326 1.463831 CACGTACGAGTAGAGTGTGCT 59.536 52.381 24.41 0.00 0.00 4.40
4528 7330 1.912417 ACGAGTAGAGTGTGCTCCTT 58.088 50.000 0.00 0.00 42.59 3.36
4630 7435 1.202580 AGCCTTGTACTGATCGATGGC 60.203 52.381 0.54 6.85 39.40 4.40
4734 7542 4.280677 TCCAAGCTGAACCAAACAAATAGG 59.719 41.667 0.00 0.00 0.00 2.57
4736 7544 5.242838 CCAAGCTGAACCAAACAAATAGGTA 59.757 40.000 0.00 0.00 34.63 3.08
4737 7545 5.959618 AGCTGAACCAAACAAATAGGTAC 57.040 39.130 0.00 0.00 34.63 3.34
4774 7586 1.258982 GACGACCGATTCACATGCATC 59.741 52.381 0.00 0.00 0.00 3.91
4882 7702 4.845580 CCCCTACGCTGCTGGCTG 62.846 72.222 0.00 0.00 39.13 4.85
4883 7703 4.845580 CCCTACGCTGCTGGCTGG 62.846 72.222 0.00 0.00 39.13 4.85
4885 7705 4.765449 CTACGCTGCTGGCTGGCA 62.765 66.667 3.18 3.18 40.15 4.92
5061 8284 0.466922 CTTCATGGGGTGGCTCATCC 60.467 60.000 0.00 0.00 33.05 3.51
5108 8331 2.081212 GCTCGTCGGAGTTGTCGTG 61.081 63.158 0.00 0.00 42.53 4.35
5121 8344 3.690280 TCGTGTGCCCGCTGATGA 61.690 61.111 0.00 0.00 0.00 2.92
5126 8349 2.202919 TGCCCGCTGATGATCGTG 60.203 61.111 0.00 0.00 0.00 4.35
5133 8356 1.065551 CGCTGATGATCGTGTACCTCA 59.934 52.381 0.00 0.00 0.00 3.86
5138 8361 1.389555 TGATCGTGTACCTCATCGCT 58.610 50.000 0.00 0.00 0.00 4.93
5349 8578 0.390860 GCTACATGGACATCTCGCCT 59.609 55.000 0.00 0.00 0.00 5.52
5350 8579 1.604185 GCTACATGGACATCTCGCCTC 60.604 57.143 0.00 0.00 0.00 4.70
5351 8580 0.668535 TACATGGACATCTCGCCTCG 59.331 55.000 0.00 0.00 0.00 4.63
5352 8581 1.953138 CATGGACATCTCGCCTCGC 60.953 63.158 0.00 0.00 0.00 5.03
5353 8582 3.157217 ATGGACATCTCGCCTCGCC 62.157 63.158 0.00 0.00 0.00 5.54
5428 8657 3.060070 GGAGTATATGTTTTACGGTGCGC 60.060 47.826 0.00 0.00 0.00 6.09
5429 8658 3.523547 AGTATATGTTTTACGGTGCGCA 58.476 40.909 5.66 5.66 0.00 6.09
5430 8659 2.817538 ATATGTTTTACGGTGCGCAC 57.182 45.000 32.15 32.15 0.00 5.34
5431 8660 0.439214 TATGTTTTACGGTGCGCACG 59.561 50.000 32.35 27.66 37.36 5.34
5458 8687 6.309436 CGTGTATACGTGTCAATATCCGTAT 58.691 40.000 3.56 9.53 45.39 3.06
5459 8688 6.463890 CGTGTATACGTGTCAATATCCGTATC 59.536 42.308 3.56 3.56 43.25 2.24
5460 8689 7.300320 GTGTATACGTGTCAATATCCGTATCA 58.700 38.462 0.00 5.43 43.25 2.15
5461 8690 7.966753 GTGTATACGTGTCAATATCCGTATCAT 59.033 37.037 0.00 0.00 43.25 2.45
5508 8901 4.390909 GTGATTAAGGTGGACTTGTTACGG 59.609 45.833 0.00 0.00 40.37 4.02
5585 10519 8.854614 AGAATAACAGTTTTGCTAGAACTCAT 57.145 30.769 0.00 0.00 35.26 2.90
5586 10520 9.289782 AGAATAACAGTTTTGCTAGAACTCATT 57.710 29.630 0.00 0.00 35.26 2.57
5587 10521 9.899226 GAATAACAGTTTTGCTAGAACTCATTT 57.101 29.630 0.00 0.00 35.26 2.32
5590 10524 8.677148 AACAGTTTTGCTAGAACTCATTTAGA 57.323 30.769 0.00 0.00 35.26 2.10
5592 10526 8.725148 ACAGTTTTGCTAGAACTCATTTAGATG 58.275 33.333 0.00 0.00 35.26 2.90
5593 10527 8.939929 CAGTTTTGCTAGAACTCATTTAGATGA 58.060 33.333 0.00 0.00 39.92 2.92
5609 10543 9.971922 CATTTAGATGAGATTTAATTTGGTCCC 57.028 33.333 0.00 0.00 35.16 4.46
5611 10545 9.713684 TTTAGATGAGATTTAATTTGGTCCCAT 57.286 29.630 0.00 0.00 0.00 4.00
5613 10547 8.242729 AGATGAGATTTAATTTGGTCCCATTC 57.757 34.615 0.00 0.00 0.00 2.67
5614 10548 7.840716 AGATGAGATTTAATTTGGTCCCATTCA 59.159 33.333 0.00 0.00 0.00 2.57
5615 10549 7.169158 TGAGATTTAATTTGGTCCCATTCAC 57.831 36.000 0.00 0.00 0.00 3.18
5616 10550 6.154363 TGAGATTTAATTTGGTCCCATTCACC 59.846 38.462 0.00 0.00 0.00 4.02
5617 10551 6.263754 AGATTTAATTTGGTCCCATTCACCT 58.736 36.000 0.00 0.00 34.66 4.00
5620 10554 6.755542 TTAATTTGGTCCCATTCACCTTTT 57.244 33.333 0.00 0.00 34.66 2.27
5621 10555 7.857404 TTAATTTGGTCCCATTCACCTTTTA 57.143 32.000 0.00 0.00 34.66 1.52
5622 10556 6.950860 AATTTGGTCCCATTCACCTTTTAT 57.049 33.333 0.00 0.00 34.66 1.40
5623 10557 9.548631 TTAATTTGGTCCCATTCACCTTTTATA 57.451 29.630 0.00 0.00 34.66 0.98
5624 10558 7.660030 ATTTGGTCCCATTCACCTTTTATAG 57.340 36.000 0.00 0.00 34.66 1.31
5625 10559 4.532834 TGGTCCCATTCACCTTTTATAGC 58.467 43.478 0.00 0.00 34.66 2.97
5626 10560 3.889538 GGTCCCATTCACCTTTTATAGCC 59.110 47.826 0.00 0.00 0.00 3.93
5628 10562 5.140454 GTCCCATTCACCTTTTATAGCCAT 58.860 41.667 0.00 0.00 0.00 4.40
5629 10563 5.598417 GTCCCATTCACCTTTTATAGCCATT 59.402 40.000 0.00 0.00 0.00 3.16
5630 10564 5.598005 TCCCATTCACCTTTTATAGCCATTG 59.402 40.000 0.00 0.00 0.00 2.82
5631 10565 5.221501 CCCATTCACCTTTTATAGCCATTGG 60.222 44.000 0.00 0.00 0.00 3.16
5632 10566 5.598005 CCATTCACCTTTTATAGCCATTGGA 59.402 40.000 6.95 0.00 0.00 3.53
5633 10567 6.268387 CCATTCACCTTTTATAGCCATTGGAT 59.732 38.462 6.95 1.78 0.00 3.41
5635 10569 5.765510 TCACCTTTTATAGCCATTGGATGT 58.234 37.500 6.95 0.10 0.00 3.06
5636 10570 5.593909 TCACCTTTTATAGCCATTGGATGTG 59.406 40.000 6.95 2.95 0.00 3.21
5638 10572 6.266103 CACCTTTTATAGCCATTGGATGTGAT 59.734 38.462 6.95 0.00 0.00 3.06
5639 10573 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
5640 10574 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
5641 10575 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
5642 10576 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
5643 10577 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
5644 10578 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
5647 10581 5.005740 GCCATTGGATGTGATGCTATAAGA 58.994 41.667 6.95 0.00 0.00 2.10
5648 10582 5.651139 GCCATTGGATGTGATGCTATAAGAT 59.349 40.000 6.95 0.00 0.00 2.40
5649 10583 6.404403 GCCATTGGATGTGATGCTATAAGATG 60.404 42.308 6.95 0.00 0.00 2.90
5651 10585 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
5652 10586 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
5655 10589 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
5656 10590 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
5658 10592 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
5660 10594 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
5661 10595 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
5664 10598 2.280119 ATGCGTGTGTGCTGACGT 60.280 55.556 0.00 0.00 37.89 4.34
5668 10602 2.203015 GTGTGTGCTGACGTGGGT 60.203 61.111 0.00 0.00 0.00 4.51
5670 10604 1.817520 TGTGTGCTGACGTGGGTTG 60.818 57.895 0.00 0.00 0.00 3.77
5672 10606 0.531090 GTGTGCTGACGTGGGTTGTA 60.531 55.000 0.00 0.00 0.00 2.41
5673 10607 0.394938 TGTGCTGACGTGGGTTGTAT 59.605 50.000 0.00 0.00 0.00 2.29
5674 10608 1.076332 GTGCTGACGTGGGTTGTATC 58.924 55.000 0.00 0.00 0.00 2.24
5676 10610 1.082117 GCTGACGTGGGTTGTATCCG 61.082 60.000 0.00 0.00 0.00 4.18
5677 10611 0.245539 CTGACGTGGGTTGTATCCGT 59.754 55.000 0.00 0.00 0.00 4.69
5678 10612 0.680618 TGACGTGGGTTGTATCCGTT 59.319 50.000 0.00 0.00 0.00 4.44
5680 10614 2.145536 GACGTGGGTTGTATCCGTTTT 58.854 47.619 0.00 0.00 0.00 2.43
5681 10615 2.549329 GACGTGGGTTGTATCCGTTTTT 59.451 45.455 0.00 0.00 0.00 1.94
5685 10619 4.684877 GTGGGTTGTATCCGTTTTTGTTT 58.315 39.130 0.00 0.00 0.00 2.83
5688 10622 5.811100 TGGGTTGTATCCGTTTTTGTTTTTC 59.189 36.000 0.00 0.00 0.00 2.29
5689 10623 5.811100 GGGTTGTATCCGTTTTTGTTTTTCA 59.189 36.000 0.00 0.00 0.00 2.69
5691 10625 6.752815 GGTTGTATCCGTTTTTGTTTTTCAGA 59.247 34.615 0.00 0.00 0.00 3.27
5692 10626 7.436970 GGTTGTATCCGTTTTTGTTTTTCAGAT 59.563 33.333 0.00 0.00 0.00 2.90
5693 10627 9.453325 GTTGTATCCGTTTTTGTTTTTCAGATA 57.547 29.630 0.00 0.00 0.00 1.98
5700 10634 9.243637 CCGTTTTTGTTTTTCAGATAAATGAGA 57.756 29.630 0.00 0.00 0.00 3.27
5712 10646 8.420374 TCAGATAAATGAGACCAAATTACGTC 57.580 34.615 0.00 0.00 0.00 4.34
5724 10658 8.258007 AGACCAAATTACGTCTCATCTAAATGA 58.742 33.333 0.00 0.00 39.63 2.57
5739 10673 7.506261 TCATCTAAATGAGTTCTAGGTACTCCC 59.494 40.741 17.72 2.30 41.02 4.30
5740 10674 7.507616 CATCTAAATGAGTTCTAGGTACTCCCT 59.492 40.741 17.72 7.45 41.02 4.20
5742 10676 8.563502 TCTAAATGAGTTCTAGGTACTCCCTTA 58.436 37.037 17.72 14.31 42.73 2.69
5743 10677 7.663043 AAATGAGTTCTAGGTACTCCCTTAG 57.337 40.000 17.72 0.00 42.73 2.18
5744 10678 6.593759 ATGAGTTCTAGGTACTCCCTTAGA 57.406 41.667 17.72 4.58 42.73 2.10
5745 10679 6.398655 TGAGTTCTAGGTACTCCCTTAGAA 57.601 41.667 17.72 0.00 42.73 2.10
5836 11493 4.154737 AGTGTGCGTATCGTGTACTAAAGA 59.845 41.667 0.00 0.00 0.00 2.52
5842 11499 5.558653 GCGTATCGTGTACTAAAGAGAGGAG 60.559 48.000 0.00 0.00 0.00 3.69
5852 11509 5.265989 ACTAAAGAGAGGAGAGGGTACAAG 58.734 45.833 0.00 0.00 0.00 3.16
5872 11529 6.676558 ACAAGAGACCCATCCATATGAAAAT 58.323 36.000 3.65 0.00 34.84 1.82
5954 11611 0.629596 TCATCCGAGACCCACCTAGT 59.370 55.000 0.00 0.00 0.00 2.57
6059 11718 3.189287 GCATGACTCTTTGAATTGACGGT 59.811 43.478 0.00 0.00 0.00 4.83
6071 11730 1.763546 TTGACGGTGTGGCTCCATCA 61.764 55.000 0.00 0.00 0.00 3.07
6074 11733 0.179004 ACGGTGTGGCTCCATCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
6075 11734 0.523072 CGGTGTGGCTCCATCAAAAG 59.477 55.000 0.00 0.00 0.00 2.27
6076 11735 1.881925 CGGTGTGGCTCCATCAAAAGA 60.882 52.381 0.00 0.00 0.00 2.52
6078 11737 1.541588 GTGTGGCTCCATCAAAAGACC 59.458 52.381 0.00 0.00 0.00 3.85
6079 11738 1.144708 TGTGGCTCCATCAAAAGACCA 59.855 47.619 0.00 0.00 0.00 4.02
6080 11739 1.541588 GTGGCTCCATCAAAAGACCAC 59.458 52.381 0.00 0.00 39.31 4.16
6081 11740 0.804989 GGCTCCATCAAAAGACCACG 59.195 55.000 0.00 0.00 0.00 4.94
6082 11741 0.804989 GCTCCATCAAAAGACCACGG 59.195 55.000 0.00 0.00 0.00 4.94
6083 11742 1.882352 GCTCCATCAAAAGACCACGGT 60.882 52.381 0.00 0.00 0.00 4.83
6084 11743 1.806542 CTCCATCAAAAGACCACGGTG 59.193 52.381 0.00 0.00 0.00 4.94
6086 11745 1.953686 CCATCAAAAGACCACGGTGTT 59.046 47.619 7.45 0.00 32.81 3.32
6087 11746 2.031157 CCATCAAAAGACCACGGTGTTC 60.031 50.000 7.45 2.00 31.02 3.18
6088 11747 1.670791 TCAAAAGACCACGGTGTTCC 58.329 50.000 7.45 0.00 31.02 3.62
6089 11748 0.666374 CAAAAGACCACGGTGTTCCC 59.334 55.000 7.45 0.00 31.02 3.97
6114 11773 2.957402 TTCAAAGCTCCCACATGACT 57.043 45.000 0.00 0.00 0.00 3.41
6118 11777 0.176680 AAGCTCCCACATGACTAGCG 59.823 55.000 0.00 0.00 38.23 4.26
6120 11779 1.517361 CTCCCACATGACTAGCGCA 59.483 57.895 11.47 0.00 0.00 6.09
6142 11801 1.679559 GATTGCCCTGGTGCCATTCC 61.680 60.000 4.97 0.00 0.00 3.01
6143 11802 2.172229 ATTGCCCTGGTGCCATTCCT 62.172 55.000 4.97 0.00 0.00 3.36
6151 11810 1.001641 GTGCCATTCCTGGAGCAGT 60.002 57.895 9.14 0.00 46.37 4.40
6154 11813 1.310933 GCCATTCCTGGAGCAGTGTG 61.311 60.000 0.00 0.00 46.37 3.82
6161 11820 1.475751 CCTGGAGCAGTGTGTCAAACT 60.476 52.381 0.00 0.00 0.00 2.66
6163 11822 1.230324 GGAGCAGTGTGTCAAACTCC 58.770 55.000 0.00 0.00 37.17 3.85
6169 11828 2.017049 AGTGTGTCAAACTCCTTGCAC 58.983 47.619 0.00 0.00 40.00 4.57
6170 11829 1.065551 GTGTGTCAAACTCCTTGCACC 59.934 52.381 0.00 0.00 39.39 5.01
6177 11836 3.357079 CTCCTTGCACCGCACCAC 61.357 66.667 0.00 0.00 38.71 4.16
6179 11838 3.357079 CCTTGCACCGCACCACTC 61.357 66.667 0.00 0.00 38.71 3.51
6198 11857 5.003160 CACTCCACAATGGTATTGTCTTGA 58.997 41.667 4.32 2.32 39.03 3.02
6231 11890 3.942351 TGGATCACCAAGAGCACTG 57.058 52.632 0.00 0.00 43.91 3.66
6236 11895 1.024271 TCACCAAGAGCACTGCAAAC 58.976 50.000 3.30 0.00 0.00 2.93
6238 11897 0.106519 ACCAAGAGCACTGCAAACCT 60.107 50.000 3.30 0.00 0.00 3.50
6246 11905 1.069049 GCACTGCAAACCTTGAACCAT 59.931 47.619 0.00 0.00 0.00 3.55
6253 11912 3.364964 GCAAACCTTGAACCATACTGTCG 60.365 47.826 0.00 0.00 0.00 4.35
6256 11915 3.660865 ACCTTGAACCATACTGTCGTTC 58.339 45.455 7.85 7.85 37.10 3.95
6265 11924 4.992951 ACCATACTGTCGTTCCAAAACTAC 59.007 41.667 0.00 0.00 33.02 2.73
6267 11926 5.467399 CCATACTGTCGTTCCAAAACTACAA 59.533 40.000 0.00 0.00 39.66 2.41
6270 11929 4.331717 ACTGTCGTTCCAAAACTACAACTG 59.668 41.667 0.00 0.00 39.66 3.16
6276 11935 5.273944 GTTCCAAAACTACAACTGAGCAAG 58.726 41.667 0.00 0.00 32.36 4.01
6277 11936 4.776349 TCCAAAACTACAACTGAGCAAGA 58.224 39.130 0.00 0.00 0.00 3.02
6278 11937 5.376625 TCCAAAACTACAACTGAGCAAGAT 58.623 37.500 0.00 0.00 0.00 2.40
6286 11945 2.880268 CAACTGAGCAAGATGTGGTTGA 59.120 45.455 0.00 0.00 38.34 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 433 1.300697 GGTGCGGACTATAAGGGCG 60.301 63.158 7.11 0.00 0.00 6.13
514 519 4.211374 CGGTTCTTTGTTTACTGAGAGGTG 59.789 45.833 0.00 0.00 0.00 4.00
541 772 2.231721 GGCTGGAATATACTCCGGAGAC 59.768 54.545 37.69 18.62 43.68 3.36
575 810 0.959372 CTGTTTGGCTGCTCTGGAGG 60.959 60.000 0.00 0.00 0.00 4.30
657 893 1.831736 GCTGGGAGTAGCTACTTGGAA 59.168 52.381 26.71 12.40 40.52 3.53
664 900 2.231716 TTGTCTGCTGGGAGTAGCTA 57.768 50.000 0.00 0.00 44.01 3.32
715 951 0.687354 GTGTGGAGGGTCACAGTCAT 59.313 55.000 0.00 0.00 46.72 3.06
774 1010 2.351244 CGAGGGCTGCCAGAGTGTA 61.351 63.158 22.05 0.00 0.00 2.90
775 1011 3.699894 CGAGGGCTGCCAGAGTGT 61.700 66.667 22.05 0.00 0.00 3.55
777 1013 2.520536 AAACGAGGGCTGCCAGAGT 61.521 57.895 22.05 13.31 0.00 3.24
779 1015 1.841302 ATCAAACGAGGGCTGCCAGA 61.841 55.000 22.05 6.44 0.00 3.86
781 1017 1.377202 GATCAAACGAGGGCTGCCA 60.377 57.895 22.05 0.00 0.00 4.92
782 1018 2.115291 GGATCAAACGAGGGCTGCC 61.115 63.158 11.05 11.05 0.00 4.85
783 1019 2.464459 CGGATCAAACGAGGGCTGC 61.464 63.158 0.00 0.00 0.00 5.25
786 1022 2.165301 CGACGGATCAAACGAGGGC 61.165 63.158 0.00 0.00 34.93 5.19
1074 1660 4.216902 TCATCACCGTCTTCGAACTTCTTA 59.783 41.667 0.00 0.00 39.71 2.10
1083 1669 1.134530 GCGTCTCATCACCGTCTTCG 61.135 60.000 0.00 0.00 0.00 3.79
1115 1701 2.270527 GAGCAAGGGGAGAGCACC 59.729 66.667 0.00 0.00 38.12 5.01
1121 1707 0.035630 CACAAGAGGAGCAAGGGGAG 60.036 60.000 0.00 0.00 0.00 4.30
1123 1709 1.676967 GCACAAGAGGAGCAAGGGG 60.677 63.158 0.00 0.00 0.00 4.79
1124 1710 0.323178 ATGCACAAGAGGAGCAAGGG 60.323 55.000 0.00 0.00 42.15 3.95
1125 1711 2.408271 TATGCACAAGAGGAGCAAGG 57.592 50.000 0.00 0.00 42.15 3.61
1148 1734 1.512926 TGAGCAAACGAGCTTCTTCC 58.487 50.000 0.00 0.00 46.75 3.46
1207 1793 6.588204 TGTACAGCCCAGATATCGTAAATTT 58.412 36.000 0.00 0.00 0.00 1.82
1310 2225 4.724279 AAAGAGGAAAGGGAGCTTACAA 57.276 40.909 0.00 0.00 0.00 2.41
1382 2526 4.082408 CACTGCATCAACAATTCCATCACT 60.082 41.667 0.00 0.00 0.00 3.41
1426 2570 1.915489 ACCTCATATCTGTGGTTGGCA 59.085 47.619 0.00 0.00 44.84 4.92
1459 2610 4.508405 CCTGGGAAAAGGTAGAATCAACCA 60.508 45.833 0.00 0.00 39.64 3.67
1460 2611 4.017126 CCTGGGAAAAGGTAGAATCAACC 58.983 47.826 0.00 0.00 37.27 3.77
1604 2965 4.573900 ACAGAAGTGCCAATTAGTCTCAG 58.426 43.478 0.00 0.00 0.00 3.35
1641 3004 1.891178 CTGCAAGCACACAATCGATG 58.109 50.000 0.00 0.00 0.00 3.84
1720 3083 0.872388 CTGTAACCACGCCAAGGTTC 59.128 55.000 5.48 0.59 45.98 3.62
1750 3113 2.353030 GCGTTTGGCGTTGTGGAC 60.353 61.111 0.00 0.00 43.66 4.02
1764 3129 4.568359 TGCATTTTGTTTTGTATGTTGCGT 59.432 33.333 0.00 0.00 0.00 5.24
1794 3159 1.236628 GGGCGATCGAGTTAGCTAGA 58.763 55.000 21.57 0.00 0.00 2.43
1832 3210 0.598419 CGCTCTTGCATATCTCGGCA 60.598 55.000 0.00 0.00 39.64 5.69
1978 4172 7.997773 AGAGCATTATTGACAGCATATTGAT 57.002 32.000 0.00 0.00 0.00 2.57
1990 4184 6.680810 CCAACTTTGTGAAGAGCATTATTGA 58.319 36.000 0.00 0.00 36.69 2.57
2002 4196 1.939934 CTGAGACGCCAACTTTGTGAA 59.060 47.619 0.00 0.00 0.00 3.18
2072 4266 2.104253 CGTGTTATTCCGGCCGCTT 61.104 57.895 22.85 8.93 0.00 4.68
2076 4270 1.702491 GCTGTCGTGTTATTCCGGCC 61.702 60.000 0.00 0.00 0.00 6.13
2077 4271 1.017177 TGCTGTCGTGTTATTCCGGC 61.017 55.000 0.00 0.00 0.00 6.13
2085 4279 5.575606 GGCGTTATATATATGCTGTCGTGTT 59.424 40.000 5.44 0.00 0.00 3.32
2103 4462 2.344500 CCGGGACACTTGGCGTTA 59.656 61.111 0.00 0.00 0.00 3.18
2236 4685 7.387948 ACTTGCTATTAGTGTTTGTTAGTGAGG 59.612 37.037 0.00 0.00 0.00 3.86
2263 4712 0.877071 CTTGACTCCACCATGTGCAC 59.123 55.000 10.75 10.75 31.34 4.57
2282 4731 7.934457 ACATTTATGTAGACCATTTCAGCATC 58.066 34.615 0.00 0.00 39.68 3.91
2478 4938 6.018425 TGCGTAAACAAACAAGTTAACCGATA 60.018 34.615 0.88 0.00 0.00 2.92
2596 5056 0.814010 CCCCGTATCTTTGAAGGCCG 60.814 60.000 0.00 0.00 0.00 6.13
2602 5062 1.219664 CCGCACCCCGTATCTTTGA 59.780 57.895 0.00 0.00 34.38 2.69
2650 5110 3.853330 CACGCCGCCATGACGAAG 61.853 66.667 1.83 0.00 34.06 3.79
3249 5944 7.435488 CACACATATGTTTAGTAGGCAGACTAC 59.565 40.741 5.37 5.11 44.08 2.73
3250 5945 7.123697 ACACACATATGTTTAGTAGGCAGACTA 59.876 37.037 5.37 0.00 36.72 2.59
3251 5946 6.070767 ACACACATATGTTTAGTAGGCAGACT 60.071 38.462 5.37 0.00 36.72 3.24
3252 5947 6.036083 CACACACATATGTTTAGTAGGCAGAC 59.964 42.308 5.37 0.00 36.72 3.51
3279 5998 0.106819 ACCTGCAAGCATCCTGATCC 60.107 55.000 0.00 0.00 0.00 3.36
3375 6094 1.079057 GTTCTCCCCGAAGCAGACC 60.079 63.158 0.00 0.00 30.85 3.85
3468 6187 6.726258 TGAACTAACTAGTCGATCGTGTTA 57.274 37.500 15.94 16.81 34.99 2.41
3476 6195 8.570488 TGTTGATACTTTGAACTAACTAGTCGA 58.430 33.333 0.00 0.00 34.99 4.20
3477 6196 8.636843 GTGTTGATACTTTGAACTAACTAGTCG 58.363 37.037 0.00 0.00 34.99 4.18
3478 6197 9.472361 TGTGTTGATACTTTGAACTAACTAGTC 57.528 33.333 0.00 0.00 34.99 2.59
3479 6198 9.826574 TTGTGTTGATACTTTGAACTAACTAGT 57.173 29.630 0.00 0.00 38.39 2.57
3528 6252 3.869832 TGCATCCAACAACACAAAACATG 59.130 39.130 0.00 0.00 0.00 3.21
3566 6290 4.625742 CCGTACACGATTGAACTTGATCTT 59.374 41.667 2.76 0.00 43.02 2.40
3572 6296 1.345415 ACCCCGTACACGATTGAACTT 59.655 47.619 2.76 0.00 43.02 2.66
3575 6299 0.037139 CCACCCCGTACACGATTGAA 60.037 55.000 2.76 0.00 43.02 2.69
3578 6302 2.266689 GCCACCCCGTACACGATT 59.733 61.111 2.76 0.00 43.02 3.34
3794 6562 8.812147 ATATTTAAGAGTGCGATCGAATTACA 57.188 30.769 21.57 3.44 0.00 2.41
4006 6781 0.968393 AGAGAGAAGGTGAGGTCGCC 60.968 60.000 0.95 0.95 46.57 5.54
4069 6846 4.435436 CTAGTGCAGCCGCCGTCA 62.435 66.667 0.00 0.00 37.32 4.35
4152 6936 5.539048 GTGCGAAATATAGTAGTGGATGGT 58.461 41.667 0.00 0.00 0.00 3.55
4243 7032 4.036144 GGGCATAGAAGTTTTCAGATGCTC 59.964 45.833 19.27 15.31 44.30 4.26
4513 7315 2.275318 GCATGAAGGAGCACACTCTAC 58.725 52.381 0.00 0.00 42.98 2.59
4515 7317 0.689055 TGCATGAAGGAGCACACTCT 59.311 50.000 0.00 0.00 42.98 3.24
4516 7318 1.400846 CATGCATGAAGGAGCACACTC 59.599 52.381 22.59 0.00 44.49 3.51
4518 7320 1.456296 TCATGCATGAAGGAGCACAC 58.544 50.000 26.87 0.00 44.49 3.82
4519 7321 2.294979 GATCATGCATGAAGGAGCACA 58.705 47.619 31.79 7.44 44.49 4.57
4520 7322 2.294979 TGATCATGCATGAAGGAGCAC 58.705 47.619 31.79 16.64 44.49 4.40
4521 7323 2.721425 TGATCATGCATGAAGGAGCA 57.279 45.000 31.79 20.47 45.92 4.26
4551 7353 0.967662 TGTGTGGGGATGCACAATTG 59.032 50.000 3.24 3.24 32.70 2.32
4630 7435 1.064463 AGAACATGGCATGTAGGGTGG 60.064 52.381 31.58 4.56 44.07 4.61
4734 7542 5.238868 TCGTCCAGATGCTTGATAGTAGTAC 59.761 44.000 0.00 0.00 0.00 2.73
4736 7544 4.036971 GTCGTCCAGATGCTTGATAGTAGT 59.963 45.833 0.00 0.00 0.00 2.73
4737 7545 4.541779 GTCGTCCAGATGCTTGATAGTAG 58.458 47.826 0.00 0.00 0.00 2.57
4774 7586 7.847166 TCGACGTTGTACTAGCATTATAATG 57.153 36.000 19.29 19.29 39.40 1.90
4887 7707 3.499929 TACATAGCTCCGCCGCTGC 62.500 63.158 6.90 0.00 41.12 5.25
4888 7708 1.372251 CTACATAGCTCCGCCGCTG 60.372 63.158 6.90 0.00 41.12 5.18
4890 7710 2.049063 CCTACATAGCTCCGCCGC 60.049 66.667 0.00 0.00 0.00 6.53
4892 7712 3.460995 AGCCTACATAGCTCCGCC 58.539 61.111 0.00 0.00 34.91 6.13
4899 7843 2.050269 CCCCCGTGAGCCTACATAG 58.950 63.158 0.00 0.00 0.00 2.23
4926 7870 0.759346 CGATAAACAGGAGGAGGGGG 59.241 60.000 0.00 0.00 0.00 5.40
4927 7871 0.106894 GCGATAAACAGGAGGAGGGG 59.893 60.000 0.00 0.00 0.00 4.79
4928 7872 0.830648 TGCGATAAACAGGAGGAGGG 59.169 55.000 0.00 0.00 0.00 4.30
4929 7873 2.691409 TTGCGATAAACAGGAGGAGG 57.309 50.000 0.00 0.00 0.00 4.30
4930 7874 6.677781 TTAATTTGCGATAAACAGGAGGAG 57.322 37.500 0.00 0.00 0.00 3.69
4931 7875 7.479980 CATTTAATTTGCGATAAACAGGAGGA 58.520 34.615 0.00 0.00 0.00 3.71
4932 7876 6.198966 GCATTTAATTTGCGATAAACAGGAGG 59.801 38.462 0.00 0.00 0.00 4.30
4933 7877 6.974622 AGCATTTAATTTGCGATAAACAGGAG 59.025 34.615 5.54 0.00 44.82 3.69
4934 7878 6.862209 AGCATTTAATTTGCGATAAACAGGA 58.138 32.000 5.54 0.00 44.82 3.86
4935 7879 6.075415 CGAGCATTTAATTTGCGATAAACAGG 60.075 38.462 5.54 0.00 44.82 4.00
5108 8331 2.202932 ACGATCATCAGCGGGCAC 60.203 61.111 0.00 0.00 0.00 5.01
5121 8344 1.065701 GACAGCGATGAGGTACACGAT 59.934 52.381 8.12 0.00 0.00 3.73
5126 8349 0.733729 AGACGACAGCGATGAGGTAC 59.266 55.000 8.12 0.00 41.64 3.34
5133 8356 0.733729 GTGAGGTAGACGACAGCGAT 59.266 55.000 0.00 0.00 41.64 4.58
5138 8361 2.160205 CTGAAGGTGAGGTAGACGACA 58.840 52.381 0.00 0.00 0.00 4.35
5349 8578 0.317160 ATGTTCACAAGACGAGGCGA 59.683 50.000 0.00 0.00 0.00 5.54
5350 8579 0.439985 CATGTTCACAAGACGAGGCG 59.560 55.000 0.00 0.00 0.00 5.52
5351 8580 1.512926 ACATGTTCACAAGACGAGGC 58.487 50.000 0.00 0.00 0.00 4.70
5352 8581 6.042777 ACATATACATGTTCACAAGACGAGG 58.957 40.000 2.30 0.00 42.98 4.63
5353 8582 6.751888 TGACATATACATGTTCACAAGACGAG 59.248 38.462 2.30 0.00 45.58 4.18
5453 8682 9.265901 AGAAACTCTGATAAAATGATGATACGG 57.734 33.333 0.00 0.00 0.00 4.02
5508 8901 0.941542 TACGCAGTTGGTTGAACAGC 59.058 50.000 0.00 0.00 37.78 4.40
5524 8917 6.072728 TGGGTGATGTCAAGATTTTCTTTACG 60.073 38.462 0.00 0.00 34.29 3.18
5565 10499 8.677148 TCTAAATGAGTTCTAGCAAAACTGTT 57.323 30.769 0.32 0.00 37.10 3.16
5566 10500 8.725148 CATCTAAATGAGTTCTAGCAAAACTGT 58.275 33.333 0.32 0.00 37.10 3.55
5567 10501 8.939929 TCATCTAAATGAGTTCTAGCAAAACTG 58.060 33.333 0.32 0.00 36.98 3.16
5583 10517 9.971922 GGGACCAAATTAAATCTCATCTAAATG 57.028 33.333 0.00 0.00 0.00 2.32
5585 10519 9.713684 ATGGGACCAAATTAAATCTCATCTAAA 57.286 29.630 0.00 0.00 24.96 1.85
5586 10520 9.713684 AATGGGACCAAATTAAATCTCATCTAA 57.286 29.630 0.00 0.00 30.88 2.10
5587 10521 9.354673 GAATGGGACCAAATTAAATCTCATCTA 57.645 33.333 0.00 0.00 30.88 1.98
5590 10524 7.147672 GGTGAATGGGACCAAATTAAATCTCAT 60.148 37.037 0.00 0.00 33.60 2.90
5592 10526 6.381133 AGGTGAATGGGACCAAATTAAATCTC 59.619 38.462 0.00 0.00 35.76 2.75
5593 10527 6.263754 AGGTGAATGGGACCAAATTAAATCT 58.736 36.000 0.00 0.00 35.76 2.40
5594 10528 6.544928 AGGTGAATGGGACCAAATTAAATC 57.455 37.500 0.00 0.00 35.76 2.17
5595 10529 6.950860 AAGGTGAATGGGACCAAATTAAAT 57.049 33.333 0.00 0.00 35.76 1.40
5598 10532 9.196139 CTATAAAAGGTGAATGGGACCAAATTA 57.804 33.333 0.00 0.00 35.76 1.40
5599 10533 6.950860 ATAAAAGGTGAATGGGACCAAATT 57.049 33.333 0.00 0.00 35.76 1.82
5600 10534 6.098266 GCTATAAAAGGTGAATGGGACCAAAT 59.902 38.462 0.00 0.00 35.76 2.32
5601 10535 5.420739 GCTATAAAAGGTGAATGGGACCAAA 59.579 40.000 0.00 0.00 35.76 3.28
5604 10538 3.889538 GGCTATAAAAGGTGAATGGGACC 59.110 47.826 0.00 0.00 0.00 4.46
5605 10539 4.532834 TGGCTATAAAAGGTGAATGGGAC 58.467 43.478 0.00 0.00 0.00 4.46
5607 10541 5.221501 CCAATGGCTATAAAAGGTGAATGGG 60.222 44.000 0.00 0.00 0.00 4.00
5609 10543 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
5611 10545 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
5613 10547 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
5614 10548 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
5615 10549 6.684686 CATCACATCCAATGGCTATAAAAGG 58.315 40.000 0.00 0.00 33.60 3.11
5616 10550 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
5617 10551 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
5620 10554 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
5621 10555 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
5622 10556 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
5623 10557 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
5624 10558 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40
5625 10559 6.404403 GCATCTTATAGCATCACATCCAATGG 60.404 42.308 0.00 0.00 33.60 3.16
5626 10560 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
5628 10562 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
5629 10563 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
5630 10564 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
5631 10565 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
5632 10566 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
5633 10567 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
5635 10569 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
5636 10570 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
5638 10572 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
5639 10573 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
5640 10574 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
5641 10575 3.186909 GTCAGCACACACGCATCTTATA 58.813 45.455 0.00 0.00 0.00 0.98
5642 10576 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
5643 10577 1.428448 GTCAGCACACACGCATCTTA 58.572 50.000 0.00 0.00 0.00 2.10
5644 10578 1.560004 CGTCAGCACACACGCATCTT 61.560 55.000 0.00 0.00 0.00 2.40
5647 10581 2.280119 ACGTCAGCACACACGCAT 60.280 55.556 0.00 0.00 39.73 4.73
5648 10582 3.261216 CACGTCAGCACACACGCA 61.261 61.111 0.00 0.00 39.73 5.24
5649 10583 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
5651 10585 1.817941 AACCCACGTCAGCACACAC 60.818 57.895 0.00 0.00 0.00 3.82
5652 10586 1.817520 CAACCCACGTCAGCACACA 60.818 57.895 0.00 0.00 0.00 3.72
5655 10589 1.076332 GATACAACCCACGTCAGCAC 58.924 55.000 0.00 0.00 0.00 4.40
5656 10590 0.036765 GGATACAACCCACGTCAGCA 60.037 55.000 0.00 0.00 0.00 4.41
5658 10592 0.245539 ACGGATACAACCCACGTCAG 59.754 55.000 0.00 0.00 31.39 3.51
5660 10594 1.799544 AAACGGATACAACCCACGTC 58.200 50.000 0.00 0.00 36.69 4.34
5661 10595 2.259266 AAAACGGATACAACCCACGT 57.741 45.000 0.00 0.00 39.74 4.49
5664 10598 5.340439 AAAACAAAAACGGATACAACCCA 57.660 34.783 0.00 0.00 0.00 4.51
5672 10606 9.757227 TCATTTATCTGAAAAACAAAAACGGAT 57.243 25.926 0.00 0.00 0.00 4.18
5673 10607 9.243637 CTCATTTATCTGAAAAACAAAAACGGA 57.756 29.630 0.00 0.00 0.00 4.69
5674 10608 9.243637 TCTCATTTATCTGAAAAACAAAAACGG 57.756 29.630 0.00 0.00 0.00 4.44
5685 10619 9.226606 ACGTAATTTGGTCTCATTTATCTGAAA 57.773 29.630 0.00 0.00 0.00 2.69
5688 10622 8.425577 AGACGTAATTTGGTCTCATTTATCTG 57.574 34.615 5.52 0.00 39.18 2.90
5714 10648 7.662897 GGGAGTACCTAGAACTCATTTAGATG 58.337 42.308 20.28 0.00 44.25 2.90
5764 11421 1.961394 TGTGACTTGCGTCCTTAGTCT 59.039 47.619 0.00 0.00 39.18 3.24
5786 11443 9.605955 CGTGCATATTCCAAAAATCGATTAATA 57.394 29.630 11.83 11.31 0.00 0.98
5789 11446 7.011950 ACTCGTGCATATTCCAAAAATCGATTA 59.988 33.333 11.83 0.00 0.00 1.75
5794 11451 5.512788 CACACTCGTGCATATTCCAAAAATC 59.487 40.000 0.00 0.00 36.06 2.17
5836 11493 2.024751 GGTCTCTTGTACCCTCTCCTCT 60.025 54.545 0.00 0.00 0.00 3.69
5852 11509 8.463930 TTGTAATTTTCATATGGATGGGTCTC 57.536 34.615 2.13 0.00 33.49 3.36
6059 11718 1.144708 TGGTCTTTTGATGGAGCCACA 59.855 47.619 0.00 0.00 0.00 4.17
6071 11730 3.105187 GGGAACACCGTGGTCTTTT 57.895 52.632 16.09 0.00 33.75 2.27
6081 11740 0.741915 TTTGAAAGCACGGGAACACC 59.258 50.000 0.00 0.00 0.00 4.16
6082 11741 2.119671 CTTTGAAAGCACGGGAACAC 57.880 50.000 0.00 0.00 0.00 3.32
6096 11755 2.355108 GCTAGTCATGTGGGAGCTTTGA 60.355 50.000 0.00 0.00 0.00 2.69
6120 11779 4.039042 GGCACCAGGGCAATCATT 57.961 55.556 0.00 0.00 42.77 2.57
6128 11787 2.043652 CCAGGAATGGCACCAGGG 60.044 66.667 0.00 0.00 31.66 4.45
6129 11788 1.077212 CTCCAGGAATGGCACCAGG 60.077 63.158 0.00 0.00 35.75 4.45
6130 11789 1.751927 GCTCCAGGAATGGCACCAG 60.752 63.158 0.00 0.00 0.00 4.00
6131 11790 2.356278 GCTCCAGGAATGGCACCA 59.644 61.111 0.00 0.00 0.00 4.17
6132 11791 1.751927 CTGCTCCAGGAATGGCACC 60.752 63.158 0.00 0.00 0.00 5.01
6133 11792 1.001641 ACTGCTCCAGGAATGGCAC 60.002 57.895 0.00 0.00 35.51 5.01
6134 11793 1.001764 CACTGCTCCAGGAATGGCA 60.002 57.895 2.05 2.05 35.51 4.92
6135 11794 1.001641 ACACTGCTCCAGGAATGGC 60.002 57.895 0.00 0.00 35.51 4.40
6142 11801 1.869767 GAGTTTGACACACTGCTCCAG 59.130 52.381 0.00 0.00 37.52 3.86
6143 11802 1.475034 GGAGTTTGACACACTGCTCCA 60.475 52.381 6.05 0.00 41.39 3.86
6151 11810 1.388547 GGTGCAAGGAGTTTGACACA 58.611 50.000 0.00 0.00 41.47 3.72
6154 11813 1.282875 GCGGTGCAAGGAGTTTGAC 59.717 57.895 0.00 0.00 39.21 3.18
6161 11820 3.825160 GAGTGGTGCGGTGCAAGGA 62.825 63.158 0.00 0.00 41.47 3.36
6163 11822 3.357079 GGAGTGGTGCGGTGCAAG 61.357 66.667 0.00 0.00 41.47 4.01
6169 11828 2.334946 CCATTGTGGAGTGGTGCGG 61.335 63.158 0.00 0.00 40.96 5.69
6170 11829 1.600636 ACCATTGTGGAGTGGTGCG 60.601 57.895 2.45 0.00 46.55 5.34
6177 11836 4.095483 GCTCAAGACAATACCATTGTGGAG 59.905 45.833 9.16 12.51 40.96 3.86
6179 11838 4.012374 AGCTCAAGACAATACCATTGTGG 58.988 43.478 9.16 0.00 45.02 4.17
6213 11872 0.321919 GCAGTGCTCTTGGTGATCCA 60.322 55.000 8.18 0.00 42.66 3.41
6231 11890 3.364964 CGACAGTATGGTTCAAGGTTTGC 60.365 47.826 0.00 0.00 43.62 3.68
6236 11895 3.000727 GGAACGACAGTATGGTTCAAGG 58.999 50.000 11.61 0.00 43.62 3.61
6238 11897 3.755112 TGGAACGACAGTATGGTTCAA 57.245 42.857 11.61 0.98 43.62 2.69
6246 11905 5.521010 CAGTTGTAGTTTTGGAACGACAGTA 59.479 40.000 5.61 0.00 46.92 2.74
6253 11912 4.893424 TGCTCAGTTGTAGTTTTGGAAC 57.107 40.909 0.00 0.00 35.97 3.62
6256 11915 5.009010 ACATCTTGCTCAGTTGTAGTTTTGG 59.991 40.000 0.00 0.00 34.21 3.28
6265 11924 2.880268 TCAACCACATCTTGCTCAGTTG 59.120 45.455 0.00 0.00 35.58 3.16
6267 11926 2.936919 TCAACCACATCTTGCTCAGT 57.063 45.000 0.00 0.00 0.00 3.41
6270 11929 2.349886 GACGATCAACCACATCTTGCTC 59.650 50.000 0.00 0.00 0.00 4.26
6276 11935 3.849911 TGAAGAGACGATCAACCACATC 58.150 45.455 0.00 0.00 0.00 3.06
6277 11936 3.961480 TGAAGAGACGATCAACCACAT 57.039 42.857 0.00 0.00 0.00 3.21
6278 11937 3.069586 ACTTGAAGAGACGATCAACCACA 59.930 43.478 0.00 0.00 32.46 4.17


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

AutoCloner maintained by Alex Coulton.