Multiple sequence alignment - TraesCS3A01G126400

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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 TraesCS3A01G126400 chr3A 100.000 3906 0 0 1 3906 102099162 102095257 0.000000e+00 7214.0
1 TraesCS3A01G126400 chr3A 85.487 3018 372 45 1 2995 175851151 175854125 0.000000e+00 3086.0
2 TraesCS3A01G126400 chr3A 87.435 1146 129 10 2277 3412 110806301 110807441 0.000000e+00 1304.0
3 TraesCS3A01G126400 chr4A 85.364 3020 376 44 1 2998 70801355 70798380 0.000000e+00 3068.0
4 TraesCS3A01G126400 chr7A 85.293 3019 375 46 1 2995 16984597 16987570 0.000000e+00 3051.0
5 TraesCS3A01G126400 chr7A 85.467 1734 211 30 1278 2998 67826666 67824961 0.000000e+00 1768.0
6 TraesCS3A01G126400 chr7A 85.409 1734 212 29 1278 2998 67836001 67834296 0.000000e+00 1762.0
7 TraesCS3A01G126400 chr1A 85.237 3021 380 44 1 2998 255747509 255744532 0.000000e+00 3048.0
8 TraesCS3A01G126400 chr2B 85.264 2158 253 43 1249 3385 495219805 495221918 0.000000e+00 2163.0
9 TraesCS3A01G126400 chr2B 91.025 1181 101 5 1 1179 495218605 495219782 0.000000e+00 1589.0
10 TraesCS3A01G126400 chr3B 85.437 1703 212 22 1305 2998 783210763 783212438 0.000000e+00 1738.0
11 TraesCS3A01G126400 chr3B 86.275 1224 138 24 1 1208 783209420 783210629 0.000000e+00 1303.0
12 TraesCS3A01G126400 chr6A 84.473 1726 238 18 1305 3023 135442022 135440320 0.000000e+00 1676.0
13 TraesCS3A01G126400 chr6A 85.633 1225 144 25 1 1208 135443366 135442157 0.000000e+00 1258.0
14 TraesCS3A01G126400 chr5B 90.788 1205 105 6 1 1204 600366185 600367384 0.000000e+00 1605.0
15 TraesCS3A01G126400 chr5B 87.580 1095 107 14 1305 2394 600367441 600368511 0.000000e+00 1242.0
16 TraesCS3A01G126400 chrUn 86.384 896 111 9 2108 2998 352288370 352287481 0.000000e+00 968.0
17 TraesCS3A01G126400 chr4B 92.337 261 16 3 98 358 481577388 481577132 6.170000e-98 368.0
18 TraesCS3A01G126400 chr4B 81.579 76 11 3 429 503 481577053 481576980 4.210000e-05 60.2


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 TraesCS3A01G126400 chr3A 102095257 102099162 3905 True 7214.0 7214 100.0000 1 3906 1 chr3A.!!$R1 3905
1 TraesCS3A01G126400 chr3A 175851151 175854125 2974 False 3086.0 3086 85.4870 1 2995 1 chr3A.!!$F2 2994
2 TraesCS3A01G126400 chr3A 110806301 110807441 1140 False 1304.0 1304 87.4350 2277 3412 1 chr3A.!!$F1 1135
3 TraesCS3A01G126400 chr4A 70798380 70801355 2975 True 3068.0 3068 85.3640 1 2998 1 chr4A.!!$R1 2997
4 TraesCS3A01G126400 chr7A 16984597 16987570 2973 False 3051.0 3051 85.2930 1 2995 1 chr7A.!!$F1 2994
5 TraesCS3A01G126400 chr7A 67824961 67826666 1705 True 1768.0 1768 85.4670 1278 2998 1 chr7A.!!$R1 1720
6 TraesCS3A01G126400 chr7A 67834296 67836001 1705 True 1762.0 1762 85.4090 1278 2998 1 chr7A.!!$R2 1720
7 TraesCS3A01G126400 chr1A 255744532 255747509 2977 True 3048.0 3048 85.2370 1 2998 1 chr1A.!!$R1 2997
8 TraesCS3A01G126400 chr2B 495218605 495221918 3313 False 1876.0 2163 88.1445 1 3385 2 chr2B.!!$F1 3384
9 TraesCS3A01G126400 chr3B 783209420 783212438 3018 False 1520.5 1738 85.8560 1 2998 2 chr3B.!!$F1 2997
10 TraesCS3A01G126400 chr6A 135440320 135443366 3046 True 1467.0 1676 85.0530 1 3023 2 chr6A.!!$R1 3022
11 TraesCS3A01G126400 chr5B 600366185 600368511 2326 False 1423.5 1605 89.1840 1 2394 2 chr5B.!!$F1 2393
12 TraesCS3A01G126400 chrUn 352287481 352288370 889 True 968.0 968 86.3840 2108 2998 1 chrUn.!!$R1 890

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
525 535 0.395586 TTGCAAGGCAACACTCAGGT 60.396 50.000 0.0 0.0 43.99 4.00 F
1359 1409 1.004628 TGGCAGAGCTTCCTAATGCAA 59.995 47.619 0.0 0.0 36.23 4.08 F
1763 1813 0.033504 GGGAGAGTTGTGACGCAGAA 59.966 55.000 0.0 0.0 0.00 3.02 F
2836 2895 0.400213 TGATGGGTGTTGTCCAGTCC 59.600 55.000 0.0 0.0 37.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1795 1.423395 CTTCTGCGTCACAACTCTCC 58.577 55.00 0.0 0.0 0.00 3.71 R
2872 2931 1.024271 GCTGCGGGCAATCTTTGATA 58.976 50.00 0.0 0.0 41.35 2.15 R
2884 2943 2.622064 AAGGTAAATAGAGCTGCGGG 57.378 50.00 0.0 0.0 0.00 6.13 R
3703 3773 5.086104 AGCAGAATGTATACGAAACCAGT 57.914 39.13 0.0 0.0 39.31 4.00 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
28 29 7.776107 AGAGTCAGATTCGAATGAAAGATACA 58.224 34.615 16.96 0.00 37.71 2.29
30 31 8.362860 AGTCAGATTCGAATGAAAGATACATG 57.637 34.615 16.96 0.00 37.71 3.21
39 41 7.921214 TCGAATGAAAGATACATGGAGTAAGAC 59.079 37.037 0.00 0.00 36.05 3.01
113 115 7.225538 TGTTCTCAACATGTTTGTTTGTTTTGT 59.774 29.630 8.77 0.00 43.57 2.83
126 128 3.764237 TGTTTTGTACAGAGGAGGACC 57.236 47.619 0.00 0.00 31.68 4.46
277 279 2.414161 GGTGCTTGGTTTCAGTATTCGC 60.414 50.000 0.00 0.00 0.00 4.70
341 343 2.037901 TGCAGGAATTCACTTGCCAAA 58.962 42.857 19.61 5.33 41.15 3.28
361 363 7.651704 TGCCAAAGAGCAGTAAGTAAATTTTTC 59.348 33.333 0.00 0.00 38.00 2.29
367 369 9.516314 AGAGCAGTAAGTAAATTTTTCACAAAC 57.484 29.630 0.00 0.00 0.00 2.93
370 372 8.325282 GCAGTAAGTAAATTTTTCACAAACCAC 58.675 33.333 0.00 0.00 0.00 4.16
376 378 8.478877 AGTAAATTTTTCACAAACCACCATGTA 58.521 29.630 0.00 0.00 0.00 2.29
388 390 9.555727 ACAAACCACCATGTAGTAATATCATAC 57.444 33.333 0.00 0.00 0.00 2.39
427 437 9.586435 TCAATGTACAATGTCTTAGTATGTCTG 57.414 33.333 10.64 0.00 0.00 3.51
448 458 8.442632 GTCTGATGACATTGAATCTTATTCCA 57.557 34.615 0.00 0.00 42.48 3.53
450 460 7.225341 TCTGATGACATTGAATCTTATTCCACG 59.775 37.037 0.00 0.00 0.00 4.94
466 476 3.541632 TCCACGATTATCTTTTCAGGGC 58.458 45.455 0.00 0.00 0.00 5.19
471 481 4.878397 ACGATTATCTTTTCAGGGCTTCAG 59.122 41.667 0.00 0.00 0.00 3.02
525 535 0.395586 TTGCAAGGCAACACTCAGGT 60.396 50.000 0.00 0.00 43.99 4.00
533 543 3.003480 GGCAACACTCAGGTTACATCTC 58.997 50.000 0.00 0.00 0.00 2.75
546 556 9.076781 TCAGGTTACATCTCAATGAAAATTCAA 57.923 29.630 0.00 0.00 41.13 2.69
581 591 2.686405 AGTTTTTCGGGAGGAACACAAC 59.314 45.455 0.00 0.00 33.42 3.32
722 733 7.893833 AGGGTTAATTCTATAGTTGCTGGTTTT 59.106 33.333 0.00 0.00 0.00 2.43
812 823 2.029739 TGAAACGCTTCAGGACGACATA 60.030 45.455 0.00 0.00 36.62 2.29
824 835 5.416639 TCAGGACGACATAGCTAAAACACTA 59.583 40.000 0.00 0.00 0.00 2.74
893 904 2.291089 TGCACAGGTGGATGATGACAAT 60.291 45.455 1.10 0.00 0.00 2.71
975 986 5.438761 AGAGTGCAATAACTTTTGACACC 57.561 39.130 0.00 0.00 35.81 4.16
1062 1073 4.270834 AGAGTGTAATCTTCGCTGGAGTA 58.729 43.478 0.00 0.00 0.00 2.59
1131 1142 2.142356 TTGTTGCTATGATGGGTGGG 57.858 50.000 0.00 0.00 0.00 4.61
1199 1211 2.927477 CGGTTATCGCTTGCTCTTTACA 59.073 45.455 0.00 0.00 0.00 2.41
1208 1220 4.790140 CGCTTGCTCTTTACATCATGTTTC 59.210 41.667 0.00 0.00 0.00 2.78
1209 1221 5.391310 CGCTTGCTCTTTACATCATGTTTCT 60.391 40.000 0.00 0.00 0.00 2.52
1213 1225 6.902341 TGCTCTTTACATCATGTTTCTTGTC 58.098 36.000 0.00 0.00 0.00 3.18
1229 1241 9.337396 TGTTTCTTGTCTTAGTAACATCACAAT 57.663 29.630 0.00 0.00 32.64 2.71
1319 1369 5.416952 ACAATTTTGTTCAGATCAGGCTAGG 59.583 40.000 0.00 0.00 38.47 3.02
1342 1392 2.546778 CATTGGAAATGCAGTCATGGC 58.453 47.619 0.00 0.00 32.23 4.40
1359 1409 1.004628 TGGCAGAGCTTCCTAATGCAA 59.995 47.619 0.00 0.00 36.23 4.08
1360 1410 1.403323 GGCAGAGCTTCCTAATGCAAC 59.597 52.381 0.00 0.00 36.23 4.17
1414 1464 2.508526 GGCTCATGAACTTCTTGGTGT 58.491 47.619 0.00 0.00 0.00 4.16
1424 1474 5.941058 TGAACTTCTTGGTGTTGTTTACAGA 59.059 36.000 0.00 0.00 37.45 3.41
1427 1477 7.404671 ACTTCTTGGTGTTGTTTACAGAAAT 57.595 32.000 0.00 0.00 37.45 2.17
1436 1486 7.201487 GGTGTTGTTTACAGAAATCACAAAACC 60.201 37.037 6.88 6.88 37.45 3.27
1442 1492 5.343307 ACAGAAATCACAAAACCTTTGCT 57.657 34.783 0.00 0.00 0.00 3.91
1478 1528 9.045223 CATAAGCTAGTAAATCACATGCTAACA 57.955 33.333 0.00 0.00 37.10 2.41
1482 1532 9.046296 AGCTAGTAAATCACATGCTAACAATAC 57.954 33.333 0.00 0.00 36.59 1.89
1556 1606 2.799412 GCATCCTTTCATGACTAGAGCG 59.201 50.000 0.00 0.00 0.00 5.03
1623 1673 4.882842 TTCTGTGCTAGAATGTGTACCA 57.117 40.909 0.00 0.00 40.43 3.25
1624 1674 4.188247 TCTGTGCTAGAATGTGTACCAC 57.812 45.455 0.00 0.00 30.84 4.16
1625 1675 3.832490 TCTGTGCTAGAATGTGTACCACT 59.168 43.478 0.00 0.00 31.70 4.00
1626 1676 4.082190 TCTGTGCTAGAATGTGTACCACTC 60.082 45.833 0.00 0.00 31.70 3.51
1627 1677 3.576550 TGTGCTAGAATGTGTACCACTCA 59.423 43.478 0.00 0.00 35.11 3.41
1628 1678 4.039852 TGTGCTAGAATGTGTACCACTCAA 59.960 41.667 0.00 0.00 35.11 3.02
1629 1679 4.389077 GTGCTAGAATGTGTACCACTCAAC 59.611 45.833 0.00 0.00 35.11 3.18
1630 1680 3.612860 GCTAGAATGTGTACCACTCAACG 59.387 47.826 0.00 0.00 35.11 4.10
1631 1681 3.746045 AGAATGTGTACCACTCAACGT 57.254 42.857 0.00 0.00 35.11 3.99
1665 1715 3.623510 TCAACGTAGTGAATGTGCAAACA 59.376 39.130 0.00 0.00 45.00 2.83
1667 1717 4.145876 ACGTAGTGAATGTGCAAACATG 57.854 40.909 0.00 0.00 42.51 3.21
1730 1780 7.971183 TGCATTCATTACACAGTACACTAAA 57.029 32.000 0.00 0.00 0.00 1.85
1745 1795 5.171147 ACACTAAACTGATAGACGATCGG 57.829 43.478 20.98 1.61 45.36 4.18
1763 1813 0.033504 GGGAGAGTTGTGACGCAGAA 59.966 55.000 0.00 0.00 0.00 3.02
1787 1837 4.142160 GCTGAAAGGAAGAACAAACAGGTT 60.142 41.667 0.00 0.00 0.00 3.50
1788 1838 5.576447 TGAAAGGAAGAACAAACAGGTTC 57.424 39.130 0.00 0.00 45.87 3.62
1804 1855 8.716909 CAAACAGGTTCAAAATGTTTAACAGTT 58.283 29.630 4.89 4.89 43.37 3.16
1953 2007 7.721286 AAGCATGCTTCTGTTATCTATACAC 57.279 36.000 27.21 0.00 0.00 2.90
2194 2248 3.514309 GTCCTAGCGGTATGATACCCATT 59.486 47.826 15.62 4.53 46.27 3.16
2197 2251 5.421056 TCCTAGCGGTATGATACCCATTAAG 59.579 44.000 15.62 6.60 46.27 1.85
2352 2408 4.808364 GCAAGCTAGGTCATCTACTTTCAG 59.192 45.833 0.00 0.00 0.00 3.02
2356 2412 4.568760 GCTAGGTCATCTACTTTCAGCAAC 59.431 45.833 0.00 0.00 0.00 4.17
2428 2484 3.181520 GGCACCAGCTATTATATTTCGCG 60.182 47.826 0.00 0.00 41.70 5.87
2435 2491 6.183360 CCAGCTATTATATTTCGCGGCAATAA 60.183 38.462 6.13 6.43 0.00 1.40
2500 2556 7.326063 GCAATTGCAAAGTCTAATTTTACTCGT 59.674 33.333 25.36 0.00 41.59 4.18
2569 2625 4.019051 TGCCAGGTAGGATATGGATCAATG 60.019 45.833 0.00 0.00 41.22 2.82
2624 2680 4.724399 TCAACTGGAAGGCAATGAAGTTA 58.276 39.130 0.00 0.00 39.30 2.24
2836 2895 0.400213 TGATGGGTGTTGTCCAGTCC 59.600 55.000 0.00 0.00 37.75 3.85
2872 2931 0.944311 GTCGATCGCCAACACACACT 60.944 55.000 11.09 0.00 0.00 3.55
2884 2943 5.156355 CCAACACACACTATCAAAGATTGC 58.844 41.667 0.00 0.00 0.00 3.56
2887 2946 3.009723 ACACACTATCAAAGATTGCCCG 58.990 45.455 0.00 0.00 0.00 6.13
2893 2952 1.138247 CAAAGATTGCCCGCAGCTC 59.862 57.895 0.00 0.00 44.23 4.09
2920 2979 8.601845 ATTTACCTTAATGTTCTTTGTTTGCC 57.398 30.769 0.00 0.00 0.00 4.52
2930 2989 4.846779 TCTTTGTTTGCCTTATGTGGTC 57.153 40.909 0.00 0.00 0.00 4.02
2940 2999 6.068461 TGCCTTATGTGGTCCAAAGTATTA 57.932 37.500 0.00 0.00 0.00 0.98
3013 3072 7.328493 TGAACTAAGTTATGTCGTCTGAATGTG 59.672 37.037 0.00 0.00 0.00 3.21
3071 3130 9.958180 TTCTTAATTTGACTTGGATGACTATCA 57.042 29.630 0.00 0.00 34.90 2.15
3072 3131 9.383519 TCTTAATTTGACTTGGATGACTATCAC 57.616 33.333 0.00 0.00 34.90 3.06
3073 3132 6.668541 AATTTGACTTGGATGACTATCACG 57.331 37.500 0.00 0.00 34.90 4.35
3083 3146 8.593492 TTGGATGACTATCACGATTGATTAAG 57.407 34.615 0.00 0.00 39.66 1.85
3093 3156 7.864108 TCACGATTGATTAAGATTTGATGGT 57.136 32.000 0.00 0.00 0.00 3.55
3260 3329 4.322198 GGTACCCGTGTTAGAAAGATGTGA 60.322 45.833 0.00 0.00 0.00 3.58
3282 3351 7.601856 GTGAATCCACATTTTCACCATTTAGA 58.398 34.615 4.81 0.00 43.72 2.10
3283 3352 7.542130 GTGAATCCACATTTTCACCATTTAGAC 59.458 37.037 4.81 0.00 43.72 2.59
3284 3353 5.621197 TCCACATTTTCACCATTTAGACG 57.379 39.130 0.00 0.00 0.00 4.18
3286 3355 5.533154 TCCACATTTTCACCATTTAGACGTT 59.467 36.000 0.00 0.00 0.00 3.99
3330 3400 3.394674 TCATGCAACGTGTTCCTCTAA 57.605 42.857 0.00 0.00 0.00 2.10
3344 3414 9.968743 CGTGTTCCTCTAATTTGAAATAACTAC 57.031 33.333 0.00 0.00 0.00 2.73
3394 3464 6.701400 ACATCACTTATTCAAAGGTTTTGCAC 59.299 34.615 0.00 0.00 0.00 4.57
3402 3472 6.561737 TTCAAAGGTTTTGCACGATATGTA 57.438 33.333 0.00 0.00 0.00 2.29
3403 3473 6.176975 TCAAAGGTTTTGCACGATATGTAG 57.823 37.500 0.00 0.00 0.00 2.74
3404 3474 4.616181 AAGGTTTTGCACGATATGTAGC 57.384 40.909 0.00 0.00 0.00 3.58
3412 3482 9.155053 GTTTTGCACGATATGTAGCTAATTAAC 57.845 33.333 0.00 0.00 0.00 2.01
3413 3483 8.426881 TTTGCACGATATGTAGCTAATTAACA 57.573 30.769 0.00 0.00 0.00 2.41
3414 3484 8.601845 TTGCACGATATGTAGCTAATTAACAT 57.398 30.769 0.00 0.00 37.58 2.71
3415 3485 9.699703 TTGCACGATATGTAGCTAATTAACATA 57.300 29.630 8.37 8.37 39.64 2.29
3416 3486 9.353999 TGCACGATATGTAGCTAATTAACATAG 57.646 33.333 11.01 3.08 38.94 2.23
3417 3487 9.569167 GCACGATATGTAGCTAATTAACATAGA 57.431 33.333 11.01 0.00 38.94 1.98
3424 3494 9.988815 ATGTAGCTAATTAACATAGAAGGTCAG 57.011 33.333 0.00 0.00 32.21 3.51
3425 3495 8.421784 TGTAGCTAATTAACATAGAAGGTCAGG 58.578 37.037 0.00 0.00 0.00 3.86
3426 3496 7.439108 AGCTAATTAACATAGAAGGTCAGGT 57.561 36.000 0.00 0.00 0.00 4.00
3427 3497 8.548880 AGCTAATTAACATAGAAGGTCAGGTA 57.451 34.615 0.00 0.00 0.00 3.08
3428 3498 9.160412 AGCTAATTAACATAGAAGGTCAGGTAT 57.840 33.333 0.00 0.00 0.00 2.73
3473 3543 9.762933 ACTTAATGCTATTTTGTTGTGATTTGT 57.237 25.926 0.00 0.00 0.00 2.83
3476 3546 8.436046 AATGCTATTTTGTTGTGATTTGTTGT 57.564 26.923 0.00 0.00 0.00 3.32
3477 3547 7.840342 TGCTATTTTGTTGTGATTTGTTGTT 57.160 28.000 0.00 0.00 0.00 2.83
3478 3548 8.261492 TGCTATTTTGTTGTGATTTGTTGTTT 57.739 26.923 0.00 0.00 0.00 2.83
3479 3549 8.173775 TGCTATTTTGTTGTGATTTGTTGTTTG 58.826 29.630 0.00 0.00 0.00 2.93
3480 3550 8.386606 GCTATTTTGTTGTGATTTGTTGTTTGA 58.613 29.630 0.00 0.00 0.00 2.69
3482 3552 8.947304 ATTTTGTTGTGATTTGTTGTTTGAAC 57.053 26.923 0.00 0.00 0.00 3.18
3483 3553 5.753713 TGTTGTGATTTGTTGTTTGAACG 57.246 34.783 0.00 0.00 0.00 3.95
3484 3554 5.461526 TGTTGTGATTTGTTGTTTGAACGA 58.538 33.333 0.00 0.00 0.00 3.85
3485 3555 6.096036 TGTTGTGATTTGTTGTTTGAACGAT 58.904 32.000 0.00 0.00 0.00 3.73
3486 3556 6.587990 TGTTGTGATTTGTTGTTTGAACGATT 59.412 30.769 0.00 0.00 0.00 3.34
3487 3557 7.116948 TGTTGTGATTTGTTGTTTGAACGATTT 59.883 29.630 0.00 0.00 0.00 2.17
3488 3558 6.987223 TGTGATTTGTTGTTTGAACGATTTG 58.013 32.000 0.00 0.00 0.00 2.32
3489 3559 6.587990 TGTGATTTGTTGTTTGAACGATTTGT 59.412 30.769 0.00 0.00 0.00 2.83
3490 3560 7.110511 GTGATTTGTTGTTTGAACGATTTGTC 58.889 34.615 0.00 0.00 0.00 3.18
3491 3561 6.808704 TGATTTGTTGTTTGAACGATTTGTCA 59.191 30.769 0.00 0.00 0.00 3.58
3492 3562 7.490725 TGATTTGTTGTTTGAACGATTTGTCAT 59.509 29.630 0.00 0.00 0.00 3.06
3493 3563 8.864069 ATTTGTTGTTTGAACGATTTGTCATA 57.136 26.923 0.00 0.00 0.00 2.15
3494 3564 8.689251 TTTGTTGTTTGAACGATTTGTCATAA 57.311 26.923 0.00 0.00 0.00 1.90
3495 3565 8.864069 TTGTTGTTTGAACGATTTGTCATAAT 57.136 26.923 0.00 0.00 0.00 1.28
3496 3566 8.864069 TGTTGTTTGAACGATTTGTCATAATT 57.136 26.923 0.00 0.00 0.00 1.40
3497 3567 9.952188 TGTTGTTTGAACGATTTGTCATAATTA 57.048 25.926 0.00 0.00 0.00 1.40
3500 3570 9.619316 TGTTTGAACGATTTGTCATAATTAAGG 57.381 29.630 0.00 0.00 0.00 2.69
3501 3571 9.620660 GTTTGAACGATTTGTCATAATTAAGGT 57.379 29.630 0.00 0.00 0.00 3.50
3503 3573 9.619316 TTGAACGATTTGTCATAATTAAGGTTG 57.381 29.630 0.00 0.00 0.00 3.77
3504 3574 8.788806 TGAACGATTTGTCATAATTAAGGTTGT 58.211 29.630 0.00 0.00 0.00 3.32
3505 3575 9.274065 GAACGATTTGTCATAATTAAGGTTGTC 57.726 33.333 0.00 0.00 0.00 3.18
3506 3576 7.461107 ACGATTTGTCATAATTAAGGTTGTCG 58.539 34.615 0.00 0.00 0.00 4.35
3507 3577 7.118680 ACGATTTGTCATAATTAAGGTTGTCGT 59.881 33.333 0.00 0.00 0.00 4.34
3508 3578 7.425309 CGATTTGTCATAATTAAGGTTGTCGTG 59.575 37.037 0.00 0.00 0.00 4.35
3509 3579 7.731882 TTTGTCATAATTAAGGTTGTCGTGA 57.268 32.000 0.00 0.00 0.00 4.35
3510 3580 7.915293 TTGTCATAATTAAGGTTGTCGTGAT 57.085 32.000 0.00 0.00 0.00 3.06
3511 3581 7.915293 TGTCATAATTAAGGTTGTCGTGATT 57.085 32.000 0.00 0.00 0.00 2.57
3512 3582 9.438228 TTGTCATAATTAAGGTTGTCGTGATTA 57.562 29.630 0.00 0.00 0.00 1.75
3513 3583 8.875803 TGTCATAATTAAGGTTGTCGTGATTAC 58.124 33.333 0.00 0.00 0.00 1.89
3514 3584 8.333186 GTCATAATTAAGGTTGTCGTGATTACC 58.667 37.037 0.00 0.00 0.00 2.85
3515 3585 8.041919 TCATAATTAAGGTTGTCGTGATTACCA 58.958 33.333 0.00 0.00 33.02 3.25
3516 3586 8.670135 CATAATTAAGGTTGTCGTGATTACCAA 58.330 33.333 0.00 0.00 33.02 3.67
3517 3587 7.513371 AATTAAGGTTGTCGTGATTACCAAA 57.487 32.000 0.00 0.00 33.02 3.28
3518 3588 7.696992 ATTAAGGTTGTCGTGATTACCAAAT 57.303 32.000 0.00 0.00 33.02 2.32
3519 3589 7.513371 TTAAGGTTGTCGTGATTACCAAATT 57.487 32.000 0.00 0.00 33.02 1.82
3520 3590 6.399639 AAGGTTGTCGTGATTACCAAATTT 57.600 33.333 0.00 0.00 33.02 1.82
3521 3591 5.768317 AGGTTGTCGTGATTACCAAATTTG 58.232 37.500 11.40 11.40 33.02 2.32
3522 3592 5.300792 AGGTTGTCGTGATTACCAAATTTGT 59.699 36.000 16.73 7.77 33.02 2.83
3523 3593 6.487331 AGGTTGTCGTGATTACCAAATTTGTA 59.513 34.615 16.73 6.86 33.02 2.41
3524 3594 7.013464 AGGTTGTCGTGATTACCAAATTTGTAA 59.987 33.333 16.73 14.22 33.02 2.41
3525 3595 7.325097 GGTTGTCGTGATTACCAAATTTGTAAG 59.675 37.037 16.73 4.57 0.00 2.34
3526 3596 7.499321 TGTCGTGATTACCAAATTTGTAAGT 57.501 32.000 16.73 10.07 0.00 2.24
3527 3597 8.604640 TGTCGTGATTACCAAATTTGTAAGTA 57.395 30.769 16.73 9.13 0.00 2.24
3528 3598 9.221933 TGTCGTGATTACCAAATTTGTAAGTAT 57.778 29.630 16.73 3.39 0.00 2.12
3529 3599 9.485591 GTCGTGATTACCAAATTTGTAAGTATG 57.514 33.333 16.73 12.03 0.00 2.39
3530 3600 8.178964 TCGTGATTACCAAATTTGTAAGTATGC 58.821 33.333 16.73 7.68 0.00 3.14
3531 3601 8.181573 CGTGATTACCAAATTTGTAAGTATGCT 58.818 33.333 16.73 1.66 0.00 3.79
3532 3602 9.503427 GTGATTACCAAATTTGTAAGTATGCTC 57.497 33.333 16.73 9.37 0.00 4.26
3533 3603 9.461312 TGATTACCAAATTTGTAAGTATGCTCT 57.539 29.630 16.73 0.00 0.00 4.09
3536 3606 9.953565 TTACCAAATTTGTAAGTATGCTCTAGT 57.046 29.630 16.73 5.08 0.00 2.57
3537 3607 8.268850 ACCAAATTTGTAAGTATGCTCTAGTG 57.731 34.615 16.73 0.00 0.00 2.74
3538 3608 7.148239 ACCAAATTTGTAAGTATGCTCTAGTGC 60.148 37.037 16.73 9.86 0.00 4.40
3540 3610 7.921786 AATTTGTAAGTATGCTCTAGTGCAA 57.078 32.000 22.16 9.89 46.61 4.08
3541 3611 8.511604 AATTTGTAAGTATGCTCTAGTGCAAT 57.488 30.769 22.16 13.36 46.61 3.56
3542 3612 7.921786 TTTGTAAGTATGCTCTAGTGCAATT 57.078 32.000 22.16 18.00 46.61 2.32
3543 3613 9.613428 ATTTGTAAGTATGCTCTAGTGCAATTA 57.387 29.630 22.16 17.16 46.61 1.40
3544 3614 9.443323 TTTGTAAGTATGCTCTAGTGCAATTAA 57.557 29.630 22.16 6.93 46.61 1.40
3545 3615 9.443323 TTGTAAGTATGCTCTAGTGCAATTAAA 57.557 29.630 22.16 13.65 46.61 1.52
3546 3616 9.613428 TGTAAGTATGCTCTAGTGCAATTAAAT 57.387 29.630 22.16 8.34 46.61 1.40
3604 3674 9.463443 TCATTTGTTATGTCTATCTCATACGTG 57.537 33.333 0.00 0.00 0.00 4.49
3605 3675 9.249457 CATTTGTTATGTCTATCTCATACGTGT 57.751 33.333 0.00 0.00 0.00 4.49
3608 3678 9.726232 TTGTTATGTCTATCTCATACGTGTAAC 57.274 33.333 0.00 0.00 0.00 2.50
3609 3679 9.117183 TGTTATGTCTATCTCATACGTGTAACT 57.883 33.333 0.00 0.00 31.75 2.24
3610 3680 9.596677 GTTATGTCTATCTCATACGTGTAACTC 57.403 37.037 0.00 0.00 31.75 3.01
3611 3681 7.803279 ATGTCTATCTCATACGTGTAACTCA 57.197 36.000 0.00 0.00 31.75 3.41
3612 3682 7.803279 TGTCTATCTCATACGTGTAACTCAT 57.197 36.000 0.00 0.00 31.75 2.90
3613 3683 8.221965 TGTCTATCTCATACGTGTAACTCATT 57.778 34.615 0.00 0.00 31.75 2.57
3614 3684 8.683615 TGTCTATCTCATACGTGTAACTCATTT 58.316 33.333 0.00 0.00 31.75 2.32
3615 3685 9.517609 GTCTATCTCATACGTGTAACTCATTTT 57.482 33.333 0.00 0.00 31.75 1.82
3616 3686 9.516314 TCTATCTCATACGTGTAACTCATTTTG 57.484 33.333 0.00 0.00 31.75 2.44
3617 3687 9.516314 CTATCTCATACGTGTAACTCATTTTGA 57.484 33.333 0.00 0.00 31.75 2.69
3618 3688 8.771920 ATCTCATACGTGTAACTCATTTTGAA 57.228 30.769 0.00 0.00 31.75 2.69
3619 3689 8.596271 TCTCATACGTGTAACTCATTTTGAAA 57.404 30.769 0.00 0.00 31.75 2.69
3620 3690 8.492748 TCTCATACGTGTAACTCATTTTGAAAC 58.507 33.333 0.00 0.00 31.75 2.78
3621 3691 8.373048 TCATACGTGTAACTCATTTTGAAACT 57.627 30.769 0.00 0.00 31.75 2.66
3622 3692 8.832521 TCATACGTGTAACTCATTTTGAAACTT 58.167 29.630 0.00 0.00 31.75 2.66
3626 3696 9.843334 ACGTGTAACTCATTTTGAAACTTAAAA 57.157 25.926 0.00 0.00 31.75 1.52
3638 3708 9.587772 TTTTGAAACTTAAAATTCATTGTCGGA 57.412 25.926 4.06 0.00 35.63 4.55
3639 3709 9.757227 TTTGAAACTTAAAATTCATTGTCGGAT 57.243 25.926 4.06 0.00 35.63 4.18
3640 3710 8.741101 TGAAACTTAAAATTCATTGTCGGATG 57.259 30.769 0.00 0.00 30.94 3.51
3641 3711 8.572185 TGAAACTTAAAATTCATTGTCGGATGA 58.428 29.630 0.00 0.00 34.37 2.92
3642 3712 9.573133 GAAACTTAAAATTCATTGTCGGATGAT 57.427 29.630 0.00 0.00 36.05 2.45
3643 3713 9.927668 AAACTTAAAATTCATTGTCGGATGATT 57.072 25.926 0.00 0.00 36.05 2.57
3644 3714 9.927668 AACTTAAAATTCATTGTCGGATGATTT 57.072 25.926 0.00 0.00 36.05 2.17
3645 3715 9.927668 ACTTAAAATTCATTGTCGGATGATTTT 57.072 25.926 9.39 9.39 39.44 1.82
3647 3717 9.703892 TTAAAATTCATTGTCGGATGATTTTGT 57.296 25.926 13.03 8.98 38.55 2.83
3649 3719 9.874205 AAAATTCATTGTCGGATGATTTTGTAT 57.126 25.926 13.03 0.00 38.55 2.29
3650 3720 9.874205 AAATTCATTGTCGGATGATTTTGTATT 57.126 25.926 12.21 2.63 37.81 1.89
3653 3723 9.949174 TTCATTGTCGGATGATTTTGTATTATG 57.051 29.630 0.00 0.00 36.05 1.90
3654 3724 8.075574 TCATTGTCGGATGATTTTGTATTATGC 58.924 33.333 0.00 0.00 31.35 3.14
3655 3725 6.934048 TGTCGGATGATTTTGTATTATGCA 57.066 33.333 0.00 0.00 0.00 3.96
3656 3726 7.509141 TGTCGGATGATTTTGTATTATGCAT 57.491 32.000 3.79 3.79 0.00 3.96
3657 3727 7.584108 TGTCGGATGATTTTGTATTATGCATC 58.416 34.615 0.19 0.00 0.00 3.91
3658 3728 7.445096 TGTCGGATGATTTTGTATTATGCATCT 59.555 33.333 0.19 0.00 33.20 2.90
3659 3729 8.935844 GTCGGATGATTTTGTATTATGCATCTA 58.064 33.333 0.19 0.00 33.20 1.98
3660 3730 8.935844 TCGGATGATTTTGTATTATGCATCTAC 58.064 33.333 0.19 7.43 33.20 2.59
3661 3731 8.939929 CGGATGATTTTGTATTATGCATCTACT 58.060 33.333 0.19 0.00 33.20 2.57
3712 3782 8.664798 TGAATTATCTTGTCATTACTGGTTTCG 58.335 33.333 0.00 0.00 0.00 3.46
3713 3783 8.561738 AATTATCTTGTCATTACTGGTTTCGT 57.438 30.769 0.00 0.00 0.00 3.85
3714 3784 9.661563 AATTATCTTGTCATTACTGGTTTCGTA 57.338 29.630 0.00 0.00 0.00 3.43
3715 3785 9.832445 ATTATCTTGTCATTACTGGTTTCGTAT 57.168 29.630 0.00 0.00 0.00 3.06
3717 3787 8.644318 ATCTTGTCATTACTGGTTTCGTATAC 57.356 34.615 0.00 0.00 0.00 1.47
3718 3788 7.604549 TCTTGTCATTACTGGTTTCGTATACA 58.395 34.615 3.32 0.00 0.00 2.29
3719 3789 8.255206 TCTTGTCATTACTGGTTTCGTATACAT 58.745 33.333 3.32 0.00 0.00 2.29
3720 3790 8.780846 TTGTCATTACTGGTTTCGTATACATT 57.219 30.769 3.32 0.00 0.00 2.71
3721 3791 8.415192 TGTCATTACTGGTTTCGTATACATTC 57.585 34.615 3.32 0.00 0.00 2.67
3722 3792 8.255206 TGTCATTACTGGTTTCGTATACATTCT 58.745 33.333 3.32 0.00 0.00 2.40
3723 3793 8.540492 GTCATTACTGGTTTCGTATACATTCTG 58.460 37.037 3.32 0.00 0.00 3.02
3724 3794 6.897259 TTACTGGTTTCGTATACATTCTGC 57.103 37.500 3.32 0.00 0.00 4.26
3725 3795 5.086104 ACTGGTTTCGTATACATTCTGCT 57.914 39.130 3.32 0.00 0.00 4.24
3726 3796 5.488341 ACTGGTTTCGTATACATTCTGCTT 58.512 37.500 3.32 0.00 0.00 3.91
3727 3797 5.581085 ACTGGTTTCGTATACATTCTGCTTC 59.419 40.000 3.32 0.00 0.00 3.86
3728 3798 5.483811 TGGTTTCGTATACATTCTGCTTCA 58.516 37.500 3.32 0.00 0.00 3.02
3729 3799 5.580691 TGGTTTCGTATACATTCTGCTTCAG 59.419 40.000 3.32 0.00 0.00 3.02
3730 3800 5.581085 GGTTTCGTATACATTCTGCTTCAGT 59.419 40.000 3.32 0.00 32.61 3.41
3731 3801 6.755141 GGTTTCGTATACATTCTGCTTCAGTA 59.245 38.462 3.32 0.00 32.61 2.74
3732 3802 7.438459 GGTTTCGTATACATTCTGCTTCAGTAT 59.562 37.037 3.32 0.00 32.61 2.12
3733 3803 8.818057 GTTTCGTATACATTCTGCTTCAGTATT 58.182 33.333 3.32 0.00 32.61 1.89
3734 3804 8.942338 TTCGTATACATTCTGCTTCAGTATTT 57.058 30.769 3.32 0.00 32.61 1.40
3735 3805 8.942338 TCGTATACATTCTGCTTCAGTATTTT 57.058 30.769 3.32 0.00 32.61 1.82
3736 3806 8.817100 TCGTATACATTCTGCTTCAGTATTTTG 58.183 33.333 3.32 0.00 32.61 2.44
3737 3807 8.817100 CGTATACATTCTGCTTCAGTATTTTGA 58.183 33.333 3.32 0.00 32.61 2.69
3881 3951 9.911788 ATGATGTAGTTTCAATATTTCACTCCT 57.088 29.630 0.00 0.00 0.00 3.69
3899 3969 9.793259 TTCACTCCTATTTACTTCATTTTCACT 57.207 29.630 0.00 0.00 0.00 3.41
3900 3970 9.793259 TCACTCCTATTTACTTCATTTTCACTT 57.207 29.630 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.877178 CAAAGTTTAGTCTTACTCCATGTATCT 57.123 33.333 0.00 0.00 0.00 1.98
89 91 7.721286 ACAAAACAAACAAACATGTTGAGAA 57.279 28.000 12.82 0.00 39.57 2.87
91 93 8.012151 TGTACAAAACAAACAAACATGTTGAG 57.988 30.769 12.82 10.63 39.57 3.02
93 95 8.012151 TCTGTACAAAACAAACAAACATGTTG 57.988 30.769 12.82 8.99 39.57 3.33
113 115 1.431633 TCCAACTGGTCCTCCTCTGTA 59.568 52.381 0.00 0.00 36.34 2.74
126 128 0.947244 GTGTTCCACAGCTCCAACTG 59.053 55.000 0.00 0.00 43.59 3.16
341 343 9.516314 GTTTGTGAAAAATTTACTTACTGCTCT 57.484 29.630 0.00 0.00 0.00 4.09
361 363 7.857734 TGATATTACTACATGGTGGTTTGTG 57.142 36.000 0.00 0.00 0.00 3.33
394 396 9.066892 ACTAAGACATTGTACATTGATGTGTTT 57.933 29.630 20.28 14.24 41.89 2.83
427 437 7.482654 TCGTGGAATAAGATTCAATGTCATC 57.517 36.000 1.90 0.00 0.00 2.92
448 458 4.843728 TGAAGCCCTGAAAAGATAATCGT 58.156 39.130 0.00 0.00 0.00 3.73
450 460 5.882557 TGTCTGAAGCCCTGAAAAGATAATC 59.117 40.000 0.00 0.00 0.00 1.75
460 470 3.840666 AGTATTCTTGTCTGAAGCCCTGA 59.159 43.478 0.00 0.00 0.00 3.86
546 556 6.041069 TCCCGAAAAACTTTGACATACCATTT 59.959 34.615 0.00 0.00 0.00 2.32
581 591 1.479323 CAAGATTCCACAAGGGCATGG 59.521 52.381 0.00 0.00 37.32 3.66
722 733 7.831691 TGGAACTTTCTTTGTTGATCCATAA 57.168 32.000 0.00 0.00 0.00 1.90
812 823 5.010820 ACGGAAGTTCTCTAGTGTTTTAGCT 59.989 40.000 2.25 0.00 46.40 3.32
824 835 5.536538 TGCTATCATATCACGGAAGTTCTCT 59.463 40.000 2.25 0.00 46.40 3.10
956 967 3.728718 CGTGGTGTCAAAAGTTATTGCAC 59.271 43.478 0.00 0.00 36.98 4.57
975 986 6.474819 TTGTAGATGTTTGTTCCATACGTG 57.525 37.500 0.00 0.00 0.00 4.49
1062 1073 8.372877 TCTCTTCCTTCTCATTAGTCAAGAAT 57.627 34.615 0.00 0.00 0.00 2.40
1131 1142 7.333672 CCTGTAAGAATAGTAACTGGTGGTTTC 59.666 40.741 0.00 0.00 36.14 2.78
1171 1182 0.025001 CAAGCGATAACCGTCTTGCG 59.975 55.000 0.00 0.00 41.53 4.85
1180 1191 5.718649 TGATGTAAAGAGCAAGCGATAAC 57.281 39.130 0.00 0.00 0.00 1.89
1185 1196 4.346734 AACATGATGTAAAGAGCAAGCG 57.653 40.909 0.00 0.00 0.00 4.68
1199 1211 9.725019 TGATGTTACTAAGACAAGAAACATGAT 57.275 29.630 0.00 0.00 37.60 2.45
1286 1334 8.202811 TGATCTGAACAAAATTGTGATGGAAAA 58.797 29.630 1.62 0.00 41.31 2.29
1296 1345 5.163581 CCCTAGCCTGATCTGAACAAAATTG 60.164 44.000 0.38 0.00 0.00 2.32
1302 1352 0.833287 GCCCTAGCCTGATCTGAACA 59.167 55.000 0.38 0.00 0.00 3.18
1303 1353 3.696306 GCCCTAGCCTGATCTGAAC 57.304 57.895 0.38 0.00 0.00 3.18
1319 1369 0.896923 TGACTGCATTTCCAATGGCC 59.103 50.000 0.00 0.00 0.00 5.36
1342 1392 3.076621 TGTGTTGCATTAGGAAGCTCTG 58.923 45.455 0.00 0.00 0.00 3.35
1359 1409 2.428171 GCCATTTGCACCATCTATGTGT 59.572 45.455 0.00 0.00 40.77 3.72
1360 1410 3.088194 GCCATTTGCACCATCTATGTG 57.912 47.619 0.00 0.00 40.77 3.21
1414 1464 8.930760 CAAAGGTTTTGTGATTTCTGTAAACAA 58.069 29.630 0.00 0.00 0.00 2.83
1424 1474 5.916318 TCATCAGCAAAGGTTTTGTGATTT 58.084 33.333 12.56 0.00 0.00 2.17
1427 1477 5.534207 AATCATCAGCAAAGGTTTTGTGA 57.466 34.783 3.77 6.41 0.00 3.58
1463 1513 6.886459 ACTCCTGTATTGTTAGCATGTGATTT 59.114 34.615 0.00 0.00 0.00 2.17
1466 1516 5.420725 ACTCCTGTATTGTTAGCATGTGA 57.579 39.130 0.00 0.00 0.00 3.58
1478 1528 5.359009 CCATGCATCTTCAAACTCCTGTATT 59.641 40.000 0.00 0.00 0.00 1.89
1482 1532 3.349927 TCCATGCATCTTCAAACTCCTG 58.650 45.455 0.00 0.00 0.00 3.86
1617 1667 4.616604 GCTACACATACGTTGAGTGGTACA 60.617 45.833 15.85 0.00 37.58 2.90
1618 1668 3.855950 GCTACACATACGTTGAGTGGTAC 59.144 47.826 15.85 0.00 37.58 3.34
1619 1669 3.506844 TGCTACACATACGTTGAGTGGTA 59.493 43.478 15.85 8.28 37.58 3.25
1620 1670 2.297880 TGCTACACATACGTTGAGTGGT 59.702 45.455 15.85 7.10 37.58 4.16
1621 1671 2.666508 GTGCTACACATACGTTGAGTGG 59.333 50.000 15.85 11.30 37.58 4.00
1622 1672 3.575630 AGTGCTACACATACGTTGAGTG 58.424 45.455 11.58 11.58 36.74 3.51
1623 1673 3.254903 TGAGTGCTACACATACGTTGAGT 59.745 43.478 0.00 0.00 36.74 3.41
1624 1674 3.833442 TGAGTGCTACACATACGTTGAG 58.167 45.455 0.00 0.00 36.74 3.02
1625 1675 3.926821 TGAGTGCTACACATACGTTGA 57.073 42.857 0.00 0.00 36.74 3.18
1626 1676 3.181544 CGTTGAGTGCTACACATACGTTG 60.182 47.826 0.00 0.00 36.74 4.10
1627 1677 2.984471 CGTTGAGTGCTACACATACGTT 59.016 45.455 0.00 0.00 36.74 3.99
1628 1678 2.030540 ACGTTGAGTGCTACACATACGT 60.031 45.455 14.66 14.66 40.25 3.57
1629 1679 2.592194 ACGTTGAGTGCTACACATACG 58.408 47.619 13.74 13.74 39.04 3.06
1630 1680 4.557690 CACTACGTTGAGTGCTACACATAC 59.442 45.833 5.58 0.00 40.42 2.39
1631 1681 4.456566 TCACTACGTTGAGTGCTACACATA 59.543 41.667 12.69 0.00 45.44 2.29
1730 1780 2.105134 ACTCTCCCGATCGTCTATCAGT 59.895 50.000 15.09 5.22 33.87 3.41
1733 1783 2.879646 ACAACTCTCCCGATCGTCTATC 59.120 50.000 15.09 0.00 0.00 2.08
1745 1795 1.423395 CTTCTGCGTCACAACTCTCC 58.577 55.000 0.00 0.00 0.00 3.71
1763 1813 3.633986 CCTGTTTGTTCTTCCTTTCAGCT 59.366 43.478 0.00 0.00 0.00 4.24
1827 1880 9.515226 AACAGAAACTAAATGTAGCAAGGAATA 57.485 29.630 0.00 0.00 0.00 1.75
2021 2075 6.459573 GCTTCACAACAAAAGTATGTTCCTCA 60.460 38.462 0.00 0.00 36.12 3.86
2209 2264 9.458374 AGTTGTTCGTTGGTAAAATATCAAAAG 57.542 29.630 0.00 0.00 29.22 2.27
2261 2316 3.304659 CCTCGGTTCACAAAAATCTGTGG 60.305 47.826 4.05 0.00 45.60 4.17
2352 2408 6.430451 CCGATATATTTCTCCAACTTGTTGC 58.570 40.000 7.89 0.00 0.00 4.17
2356 2412 4.988540 TCGCCGATATATTTCTCCAACTTG 59.011 41.667 0.00 0.00 0.00 3.16
2500 2556 3.758554 GCTCCTGTAATTCCTTCTTGCAA 59.241 43.478 0.00 0.00 0.00 4.08
2569 2625 5.479306 TGTGTACTTACTTCATCTTCAGGC 58.521 41.667 0.00 0.00 0.00 4.85
2607 2663 4.365514 TCACTAACTTCATTGCCTTCCA 57.634 40.909 0.00 0.00 0.00 3.53
2624 2680 8.394971 TCAACTATTTGAACACATGATTCACT 57.605 30.769 14.17 9.09 38.87 3.41
2836 2895 1.788308 CGACATTTGCTGCAAAACCTG 59.212 47.619 29.05 23.96 36.90 4.00
2872 2931 1.024271 GCTGCGGGCAATCTTTGATA 58.976 50.000 0.00 0.00 41.35 2.15
2884 2943 2.622064 AAGGTAAATAGAGCTGCGGG 57.378 50.000 0.00 0.00 0.00 6.13
2887 2946 7.793927 AGAACATTAAGGTAAATAGAGCTGC 57.206 36.000 0.00 0.00 0.00 5.25
2984 3043 4.563184 CAGACGACATAACTTAGTTCAGCC 59.437 45.833 0.00 0.00 0.00 4.85
3048 3107 8.038351 TCGTGATAGTCATCCAAGTCAAATTAA 58.962 33.333 0.00 0.00 0.00 1.40
3057 3116 8.593492 TTAATCAATCGTGATAGTCATCCAAG 57.407 34.615 0.00 0.00 44.02 3.61
3114 3177 8.647143 AAACAGTACAACCATTCATTTTGAAG 57.353 30.769 0.00 0.00 40.05 3.02
3260 3329 6.208599 ACGTCTAAATGGTGAAAATGTGGATT 59.791 34.615 0.00 0.00 0.00 3.01
3300 3369 6.364706 GGAACACGTTGCATGAAATAAAATCA 59.635 34.615 0.00 0.00 0.00 2.57
3303 3372 5.837437 AGGAACACGTTGCATGAAATAAAA 58.163 33.333 0.00 0.00 33.04 1.52
3304 3373 5.240623 AGAGGAACACGTTGCATGAAATAAA 59.759 36.000 0.00 0.00 33.04 1.40
3311 3380 4.685169 AATTAGAGGAACACGTTGCATG 57.315 40.909 4.20 0.00 33.04 4.06
3316 3385 9.063615 AGTTATTTCAAATTAGAGGAACACGTT 57.936 29.630 0.00 0.00 0.00 3.99
3368 3438 6.700960 TGCAAAACCTTTGAATAAGTGATGTG 59.299 34.615 3.35 0.00 0.00 3.21
3402 3472 7.439108 ACCTGACCTTCTATGTTAATTAGCT 57.561 36.000 0.83 0.00 0.00 3.32
3447 3517 9.762933 ACAAATCACAACAAAATAGCATTAAGT 57.237 25.926 0.00 0.00 0.00 2.24
3450 3520 9.539825 ACAACAAATCACAACAAAATAGCATTA 57.460 25.926 0.00 0.00 0.00 1.90
3451 3521 8.436046 ACAACAAATCACAACAAAATAGCATT 57.564 26.923 0.00 0.00 0.00 3.56
3452 3522 8.436046 AACAACAAATCACAACAAAATAGCAT 57.564 26.923 0.00 0.00 0.00 3.79
3453 3523 7.840342 AACAACAAATCACAACAAAATAGCA 57.160 28.000 0.00 0.00 0.00 3.49
3454 3524 8.386606 TCAAACAACAAATCACAACAAAATAGC 58.613 29.630 0.00 0.00 0.00 2.97
3457 3527 7.743838 CGTTCAAACAACAAATCACAACAAAAT 59.256 29.630 0.00 0.00 0.00 1.82
3458 3528 7.042725 TCGTTCAAACAACAAATCACAACAAAA 60.043 29.630 0.00 0.00 0.00 2.44
3459 3529 6.420903 TCGTTCAAACAACAAATCACAACAAA 59.579 30.769 0.00 0.00 0.00 2.83
3460 3530 5.920840 TCGTTCAAACAACAAATCACAACAA 59.079 32.000 0.00 0.00 0.00 2.83
3461 3531 5.461526 TCGTTCAAACAACAAATCACAACA 58.538 33.333 0.00 0.00 0.00 3.33
3462 3532 6.567769 ATCGTTCAAACAACAAATCACAAC 57.432 33.333 0.00 0.00 0.00 3.32
3463 3533 7.116948 ACAAATCGTTCAAACAACAAATCACAA 59.883 29.630 0.00 0.00 0.00 3.33
3464 3534 6.587990 ACAAATCGTTCAAACAACAAATCACA 59.412 30.769 0.00 0.00 0.00 3.58
3465 3535 6.988329 ACAAATCGTTCAAACAACAAATCAC 58.012 32.000 0.00 0.00 0.00 3.06
3466 3536 6.808704 TGACAAATCGTTCAAACAACAAATCA 59.191 30.769 0.00 0.00 0.00 2.57
3467 3537 7.215696 TGACAAATCGTTCAAACAACAAATC 57.784 32.000 0.00 0.00 0.00 2.17
3468 3538 7.769272 ATGACAAATCGTTCAAACAACAAAT 57.231 28.000 0.00 0.00 0.00 2.32
3469 3539 8.689251 TTATGACAAATCGTTCAAACAACAAA 57.311 26.923 0.00 0.00 0.00 2.83
3470 3540 8.864069 ATTATGACAAATCGTTCAAACAACAA 57.136 26.923 0.00 0.00 0.00 2.83
3471 3541 8.864069 AATTATGACAAATCGTTCAAACAACA 57.136 26.923 0.00 0.00 0.00 3.33
3474 3544 9.619316 CCTTAATTATGACAAATCGTTCAAACA 57.381 29.630 0.04 0.00 0.00 2.83
3475 3545 9.620660 ACCTTAATTATGACAAATCGTTCAAAC 57.379 29.630 0.04 0.00 0.00 2.93
3477 3547 9.619316 CAACCTTAATTATGACAAATCGTTCAA 57.381 29.630 0.04 0.00 0.00 2.69
3478 3548 8.788806 ACAACCTTAATTATGACAAATCGTTCA 58.211 29.630 0.04 0.00 0.00 3.18
3479 3549 9.274065 GACAACCTTAATTATGACAAATCGTTC 57.726 33.333 0.04 0.00 0.00 3.95
3480 3550 7.960738 CGACAACCTTAATTATGACAAATCGTT 59.039 33.333 0.04 0.00 0.00 3.85
3481 3551 7.118680 ACGACAACCTTAATTATGACAAATCGT 59.881 33.333 0.00 0.00 0.00 3.73
3482 3552 7.425309 CACGACAACCTTAATTATGACAAATCG 59.575 37.037 0.00 0.00 0.00 3.34
3483 3553 8.447833 TCACGACAACCTTAATTATGACAAATC 58.552 33.333 0.00 0.00 0.00 2.17
3484 3554 8.330466 TCACGACAACCTTAATTATGACAAAT 57.670 30.769 0.00 0.00 0.00 2.32
3485 3555 7.731882 TCACGACAACCTTAATTATGACAAA 57.268 32.000 0.00 0.00 0.00 2.83
3486 3556 7.915293 ATCACGACAACCTTAATTATGACAA 57.085 32.000 0.00 0.00 0.00 3.18
3487 3557 7.915293 AATCACGACAACCTTAATTATGACA 57.085 32.000 0.00 0.00 0.00 3.58
3488 3558 8.333186 GGTAATCACGACAACCTTAATTATGAC 58.667 37.037 0.00 0.00 0.00 3.06
3489 3559 8.041919 TGGTAATCACGACAACCTTAATTATGA 58.958 33.333 0.00 0.00 32.99 2.15
3490 3560 8.203937 TGGTAATCACGACAACCTTAATTATG 57.796 34.615 0.00 0.00 32.99 1.90
3491 3561 8.795842 TTGGTAATCACGACAACCTTAATTAT 57.204 30.769 0.00 0.00 32.99 1.28
3492 3562 8.618702 TTTGGTAATCACGACAACCTTAATTA 57.381 30.769 0.00 0.00 32.99 1.40
3493 3563 7.513371 TTTGGTAATCACGACAACCTTAATT 57.487 32.000 0.00 0.00 32.99 1.40
3494 3564 7.696992 ATTTGGTAATCACGACAACCTTAAT 57.303 32.000 0.00 0.00 32.99 1.40
3495 3565 7.513371 AATTTGGTAATCACGACAACCTTAA 57.487 32.000 0.00 0.00 32.99 1.85
3496 3566 7.013464 ACAAATTTGGTAATCACGACAACCTTA 59.987 33.333 21.74 0.00 32.99 2.69
3497 3567 6.183360 ACAAATTTGGTAATCACGACAACCTT 60.183 34.615 21.74 0.00 32.99 3.50
3498 3568 5.300792 ACAAATTTGGTAATCACGACAACCT 59.699 36.000 21.74 0.00 32.99 3.50
3499 3569 5.525199 ACAAATTTGGTAATCACGACAACC 58.475 37.500 21.74 0.00 0.00 3.77
3500 3570 7.858879 ACTTACAAATTTGGTAATCACGACAAC 59.141 33.333 21.74 0.00 30.93 3.32
3501 3571 7.932335 ACTTACAAATTTGGTAATCACGACAA 58.068 30.769 21.74 0.00 30.93 3.18
3502 3572 7.499321 ACTTACAAATTTGGTAATCACGACA 57.501 32.000 21.74 0.00 30.93 4.35
3503 3573 9.485591 CATACTTACAAATTTGGTAATCACGAC 57.514 33.333 21.74 0.00 30.93 4.34
3504 3574 8.178964 GCATACTTACAAATTTGGTAATCACGA 58.821 33.333 21.74 0.00 30.93 4.35
3505 3575 8.181573 AGCATACTTACAAATTTGGTAATCACG 58.818 33.333 21.74 8.70 30.93 4.35
3506 3576 9.503427 GAGCATACTTACAAATTTGGTAATCAC 57.497 33.333 21.74 5.61 30.93 3.06
3507 3577 9.461312 AGAGCATACTTACAAATTTGGTAATCA 57.539 29.630 21.74 8.92 30.93 2.57
3510 3580 9.953565 ACTAGAGCATACTTACAAATTTGGTAA 57.046 29.630 21.74 15.18 0.00 2.85
3511 3581 9.378551 CACTAGAGCATACTTACAAATTTGGTA 57.621 33.333 21.74 14.11 0.00 3.25
3512 3582 7.148239 GCACTAGAGCATACTTACAAATTTGGT 60.148 37.037 21.74 12.47 0.00 3.67
3513 3583 7.148255 TGCACTAGAGCATACTTACAAATTTGG 60.148 37.037 21.74 7.20 40.11 3.28
3514 3584 7.751732 TGCACTAGAGCATACTTACAAATTTG 58.248 34.615 16.67 16.67 40.11 2.32
3515 3585 7.921786 TGCACTAGAGCATACTTACAAATTT 57.078 32.000 11.06 0.00 40.11 1.82
3516 3586 7.921786 TTGCACTAGAGCATACTTACAAATT 57.078 32.000 15.82 0.00 45.19 1.82
3517 3587 8.511604 AATTGCACTAGAGCATACTTACAAAT 57.488 30.769 15.82 0.32 45.19 2.32
3518 3588 7.921786 AATTGCACTAGAGCATACTTACAAA 57.078 32.000 15.82 0.00 45.19 2.83
3519 3589 9.443323 TTTAATTGCACTAGAGCATACTTACAA 57.557 29.630 15.82 0.00 45.19 2.41
3520 3590 9.613428 ATTTAATTGCACTAGAGCATACTTACA 57.387 29.630 15.82 7.93 45.19 2.41
3578 3648 9.463443 CACGTATGAGATAGACATAACAAATGA 57.537 33.333 0.00 0.00 33.04 2.57
3579 3649 9.249457 ACACGTATGAGATAGACATAACAAATG 57.751 33.333 0.00 0.00 33.04 2.32
3582 3652 9.726232 GTTACACGTATGAGATAGACATAACAA 57.274 33.333 0.00 0.00 33.04 2.83
3583 3653 9.117183 AGTTACACGTATGAGATAGACATAACA 57.883 33.333 0.00 0.00 33.04 2.41
3584 3654 9.596677 GAGTTACACGTATGAGATAGACATAAC 57.403 37.037 0.00 0.00 33.04 1.89
3585 3655 9.333724 TGAGTTACACGTATGAGATAGACATAA 57.666 33.333 0.00 0.00 33.04 1.90
3586 3656 8.897872 TGAGTTACACGTATGAGATAGACATA 57.102 34.615 0.00 0.00 0.00 2.29
3587 3657 7.803279 TGAGTTACACGTATGAGATAGACAT 57.197 36.000 0.00 0.00 0.00 3.06
3588 3658 7.803279 ATGAGTTACACGTATGAGATAGACA 57.197 36.000 0.00 0.00 0.00 3.41
3589 3659 9.517609 AAAATGAGTTACACGTATGAGATAGAC 57.482 33.333 0.00 0.00 0.00 2.59
3590 3660 9.516314 CAAAATGAGTTACACGTATGAGATAGA 57.484 33.333 0.00 0.00 0.00 1.98
3591 3661 9.516314 TCAAAATGAGTTACACGTATGAGATAG 57.484 33.333 0.00 0.00 0.00 2.08
3592 3662 9.863845 TTCAAAATGAGTTACACGTATGAGATA 57.136 29.630 0.00 0.00 0.00 1.98
3593 3663 8.771920 TTCAAAATGAGTTACACGTATGAGAT 57.228 30.769 0.00 0.00 0.00 2.75
3594 3664 8.492748 GTTTCAAAATGAGTTACACGTATGAGA 58.507 33.333 0.00 0.00 0.00 3.27
3595 3665 8.495949 AGTTTCAAAATGAGTTACACGTATGAG 58.504 33.333 0.00 0.00 0.00 2.90
3596 3666 8.373048 AGTTTCAAAATGAGTTACACGTATGA 57.627 30.769 0.00 0.00 0.00 2.15
3600 3670 9.843334 TTTTAAGTTTCAAAATGAGTTACACGT 57.157 25.926 0.00 0.00 0.00 4.49
3612 3682 9.587772 TCCGACAATGAATTTTAAGTTTCAAAA 57.412 25.926 6.33 0.00 35.63 2.44
3613 3683 9.757227 ATCCGACAATGAATTTTAAGTTTCAAA 57.243 25.926 6.33 0.00 35.63 2.69
3614 3684 9.190858 CATCCGACAATGAATTTTAAGTTTCAA 57.809 29.630 6.33 0.00 35.63 2.69
3615 3685 8.572185 TCATCCGACAATGAATTTTAAGTTTCA 58.428 29.630 5.06 5.06 36.38 2.69
3616 3686 8.964420 TCATCCGACAATGAATTTTAAGTTTC 57.036 30.769 0.00 0.00 32.80 2.78
3617 3687 9.927668 AATCATCCGACAATGAATTTTAAGTTT 57.072 25.926 0.00 0.00 39.04 2.66
3618 3688 9.927668 AAATCATCCGACAATGAATTTTAAGTT 57.072 25.926 0.00 0.00 39.04 2.66
3619 3689 9.927668 AAAATCATCCGACAATGAATTTTAAGT 57.072 25.926 0.00 0.00 36.02 2.24
3621 3691 9.703892 ACAAAATCATCCGACAATGAATTTTAA 57.296 25.926 6.00 0.00 36.89 1.52
3623 3693 9.874205 ATACAAAATCATCCGACAATGAATTTT 57.126 25.926 6.00 7.25 36.89 1.82
3624 3694 9.874205 AATACAAAATCATCCGACAATGAATTT 57.126 25.926 0.00 0.00 38.62 1.82
3627 3697 9.949174 CATAATACAAAATCATCCGACAATGAA 57.051 29.630 0.00 0.00 39.04 2.57
3628 3698 8.075574 GCATAATACAAAATCATCCGACAATGA 58.924 33.333 0.00 0.00 39.85 2.57
3629 3699 7.861872 TGCATAATACAAAATCATCCGACAATG 59.138 33.333 0.00 0.00 0.00 2.82
3630 3700 7.939782 TGCATAATACAAAATCATCCGACAAT 58.060 30.769 0.00 0.00 0.00 2.71
3631 3701 7.326968 TGCATAATACAAAATCATCCGACAA 57.673 32.000 0.00 0.00 0.00 3.18
3632 3702 6.934048 TGCATAATACAAAATCATCCGACA 57.066 33.333 0.00 0.00 0.00 4.35
3633 3703 7.810658 AGATGCATAATACAAAATCATCCGAC 58.189 34.615 0.00 0.00 31.80 4.79
3634 3704 7.984422 AGATGCATAATACAAAATCATCCGA 57.016 32.000 0.00 0.00 31.80 4.55
3635 3705 8.939929 AGTAGATGCATAATACAAAATCATCCG 58.060 33.333 18.76 0.00 31.80 4.18
3686 3756 8.664798 CGAAACCAGTAATGACAAGATAATTCA 58.335 33.333 0.00 0.00 0.00 2.57
3687 3757 8.665685 ACGAAACCAGTAATGACAAGATAATTC 58.334 33.333 0.00 0.00 0.00 2.17
3688 3758 8.561738 ACGAAACCAGTAATGACAAGATAATT 57.438 30.769 0.00 0.00 0.00 1.40
3689 3759 9.832445 ATACGAAACCAGTAATGACAAGATAAT 57.168 29.630 0.00 0.00 0.00 1.28
3691 3761 9.740239 GTATACGAAACCAGTAATGACAAGATA 57.260 33.333 0.00 0.00 0.00 1.98
3692 3762 8.255206 TGTATACGAAACCAGTAATGACAAGAT 58.745 33.333 0.00 0.00 0.00 2.40
3693 3763 7.604549 TGTATACGAAACCAGTAATGACAAGA 58.395 34.615 0.00 0.00 0.00 3.02
3694 3764 7.821595 TGTATACGAAACCAGTAATGACAAG 57.178 36.000 0.00 0.00 0.00 3.16
3695 3765 8.780846 AATGTATACGAAACCAGTAATGACAA 57.219 30.769 0.00 0.00 0.00 3.18
3696 3766 8.255206 AGAATGTATACGAAACCAGTAATGACA 58.745 33.333 0.00 0.00 0.00 3.58
3697 3767 8.540492 CAGAATGTATACGAAACCAGTAATGAC 58.460 37.037 0.00 0.00 0.00 3.06
3698 3768 7.223971 GCAGAATGTATACGAAACCAGTAATGA 59.776 37.037 0.00 0.00 39.31 2.57
3699 3769 7.224753 AGCAGAATGTATACGAAACCAGTAATG 59.775 37.037 0.00 0.00 39.31 1.90
3700 3770 7.272978 AGCAGAATGTATACGAAACCAGTAAT 58.727 34.615 0.00 0.00 39.31 1.89
3701 3771 6.636705 AGCAGAATGTATACGAAACCAGTAA 58.363 36.000 0.00 0.00 39.31 2.24
3702 3772 6.216801 AGCAGAATGTATACGAAACCAGTA 57.783 37.500 0.00 0.00 39.31 2.74
3703 3773 5.086104 AGCAGAATGTATACGAAACCAGT 57.914 39.130 0.00 0.00 39.31 4.00
3704 3774 5.580691 TGAAGCAGAATGTATACGAAACCAG 59.419 40.000 0.00 0.00 39.31 4.00
3705 3775 5.483811 TGAAGCAGAATGTATACGAAACCA 58.516 37.500 0.00 0.00 39.31 3.67
3706 3776 5.581085 ACTGAAGCAGAATGTATACGAAACC 59.419 40.000 0.82 0.00 39.31 3.27
3707 3777 6.648725 ACTGAAGCAGAATGTATACGAAAC 57.351 37.500 0.82 0.00 39.31 2.78
3708 3778 8.942338 AATACTGAAGCAGAATGTATACGAAA 57.058 30.769 0.82 0.00 39.31 3.46
3709 3779 8.942338 AAATACTGAAGCAGAATGTATACGAA 57.058 30.769 0.82 0.00 39.31 3.85
3710 3780 8.817100 CAAAATACTGAAGCAGAATGTATACGA 58.183 33.333 0.82 0.00 39.31 3.43
3711 3781 8.817100 TCAAAATACTGAAGCAGAATGTATACG 58.183 33.333 0.82 0.00 39.31 3.06
3855 3925 9.911788 AGGAGTGAAATATTGAAACTACATCAT 57.088 29.630 9.26 0.00 0.00 2.45
3873 3943 9.793259 AGTGAAAATGAAGTAAATAGGAGTGAA 57.207 29.630 0.00 0.00 0.00 3.18
3874 3944 9.793259 AAGTGAAAATGAAGTAAATAGGAGTGA 57.207 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.