Multiple sequence alignment - TraesCS4B01G059000

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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 TraesCS4B01G059000 chr4B 100.000 3694 0 0 1 3694 49761300 49757607 0.000000e+00 6822
1 TraesCS4B01G059000 chr4D 92.006 3115 144 43 1 3063 34715631 34712570 0.000000e+00 4276
2 TraesCS4B01G059000 chr4D 88.998 409 34 5 3007 3409 34712572 34712169 2.560000e-136 496
3 TraesCS4B01G059000 chr4D 91.429 140 8 2 3426 3565 34711991 34711856 4.870000e-44 189
4 TraesCS4B01G059000 chr4D 94.262 122 4 2 3574 3694 34711626 34711507 2.270000e-42 183
5 TraesCS4B01G059000 chr4A 91.781 3127 163 38 1 3092 567650677 567653744 0.000000e+00 4265
6 TraesCS4B01G059000 chr4A 81.395 258 20 14 3444 3694 567667332 567667568 6.300000e-43 185


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 TraesCS4B01G059000 chr4B 49757607 49761300 3693 True 6822 6822 100.00000 1 3694 1 chr4B.!!$R1 3693
1 TraesCS4B01G059000 chr4D 34711507 34715631 4124 True 1286 4276 91.67375 1 3694 4 chr4D.!!$R1 3693
2 TraesCS4B01G059000 chr4A 567650677 567653744 3067 False 4265 4265 91.78100 1 3092 1 chr4A.!!$F1 3091

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
60 61 0.105039 AAATAGCCTCGCCTCTTCCG 59.895 55.0 0.0 0.00 0.00 4.30 F
719 779 0.178301 GACGGTGGATCCCTTCTTCC 59.822 60.0 9.9 1.57 0.00 3.46 F
736 796 0.179040 TCCGGCTTTCTTTTGTCCGT 60.179 50.0 0.0 0.00 38.54 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1576 0.247736 CTTCCTGTTGTCCCTCTCCG 59.752 60.0 0.00 0.00 0.0 4.63 R
2555 2617 0.038892 CATTGTTGGTGCTGCTGTCC 60.039 55.0 0.00 1.75 0.0 4.02 R
2707 2769 3.134458 GGTTCACAGAACAACTCCAGAG 58.866 50.0 11.51 0.00 0.0 3.35 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
27 28 5.494341 TCCTACTCCAGCTATCCATCTATCT 59.506 44.000 0.00 0.00 0.00 1.98
28 29 6.678857 TCCTACTCCAGCTATCCATCTATCTA 59.321 42.308 0.00 0.00 0.00 1.98
29 30 7.352254 TCCTACTCCAGCTATCCATCTATCTAT 59.648 40.741 0.00 0.00 0.00 1.98
30 31 7.665559 CCTACTCCAGCTATCCATCTATCTATC 59.334 44.444 0.00 0.00 0.00 2.08
59 60 1.139058 TCAAATAGCCTCGCCTCTTCC 59.861 52.381 0.00 0.00 0.00 3.46
60 61 0.105039 AAATAGCCTCGCCTCTTCCG 59.895 55.000 0.00 0.00 0.00 4.30
66 67 2.987547 TCGCCTCTTCCGTTCGGT 60.988 61.111 11.04 0.00 0.00 4.69
88 89 0.395312 TTCGACTTGGGAGTTGGGAC 59.605 55.000 0.00 0.00 37.79 4.46
89 90 0.471211 TCGACTTGGGAGTTGGGACT 60.471 55.000 0.00 0.00 37.79 3.85
132 150 5.945784 CCTAGATGATGAAAACTTTGTGGGA 59.054 40.000 0.00 0.00 0.00 4.37
233 275 9.715121 TGTTCATCGAAGTAGGTAGTTTTAATT 57.285 29.630 0.00 0.00 0.00 1.40
239 281 9.525409 TCGAAGTAGGTAGTTTTAATTAGATGC 57.475 33.333 0.00 0.00 0.00 3.91
271 314 4.826183 GCTATTTTGATCTTCCTGGATGCT 59.174 41.667 0.00 0.00 0.00 3.79
273 316 6.149142 GCTATTTTGATCTTCCTGGATGCTAG 59.851 42.308 0.00 0.00 0.00 3.42
391 440 9.827411 CCAAACTAGTATCTGTTCTTTTAAAGC 57.173 33.333 0.00 0.00 0.00 3.51
422 472 4.780815 CTTGGTAATGTTCTCCATGCCTA 58.219 43.478 0.00 0.00 32.82 3.93
436 486 5.188434 TCCATGCCTAGTTCTTGAAGATTG 58.812 41.667 0.00 0.00 0.00 2.67
454 504 4.344968 AGATTGGTTAGGCTTTTGCTGTTT 59.655 37.500 0.00 0.00 46.54 2.83
462 512 4.886579 AGGCTTTTGCTGTTTCCAATTAG 58.113 39.130 0.00 0.00 46.54 1.73
475 525 6.536941 TGTTTCCAATTAGCTTTGGTGTTTTC 59.463 34.615 15.29 4.66 45.32 2.29
477 527 4.580995 TCCAATTAGCTTTGGTGTTTTCGA 59.419 37.500 15.29 0.00 45.32 3.71
551 610 5.356426 GCCCAAGTTAGTGAATGTTGTTTT 58.644 37.500 0.00 0.00 0.00 2.43
683 743 0.673985 GTTCCCCAAGGTTGTTCTGC 59.326 55.000 0.00 0.00 0.00 4.26
697 757 3.299977 CTGCAGCAGGCCTTTGCA 61.300 61.111 30.10 30.10 46.47 4.08
719 779 0.178301 GACGGTGGATCCCTTCTTCC 59.822 60.000 9.90 1.57 0.00 3.46
734 794 2.227194 TCTTCCGGCTTTCTTTTGTCC 58.773 47.619 0.00 0.00 0.00 4.02
735 795 0.948678 TTCCGGCTTTCTTTTGTCCG 59.051 50.000 0.00 0.00 39.79 4.79
736 796 0.179040 TCCGGCTTTCTTTTGTCCGT 60.179 50.000 0.00 0.00 38.54 4.69
737 797 0.666374 CCGGCTTTCTTTTGTCCGTT 59.334 50.000 0.00 0.00 38.54 4.44
738 798 1.599419 CCGGCTTTCTTTTGTCCGTTG 60.599 52.381 0.00 0.00 38.54 4.10
739 799 1.332375 CGGCTTTCTTTTGTCCGTTGA 59.668 47.619 0.00 0.00 35.75 3.18
740 800 2.031157 CGGCTTTCTTTTGTCCGTTGAT 60.031 45.455 0.00 0.00 35.75 2.57
741 801 3.550030 CGGCTTTCTTTTGTCCGTTGATT 60.550 43.478 0.00 0.00 35.75 2.57
742 802 3.735746 GGCTTTCTTTTGTCCGTTGATTG 59.264 43.478 0.00 0.00 0.00 2.67
743 803 4.499019 GGCTTTCTTTTGTCCGTTGATTGA 60.499 41.667 0.00 0.00 0.00 2.57
755 815 3.997021 CCGTTGATTGATAGGGATAGTGC 59.003 47.826 0.00 0.00 0.00 4.40
775 835 0.605589 CGGTGGTTCTTCAAGGGACC 60.606 60.000 4.42 4.42 0.00 4.46
798 858 3.438360 GTTGCTTTTCACCTCTGTGTTG 58.562 45.455 0.00 0.00 43.26 3.33
823 883 6.306987 AGGATTACCAGTTGAGTTGTTCATT 58.693 36.000 0.00 0.00 38.94 2.57
865 925 7.810658 TGCAGACTTTATGAAATTTCACTCTC 58.189 34.615 22.71 12.48 40.49 3.20
953 1015 2.969262 CTCCCCCTTGTCTTCTATCCTC 59.031 54.545 0.00 0.00 0.00 3.71
980 1042 2.835156 GGAACTAAGGAGGAGCTCTTGT 59.165 50.000 14.64 0.00 0.00 3.16
984 1046 2.849294 AAGGAGGAGCTCTTGTTGTC 57.151 50.000 14.64 1.40 0.00 3.18
993 1055 4.688413 GGAGCTCTTGTTGTCTTTAGACTG 59.312 45.833 14.64 0.00 44.99 3.51
1017 1079 2.368439 GACATGTATTCAGGCCAGCAA 58.632 47.619 5.01 0.00 0.00 3.91
1074 1136 1.381735 CTTGGAGGGGAATTGGGGC 60.382 63.158 0.00 0.00 0.00 5.80
1104 1166 4.685924 CAATGCATCAAAAGATGGGGTAC 58.314 43.478 0.00 0.00 33.41 3.34
1134 1196 2.096980 GGCGTATGGGTTTCAAGCTTAC 59.903 50.000 0.00 0.00 0.00 2.34
1152 1214 4.755411 CTTACGGCATGGAGTTAGAAGAA 58.245 43.478 0.00 0.00 0.00 2.52
1162 1224 5.399991 TGGAGTTAGAAGAAAGACCAGGTA 58.600 41.667 0.00 0.00 0.00 3.08
1213 1275 2.971307 TCTTATCATGCAGTTGTCGCA 58.029 42.857 0.00 0.00 44.94 5.10
1251 1313 7.078228 GTGACAATTCTGTAGTTGATGGAAAC 58.922 38.462 0.00 0.00 35.30 2.78
1253 1315 5.763204 ACAATTCTGTAGTTGATGGAAACGT 59.237 36.000 0.00 0.00 35.13 3.99
1315 1377 1.134280 AGTGATGAGCATAGTGGTGGC 60.134 52.381 0.00 0.00 0.00 5.01
1316 1378 0.911053 TGATGAGCATAGTGGTGGCA 59.089 50.000 0.00 0.00 0.00 4.92
1500 1562 0.318441 CAGAGGTTTCGTCTCAGCCA 59.682 55.000 0.00 0.00 33.92 4.75
1509 1571 1.902508 TCGTCTCAGCCAGAAAGGAAT 59.097 47.619 0.00 0.00 41.22 3.01
1586 1648 0.752658 TCGGATGGTGATGGCACTAG 59.247 55.000 0.00 0.00 44.52 2.57
1673 1735 5.017294 AGAGTAAGCTTCTGATTAGCACC 57.983 43.478 0.00 0.00 41.11 5.01
1703 1765 9.533831 AAGATCCCATTTCAGTTTACTTTATGT 57.466 29.630 0.00 0.00 0.00 2.29
1864 1926 1.000506 TCTGCGACCAACTTGTACTCC 59.999 52.381 0.00 0.00 0.00 3.85
1957 2019 3.874543 TGCAGTCATTACAACGACAAGTT 59.125 39.130 0.00 0.00 45.45 2.66
1968 2030 3.314541 ACGACAAGTTGAGGTACATCC 57.685 47.619 10.54 0.00 0.00 3.51
1969 2031 3.323979 AACGACAAGTTGAGGTACATCCT 59.676 43.478 10.54 0.00 42.39 3.24
1970 2032 4.799586 AACGACAAGTTGAGGTACATCCTG 60.800 45.833 10.54 0.31 42.81 3.86
1971 2033 7.756778 AACGACAAGTTGAGGTACATCCTGG 62.757 48.000 10.54 0.00 42.81 4.45
1981 2043 5.171339 AGGTACATCCTGGAATATCATGC 57.829 43.478 0.00 0.00 46.19 4.06
1990 2052 2.621526 TGGAATATCATGCTGCTGCTTG 59.378 45.455 20.96 20.96 43.21 4.01
2000 2062 3.525537 TGCTGCTGCTTGTCTATTAGTC 58.474 45.455 17.00 0.00 40.48 2.59
2017 2079 9.442062 TCTATTAGTCCAGATGTTATTGGGTTA 57.558 33.333 0.00 0.00 35.13 2.85
2022 2084 6.833933 AGTCCAGATGTTATTGGGTTATTTCC 59.166 38.462 0.00 0.00 35.13 3.13
2029 2091 8.990163 ATGTTATTGGGTTATTTCCGAGTATT 57.010 30.769 0.00 0.00 0.00 1.89
2031 2093 9.902684 TGTTATTGGGTTATTTCCGAGTATTTA 57.097 29.630 0.00 0.00 0.00 1.40
2034 2096 6.870971 TGGGTTATTTCCGAGTATTTATGC 57.129 37.500 0.00 0.00 0.00 3.14
2035 2097 5.766174 TGGGTTATTTCCGAGTATTTATGCC 59.234 40.000 0.00 0.00 0.00 4.40
2054 2116 4.013050 TGCCGTTTGTTGGAATATCATCA 58.987 39.130 0.00 0.00 0.00 3.07
2166 2228 9.788960 GATTCTATCCAAACAAGTAAATTCACC 57.211 33.333 0.00 0.00 0.00 4.02
2209 2271 2.093128 TCAAAGATTTCTAGACCCGCCC 60.093 50.000 0.00 0.00 0.00 6.13
2234 2296 4.854399 TCAACGCAATTCTTGTTTGTAGG 58.146 39.130 0.00 0.00 31.66 3.18
2248 2310 4.756642 TGTTTGTAGGTGATGCTTTCTCAG 59.243 41.667 0.00 0.00 0.00 3.35
2296 2358 2.203126 CCAGGATCAAGCGCCCTC 60.203 66.667 2.29 0.00 0.00 4.30
2332 2394 2.621998 CCAAGGAATGATGCATCCAGAC 59.378 50.000 23.67 11.65 0.00 3.51
2423 2485 6.994421 ACCAGGTAAATTCAGTCCATTTTT 57.006 33.333 0.00 0.00 0.00 1.94
2424 2486 6.758254 ACCAGGTAAATTCAGTCCATTTTTG 58.242 36.000 0.00 0.00 0.00 2.44
2425 2487 6.553100 ACCAGGTAAATTCAGTCCATTTTTGA 59.447 34.615 0.00 0.00 0.00 2.69
2426 2488 7.235399 ACCAGGTAAATTCAGTCCATTTTTGAT 59.765 33.333 0.00 0.00 0.00 2.57
2427 2489 8.748412 CCAGGTAAATTCAGTCCATTTTTGATA 58.252 33.333 0.00 0.00 0.00 2.15
2432 2494 8.483307 AAATTCAGTCCATTTTTGATACATGC 57.517 30.769 0.00 0.00 0.00 4.06
2438 2500 6.154877 AGTCCATTTTTGATACATGCCAATCA 59.845 34.615 0.00 0.00 0.00 2.57
2442 2504 7.927092 CCATTTTTGATACATGCCAATCACATA 59.073 33.333 5.69 0.00 31.99 2.29
2481 2543 2.723273 CAATGGACTTACCTGAACCCC 58.277 52.381 0.00 0.00 39.86 4.95
2543 2605 4.503714 TCCTCATATGAACTTCAACCCC 57.496 45.455 6.90 0.00 0.00 4.95
2591 2653 3.006110 ACAATGCTGGTATATGCAATGCC 59.994 43.478 1.53 0.00 42.03 4.40
2595 2657 2.553904 GCTGGTATATGCAATGCCCTCT 60.554 50.000 1.53 0.00 0.00 3.69
2606 2668 3.120095 GCAATGCCCTCTTTTCAAAATGC 60.120 43.478 0.00 0.00 0.00 3.56
2615 2677 4.317488 TCTTTTCAAAATGCCATGCTTCC 58.683 39.130 0.00 0.00 0.00 3.46
2631 2693 6.713903 CCATGCTTCCTAATCATAGTGATTGT 59.286 38.462 13.82 0.00 45.77 2.71
2632 2694 7.879677 CCATGCTTCCTAATCATAGTGATTGTA 59.120 37.037 13.82 0.00 45.77 2.41
2707 2769 3.045601 ACAGTGAGTTGCTGGTATGAC 57.954 47.619 0.00 0.00 38.22 3.06
2786 2848 3.547054 TGCCTAACCATTAGTTACCGG 57.453 47.619 0.00 0.00 40.05 5.28
2795 2857 3.538591 CATTAGTTACCGGTTTCCTCCC 58.461 50.000 15.04 0.00 0.00 4.30
2906 2968 6.093082 ACCGTAAATTTCTATTGCGTTAGCTT 59.907 34.615 0.00 0.00 45.42 3.74
2939 3001 7.088589 CAGGAACCCTGTGTTATTCATTAAG 57.911 40.000 4.88 0.00 45.82 1.85
2941 3003 7.827236 CAGGAACCCTGTGTTATTCATTAAGTA 59.173 37.037 4.88 0.00 45.82 2.24
2947 3009 7.336931 CCCTGTGTTATTCATTAAGTACAAGCT 59.663 37.037 0.00 0.00 0.00 3.74
2948 3010 8.730680 CCTGTGTTATTCATTAAGTACAAGCTT 58.269 33.333 0.00 0.00 0.00 3.74
2997 3059 5.593502 AGCGTACTAAGTAGACTGGCTTATT 59.406 40.000 0.00 0.00 0.00 1.40
2998 3060 6.769822 AGCGTACTAAGTAGACTGGCTTATTA 59.230 38.462 0.00 0.00 0.00 0.98
2999 3061 7.041235 AGCGTACTAAGTAGACTGGCTTATTAG 60.041 40.741 11.02 11.02 33.23 1.73
3049 3165 7.078011 ACTTTTGTCAAGAGTTTCAGAGTTC 57.922 36.000 2.96 0.00 0.00 3.01
3181 3297 1.281287 AGTGCCATCAGTCAAGAGCAT 59.719 47.619 0.00 0.00 32.11 3.79
3187 3303 4.337555 GCCATCAGTCAAGAGCATTTGTAT 59.662 41.667 0.00 0.00 0.00 2.29
3193 3309 8.654230 TCAGTCAAGAGCATTTGTATAATCTC 57.346 34.615 0.00 0.00 0.00 2.75
3200 3316 7.278135 AGAGCATTTGTATAATCTCTTGAGCA 58.722 34.615 0.00 0.00 0.00 4.26
3201 3317 7.772292 AGAGCATTTGTATAATCTCTTGAGCAA 59.228 33.333 0.00 0.00 0.00 3.91
3202 3318 7.928103 AGCATTTGTATAATCTCTTGAGCAAG 58.072 34.615 3.87 3.87 39.71 4.01
3234 3350 5.850557 TTGATGTGGTTTTCAATGTGTCT 57.149 34.783 0.00 0.00 0.00 3.41
3235 3351 6.951062 TTGATGTGGTTTTCAATGTGTCTA 57.049 33.333 0.00 0.00 0.00 2.59
3237 3353 5.825151 TGATGTGGTTTTCAATGTGTCTACA 59.175 36.000 0.00 0.00 41.89 2.74
3296 3415 2.368875 CCTTGTGACCTTGTGAGTACCT 59.631 50.000 0.00 0.00 0.00 3.08
3298 3417 4.451900 CTTGTGACCTTGTGAGTACCTTT 58.548 43.478 0.00 0.00 0.00 3.11
3313 3432 1.480545 ACCTTTTGAACTTGTGGTGCC 59.519 47.619 0.00 0.00 0.00 5.01
3316 3435 0.459489 TTTGAACTTGTGGTGCCTGC 59.541 50.000 0.00 0.00 0.00 4.85
3335 3454 3.070076 GCATGAAGCGTCCATCAGA 57.930 52.632 0.00 0.00 0.00 3.27
3337 3456 1.739466 GCATGAAGCGTCCATCAGAAA 59.261 47.619 0.00 0.00 0.00 2.52
3341 3460 3.673902 TGAAGCGTCCATCAGAAAATCA 58.326 40.909 0.00 0.00 0.00 2.57
3342 3461 3.436704 TGAAGCGTCCATCAGAAAATCAC 59.563 43.478 0.00 0.00 0.00 3.06
3345 3464 2.684881 GCGTCCATCAGAAAATCACCAT 59.315 45.455 0.00 0.00 0.00 3.55
3346 3465 3.876914 GCGTCCATCAGAAAATCACCATA 59.123 43.478 0.00 0.00 0.00 2.74
3347 3466 4.260784 GCGTCCATCAGAAAATCACCATAC 60.261 45.833 0.00 0.00 0.00 2.39
3348 3467 4.875536 CGTCCATCAGAAAATCACCATACA 59.124 41.667 0.00 0.00 0.00 2.29
3349 3468 5.220662 CGTCCATCAGAAAATCACCATACAC 60.221 44.000 0.00 0.00 0.00 2.90
3350 3469 5.066505 GTCCATCAGAAAATCACCATACACC 59.933 44.000 0.00 0.00 0.00 4.16
3351 3470 5.044919 TCCATCAGAAAATCACCATACACCT 60.045 40.000 0.00 0.00 0.00 4.00
3352 3471 6.157820 TCCATCAGAAAATCACCATACACCTA 59.842 38.462 0.00 0.00 0.00 3.08
3353 3472 7.000472 CCATCAGAAAATCACCATACACCTAT 59.000 38.462 0.00 0.00 0.00 2.57
3356 3475 9.730705 ATCAGAAAATCACCATACACCTATATG 57.269 33.333 0.00 0.00 33.10 1.78
3357 3476 7.661437 TCAGAAAATCACCATACACCTATATGC 59.339 37.037 0.00 0.00 32.12 3.14
3358 3477 7.663081 CAGAAAATCACCATACACCTATATGCT 59.337 37.037 0.00 0.00 32.12 3.79
3359 3478 8.880244 AGAAAATCACCATACACCTATATGCTA 58.120 33.333 0.00 0.00 32.12 3.49
3360 3479 8.848474 AAAATCACCATACACCTATATGCTAC 57.152 34.615 0.00 0.00 32.12 3.58
3361 3480 7.798710 AATCACCATACACCTATATGCTACT 57.201 36.000 0.00 0.00 32.12 2.57
3362 3481 6.590234 TCACCATACACCTATATGCTACTG 57.410 41.667 0.00 0.00 32.12 2.74
3363 3482 6.311735 TCACCATACACCTATATGCTACTGA 58.688 40.000 0.00 0.00 32.12 3.41
3364 3483 6.208797 TCACCATACACCTATATGCTACTGAC 59.791 42.308 0.00 0.00 32.12 3.51
3365 3484 6.209589 CACCATACACCTATATGCTACTGACT 59.790 42.308 0.00 0.00 32.12 3.41
3366 3485 6.209589 ACCATACACCTATATGCTACTGACTG 59.790 42.308 0.00 0.00 32.12 3.51
3367 3486 6.434340 CCATACACCTATATGCTACTGACTGA 59.566 42.308 0.00 0.00 32.12 3.41
3374 3494 2.532250 TGCTACTGACTGATCTCCCA 57.468 50.000 0.00 0.00 0.00 4.37
3381 3501 2.568956 CTGACTGATCTCCCACTGGAAA 59.431 50.000 0.00 0.00 41.17 3.13
3395 3515 3.772025 CACTGGAAAGTGATCTCCTACCT 59.228 47.826 0.00 0.00 42.02 3.08
3401 3521 5.413309 AAAGTGATCTCCTACCTGTTCAG 57.587 43.478 0.00 0.00 0.00 3.02
3413 3533 1.581934 CTGTTCAGAACTGGTTGCGA 58.418 50.000 14.51 0.00 0.00 5.10
3414 3534 1.939934 CTGTTCAGAACTGGTTGCGAA 59.060 47.619 14.51 0.00 0.00 4.70
3415 3535 2.354510 CTGTTCAGAACTGGTTGCGAAA 59.645 45.455 14.51 0.00 0.00 3.46
3416 3536 2.096819 TGTTCAGAACTGGTTGCGAAAC 59.903 45.455 14.51 0.00 0.00 2.78
3417 3537 2.325583 TCAGAACTGGTTGCGAAACT 57.674 45.000 6.17 0.00 0.00 2.66
3418 3538 3.462483 TCAGAACTGGTTGCGAAACTA 57.538 42.857 6.17 0.00 0.00 2.24
3419 3539 3.390135 TCAGAACTGGTTGCGAAACTAG 58.610 45.455 17.53 17.53 37.30 2.57
3420 3540 3.131396 CAGAACTGGTTGCGAAACTAGT 58.869 45.455 18.92 18.92 44.74 2.57
3421 3541 3.059597 CAGAACTGGTTGCGAAACTAGTG 60.060 47.826 24.39 9.83 42.52 2.74
3424 3544 1.531149 CTGGTTGCGAAACTAGTGTGG 59.469 52.381 11.39 0.00 0.00 4.17
3478 3759 9.869844 GAATGATTGATTATAACTCCTTGTTCG 57.130 33.333 0.00 0.00 39.89 3.95
3483 3764 7.989416 TGATTATAACTCCTTGTTCGGTTTT 57.011 32.000 0.00 0.00 39.89 2.43
3484 3765 7.812648 TGATTATAACTCCTTGTTCGGTTTTG 58.187 34.615 0.00 0.00 39.89 2.44
3486 3767 7.571080 TTATAACTCCTTGTTCGGTTTTGTT 57.429 32.000 0.00 0.00 39.89 2.83
3487 3768 4.365899 AACTCCTTGTTCGGTTTTGTTC 57.634 40.909 0.00 0.00 32.63 3.18
3488 3769 3.617284 ACTCCTTGTTCGGTTTTGTTCT 58.383 40.909 0.00 0.00 0.00 3.01
3489 3770 4.014406 ACTCCTTGTTCGGTTTTGTTCTT 58.986 39.130 0.00 0.00 0.00 2.52
3490 3771 4.142469 ACTCCTTGTTCGGTTTTGTTCTTG 60.142 41.667 0.00 0.00 0.00 3.02
3493 3774 5.047943 TCCTTGTTCGGTTTTGTTCTTGAAA 60.048 36.000 0.00 0.00 0.00 2.69
3494 3775 5.810074 CCTTGTTCGGTTTTGTTCTTGAAAT 59.190 36.000 0.00 0.00 0.00 2.17
3495 3776 6.975772 CCTTGTTCGGTTTTGTTCTTGAAATA 59.024 34.615 0.00 0.00 0.00 1.40
3496 3777 7.043656 CCTTGTTCGGTTTTGTTCTTGAAATAC 60.044 37.037 0.00 0.00 0.00 1.89
3497 3778 7.090953 TGTTCGGTTTTGTTCTTGAAATACT 57.909 32.000 0.00 0.00 0.00 2.12
3499 3780 6.308371 TCGGTTTTGTTCTTGAAATACTCC 57.692 37.500 0.00 0.00 0.00 3.85
3500 3781 5.823570 TCGGTTTTGTTCTTGAAATACTCCA 59.176 36.000 0.00 0.00 0.00 3.86
3502 3783 6.447162 GGTTTTGTTCTTGAAATACTCCAGG 58.553 40.000 0.00 0.00 0.00 4.45
3503 3784 6.040504 GGTTTTGTTCTTGAAATACTCCAGGT 59.959 38.462 0.00 0.00 0.00 4.00
3504 3785 7.229907 GGTTTTGTTCTTGAAATACTCCAGGTA 59.770 37.037 0.00 0.00 34.62 3.08
3505 3786 8.626526 GTTTTGTTCTTGAAATACTCCAGGTAA 58.373 33.333 0.00 0.00 33.74 2.85
3565 3846 7.446931 TGTGATACTAGCAACATCCAAAGAAAA 59.553 33.333 0.00 0.00 0.00 2.29
3566 3847 8.462016 GTGATACTAGCAACATCCAAAGAAAAT 58.538 33.333 0.00 0.00 0.00 1.82
3567 3848 9.679661 TGATACTAGCAACATCCAAAGAAAATA 57.320 29.630 0.00 0.00 0.00 1.40
3571 3852 8.903820 ACTAGCAACATCCAAAGAAAATATACC 58.096 33.333 0.00 0.00 0.00 2.73
3572 3853 7.961326 AGCAACATCCAAAGAAAATATACCT 57.039 32.000 0.00 0.00 0.00 3.08
3599 4101 8.536175 AGACAAAAGAACATAAACTCCCAAAAA 58.464 29.630 0.00 0.00 0.00 1.94
3639 4141 4.145876 TGCACATTAAGCTTTGTCTTCG 57.854 40.909 3.20 0.00 0.00 3.79
3671 4173 5.119931 TGCTACAAAGTTACAAGGCAATG 57.880 39.130 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.858094 TGCAATAGATAGATAGATGGATAGCTG 58.142 37.037 0.00 0.00 0.00 4.24
27 28 6.092670 GCGAGGCTATTTGAATGCAATAGATA 59.907 38.462 6.55 0.00 33.25 1.98
28 29 5.106396 GCGAGGCTATTTGAATGCAATAGAT 60.106 40.000 6.55 0.00 33.25 1.98
29 30 4.214119 GCGAGGCTATTTGAATGCAATAGA 59.786 41.667 6.55 0.00 33.25 1.98
30 31 4.470462 GCGAGGCTATTTGAATGCAATAG 58.530 43.478 0.00 0.00 33.25 1.73
59 60 1.333435 CCCAAGTCGAAAAACCGAACG 60.333 52.381 0.00 0.00 40.51 3.95
60 61 1.941975 TCCCAAGTCGAAAAACCGAAC 59.058 47.619 0.00 0.00 40.51 3.95
66 67 2.092321 TCCCAACTCCCAAGTCGAAAAA 60.092 45.455 0.00 0.00 33.48 1.94
88 89 2.003301 GAAAGCGCAAGTAGGAAGGAG 58.997 52.381 11.47 0.00 41.68 3.69
89 90 1.338769 GGAAAGCGCAAGTAGGAAGGA 60.339 52.381 11.47 0.00 41.68 3.36
95 113 4.046938 TCATCTAGGAAAGCGCAAGTAG 57.953 45.455 11.47 3.00 41.68 2.57
132 150 3.772025 ACCTTCTCAGAGGATTTGATCGT 59.228 43.478 0.00 0.00 39.25 3.73
202 220 7.653767 ACTACCTACTTCGATGAACAAAAAG 57.346 36.000 5.16 0.00 0.00 2.27
239 281 4.978083 AGATCAAAATAGCAGCACCTTG 57.022 40.909 0.00 0.00 0.00 3.61
271 314 2.410322 CTGGGTGTGGCTTGGCACTA 62.410 60.000 23.96 10.89 36.03 2.74
273 316 3.297620 CTGGGTGTGGCTTGGCAC 61.298 66.667 18.51 18.51 35.07 5.01
391 440 6.543465 TGGAGAACATTACCAAGCATATGAAG 59.457 38.462 6.97 0.00 0.00 3.02
404 453 5.675538 AGAACTAGGCATGGAGAACATTAC 58.324 41.667 0.00 0.00 37.84 1.89
422 472 5.248380 AGCCTAACCAATCTTCAAGAACT 57.752 39.130 0.00 0.00 0.00 3.01
436 486 2.364002 TGGAAACAGCAAAAGCCTAACC 59.636 45.455 0.00 0.00 35.01 2.85
462 512 3.692791 AAGACTCGAAAACACCAAAGC 57.307 42.857 0.00 0.00 0.00 3.51
475 525 2.755655 TCTGCTCCTCCTAAAAGACTCG 59.244 50.000 0.00 0.00 0.00 4.18
477 527 3.259625 GTGTCTGCTCCTCCTAAAAGACT 59.740 47.826 0.00 0.00 36.01 3.24
528 587 4.584327 AACAACATTCACTAACTTGGGC 57.416 40.909 0.00 0.00 0.00 5.36
551 610 6.032039 AGAGGATATAACCCCATCATTAGCA 58.968 40.000 0.00 0.00 0.00 3.49
683 743 1.980232 TCCATGCAAAGGCCTGCTG 60.980 57.895 17.08 13.65 43.07 4.41
697 757 0.326618 AGAAGGGATCCACCGTCCAT 60.327 55.000 15.23 0.00 39.46 3.41
719 779 1.332375 TCAACGGACAAAAGAAAGCCG 59.668 47.619 0.00 0.00 46.83 5.52
734 794 3.997021 GGCACTATCCCTATCAATCAACG 59.003 47.826 0.00 0.00 0.00 4.10
735 795 3.997021 CGGCACTATCCCTATCAATCAAC 59.003 47.826 0.00 0.00 0.00 3.18
736 796 3.007940 CCGGCACTATCCCTATCAATCAA 59.992 47.826 0.00 0.00 0.00 2.57
737 797 2.567169 CCGGCACTATCCCTATCAATCA 59.433 50.000 0.00 0.00 0.00 2.57
738 798 2.567615 ACCGGCACTATCCCTATCAATC 59.432 50.000 0.00 0.00 0.00 2.67
739 799 2.303022 CACCGGCACTATCCCTATCAAT 59.697 50.000 0.00 0.00 0.00 2.57
740 800 1.691976 CACCGGCACTATCCCTATCAA 59.308 52.381 0.00 0.00 0.00 2.57
741 801 1.338107 CACCGGCACTATCCCTATCA 58.662 55.000 0.00 0.00 0.00 2.15
742 802 0.608640 CCACCGGCACTATCCCTATC 59.391 60.000 0.00 0.00 0.00 2.08
743 803 0.105142 ACCACCGGCACTATCCCTAT 60.105 55.000 0.00 0.00 0.00 2.57
755 815 0.605589 GTCCCTTGAAGAACCACCGG 60.606 60.000 0.00 0.00 0.00 5.28
775 835 1.308998 ACAGAGGTGAAAAGCAACCG 58.691 50.000 0.00 0.00 33.51 4.44
798 858 5.305585 TGAACAACTCAACTGGTAATCCTC 58.694 41.667 0.00 0.00 34.23 3.71
865 925 3.637998 AGACAAATGCAGCTTGAACAG 57.362 42.857 16.08 0.00 0.00 3.16
953 1015 2.355209 GCTCCTCCTTAGTTCCCTGTTG 60.355 54.545 0.00 0.00 0.00 3.33
984 1046 7.065085 CCTGAATACATGTCCAACAGTCTAAAG 59.935 40.741 0.00 0.00 0.00 1.85
993 1055 2.684881 CTGGCCTGAATACATGTCCAAC 59.315 50.000 0.00 0.00 0.00 3.77
1017 1079 1.134159 GCAGCAGGACCTTGATCAGAT 60.134 52.381 0.00 0.00 0.00 2.90
1074 1136 5.556355 TCTTTTGATGCATTGCTACAGAG 57.444 39.130 10.49 10.84 0.00 3.35
1116 1178 2.096980 GCCGTAAGCTTGAAACCCATAC 59.903 50.000 9.86 0.00 38.99 2.39
1134 1196 3.619038 GTCTTTCTTCTAACTCCATGCCG 59.381 47.826 0.00 0.00 0.00 5.69
1152 1214 6.097554 CAGAAGATCTGTACATACCTGGTCTT 59.902 42.308 0.63 7.16 39.58 3.01
1162 1224 4.833478 AACCAGCAGAAGATCTGTACAT 57.167 40.909 8.97 0.00 45.94 2.29
1188 1250 5.276584 GCGACAACTGCATGATAAGAACTAG 60.277 44.000 0.00 0.00 0.00 2.57
1213 1275 8.237811 ACAGAATTGTCACCTTCAAAAGTATT 57.762 30.769 0.00 0.00 29.46 1.89
1251 1313 4.109766 TGTACCTGCAAGAATTATCGACG 58.890 43.478 0.00 0.00 34.07 5.12
1253 1315 6.582636 AGAATGTACCTGCAAGAATTATCGA 58.417 36.000 0.00 0.00 34.07 3.59
1315 1377 5.072741 TCTGTTCCCTTCCTTTTCTTCATG 58.927 41.667 0.00 0.00 0.00 3.07
1316 1378 5.324832 TCTGTTCCCTTCCTTTTCTTCAT 57.675 39.130 0.00 0.00 0.00 2.57
1405 1467 9.258826 CCACATCTAGATTAGAACAAGAAGATG 57.741 37.037 1.33 7.30 42.92 2.90
1500 1562 0.902531 TCTCCGCCGAATTCCTTTCT 59.097 50.000 0.00 0.00 31.73 2.52
1509 1571 2.602267 TTGTCCCTCTCCGCCGAA 60.602 61.111 0.00 0.00 0.00 4.30
1514 1576 0.247736 CTTCCTGTTGTCCCTCTCCG 59.752 60.000 0.00 0.00 0.00 4.63
1586 1648 5.748630 GCCCGGAAATGAACATAATTTTCTC 59.251 40.000 0.73 0.00 0.00 2.87
1673 1735 7.636150 AGTAAACTGAAATGGGATCTTGATG 57.364 36.000 0.00 0.00 0.00 3.07
1703 1765 4.356405 TCAAGCATGAGAACAGGAAGAA 57.644 40.909 0.00 0.00 0.00 2.52
1864 1926 1.024579 AGGAACATTGGTAAGGCGCG 61.025 55.000 0.00 0.00 0.00 6.86
1906 1968 6.535274 TTGATTATCTCATCAAGCATGACG 57.465 37.500 0.00 0.00 38.09 4.35
1957 2019 9.368341 CAGCATGATATTCCAGGATGTACCTCA 62.368 44.444 0.00 0.00 43.83 3.86
1964 2026 3.440522 CAGCAGCATGATATTCCAGGATG 59.559 47.826 0.00 0.00 39.69 3.51
1965 2027 3.687125 CAGCAGCATGATATTCCAGGAT 58.313 45.455 0.00 0.00 39.69 3.24
1966 2028 2.812983 GCAGCAGCATGATATTCCAGGA 60.813 50.000 0.00 0.00 39.69 3.86
1967 2029 1.540267 GCAGCAGCATGATATTCCAGG 59.460 52.381 0.00 0.00 39.69 4.45
1968 2030 2.505405 AGCAGCAGCATGATATTCCAG 58.495 47.619 3.17 0.00 45.49 3.86
1969 2031 2.621526 CAAGCAGCAGCATGATATTCCA 59.378 45.455 3.17 0.00 41.78 3.53
1970 2032 2.621998 ACAAGCAGCAGCATGATATTCC 59.378 45.455 13.49 0.00 41.78 3.01
1971 2033 3.564644 AGACAAGCAGCAGCATGATATTC 59.435 43.478 13.49 0.21 41.78 1.75
1972 2034 3.552875 AGACAAGCAGCAGCATGATATT 58.447 40.909 13.49 0.00 41.78 1.28
1973 2035 3.210232 AGACAAGCAGCAGCATGATAT 57.790 42.857 13.49 0.00 41.78 1.63
1974 2036 2.704464 AGACAAGCAGCAGCATGATA 57.296 45.000 13.49 0.00 41.78 2.15
1975 2037 2.704464 TAGACAAGCAGCAGCATGAT 57.296 45.000 13.49 3.98 41.78 2.45
1976 2038 2.704464 ATAGACAAGCAGCAGCATGA 57.296 45.000 13.49 0.00 41.78 3.07
1977 2039 3.875727 ACTAATAGACAAGCAGCAGCATG 59.124 43.478 3.17 3.98 44.59 4.06
1978 2040 4.125703 GACTAATAGACAAGCAGCAGCAT 58.874 43.478 3.17 0.00 45.49 3.79
1979 2041 3.525537 GACTAATAGACAAGCAGCAGCA 58.474 45.455 3.17 0.00 45.49 4.41
1980 2042 2.869192 GGACTAATAGACAAGCAGCAGC 59.131 50.000 0.00 0.00 42.56 5.25
1981 2043 4.118410 CTGGACTAATAGACAAGCAGCAG 58.882 47.826 0.00 0.00 0.00 4.24
1990 2052 7.736893 ACCCAATAACATCTGGACTAATAGAC 58.263 38.462 0.00 0.00 34.35 2.59
2000 2062 5.825679 TCGGAAATAACCCAATAACATCTGG 59.174 40.000 0.00 0.00 0.00 3.86
2017 2079 5.355910 ACAAACGGCATAAATACTCGGAAAT 59.644 36.000 0.00 0.00 0.00 2.17
2022 2084 4.093703 TCCAACAAACGGCATAAATACTCG 59.906 41.667 0.00 0.00 0.00 4.18
2029 2091 6.319911 TGATGATATTCCAACAAACGGCATAA 59.680 34.615 0.00 0.00 0.00 1.90
2031 2093 4.644234 TGATGATATTCCAACAAACGGCAT 59.356 37.500 0.00 0.00 0.00 4.40
2032 2094 4.013050 TGATGATATTCCAACAAACGGCA 58.987 39.130 0.00 0.00 0.00 5.69
2033 2095 4.630894 TGATGATATTCCAACAAACGGC 57.369 40.909 0.00 0.00 0.00 5.68
2034 2096 5.972973 CACATGATGATATTCCAACAAACGG 59.027 40.000 0.00 0.00 0.00 4.44
2035 2097 5.456497 GCACATGATGATATTCCAACAAACG 59.544 40.000 0.00 0.00 0.00 3.60
2054 2116 3.354948 TGAAGTGGCATTAGAGCACAT 57.645 42.857 0.00 0.00 35.83 3.21
2234 2296 2.354259 CCTGTCCTGAGAAAGCATCAC 58.646 52.381 0.00 0.00 0.00 3.06
2248 2310 2.597510 AAACCAAGGCGCCTGTCC 60.598 61.111 33.60 0.00 0.00 4.02
2296 2358 4.524316 TCCTTGGTTGAAATGAGCAATG 57.476 40.909 0.00 0.00 34.42 2.82
2332 2394 2.951457 TGGAAGCATTGCACATCATG 57.049 45.000 11.91 0.00 43.23 3.07
2423 2485 6.474630 TGCTATATGTGATTGGCATGTATCA 58.525 36.000 0.00 0.00 0.00 2.15
2424 2486 6.990341 TGCTATATGTGATTGGCATGTATC 57.010 37.500 0.00 0.00 0.00 2.24
2425 2487 7.282450 CAGATGCTATATGTGATTGGCATGTAT 59.718 37.037 0.00 0.00 39.93 2.29
2426 2488 6.596497 CAGATGCTATATGTGATTGGCATGTA 59.404 38.462 0.00 0.00 39.93 2.29
2427 2489 5.414765 CAGATGCTATATGTGATTGGCATGT 59.585 40.000 0.00 0.00 39.93 3.21
2432 2494 5.123502 GGCTTCAGATGCTATATGTGATTGG 59.876 44.000 8.14 0.00 0.00 3.16
2438 2500 5.046087 TGCTATGGCTTCAGATGCTATATGT 60.046 40.000 12.92 0.00 39.59 2.29
2442 2504 4.362470 TTGCTATGGCTTCAGATGCTAT 57.638 40.909 11.30 11.30 39.59 2.97
2470 2532 1.200519 CTGGATTCGGGGTTCAGGTA 58.799 55.000 0.00 0.00 0.00 3.08
2473 2535 1.959042 CATCTGGATTCGGGGTTCAG 58.041 55.000 0.00 0.00 0.00 3.02
2481 2543 2.224233 ACATCTCAGGCATCTGGATTCG 60.224 50.000 0.00 0.00 41.23 3.34
2555 2617 0.038892 CATTGTTGGTGCTGCTGTCC 60.039 55.000 0.00 1.75 0.00 4.02
2558 2620 4.255126 GCATTGTTGGTGCTGCTG 57.745 55.556 0.00 0.00 39.45 4.41
2591 2653 3.934068 AGCATGGCATTTTGAAAAGAGG 58.066 40.909 0.00 0.00 0.00 3.69
2595 2657 4.354893 AGGAAGCATGGCATTTTGAAAA 57.645 36.364 0.00 0.00 0.00 2.29
2606 2668 6.713903 ACAATCACTATGATTAGGAAGCATGG 59.286 38.462 3.81 0.19 44.60 3.66
2632 2694 9.965902 AGAGGAACATTTCTGTAAGTTTGATAT 57.034 29.630 0.00 0.00 33.36 1.63
2707 2769 3.134458 GGTTCACAGAACAACTCCAGAG 58.866 50.000 11.51 0.00 0.00 3.35
2786 2848 1.979155 GGCAGCAAGGGGAGGAAAC 60.979 63.158 0.00 0.00 0.00 2.78
2906 2968 0.250295 CAGGGTTCCTGCTTTCGACA 60.250 55.000 0.61 0.00 45.13 4.35
2936 2998 7.232534 ACAATTGATCCCAAAAGCTTGTACTTA 59.767 33.333 13.59 0.00 32.89 2.24
2939 3001 5.634859 CACAATTGATCCCAAAAGCTTGTAC 59.365 40.000 13.59 0.00 32.89 2.90
2941 3003 4.503643 CCACAATTGATCCCAAAAGCTTGT 60.504 41.667 13.59 0.00 34.13 3.16
2947 3009 3.055240 GGCATCCACAATTGATCCCAAAA 60.055 43.478 13.59 0.00 35.67 2.44
2948 3010 2.500910 GGCATCCACAATTGATCCCAAA 59.499 45.455 13.59 0.00 35.67 3.28
2997 3059 7.554118 ACTTCACTACTTACGGCAATACTACTA 59.446 37.037 0.00 0.00 0.00 1.82
2998 3060 6.376581 ACTTCACTACTTACGGCAATACTACT 59.623 38.462 0.00 0.00 0.00 2.57
2999 3061 6.471519 CACTTCACTACTTACGGCAATACTAC 59.528 42.308 0.00 0.00 0.00 2.73
3110 3226 6.377146 GGCATAATGAGTTTAAAGTGGAGGAA 59.623 38.462 0.00 0.00 0.00 3.36
3122 3238 6.430000 ACTTTCACTTACGGCATAATGAGTTT 59.570 34.615 0.00 0.00 0.00 2.66
3124 3240 5.488341 ACTTTCACTTACGGCATAATGAGT 58.512 37.500 0.00 0.00 0.00 3.41
3127 3243 6.607689 TCAAACTTTCACTTACGGCATAATG 58.392 36.000 0.00 0.00 0.00 1.90
3193 3309 4.001652 TCAATCTCTTGCTCTTGCTCAAG 58.998 43.478 3.32 3.32 40.62 3.02
3200 3316 4.298103 ACCACATCAATCTCTTGCTCTT 57.702 40.909 0.00 0.00 32.11 2.85
3201 3317 3.996921 ACCACATCAATCTCTTGCTCT 57.003 42.857 0.00 0.00 32.11 4.09
3202 3318 5.048504 TGAAAACCACATCAATCTCTTGCTC 60.049 40.000 0.00 0.00 32.11 4.26
3296 3415 1.134848 GCAGGCACCACAAGTTCAAAA 60.135 47.619 0.00 0.00 0.00 2.44
3298 3417 1.723608 CGCAGGCACCACAAGTTCAA 61.724 55.000 0.00 0.00 0.00 2.69
3325 3444 4.875536 TGTATGGTGATTTTCTGATGGACG 59.124 41.667 0.00 0.00 0.00 4.79
3329 3448 9.730705 ATATAGGTGTATGGTGATTTTCTGATG 57.269 33.333 0.00 0.00 0.00 3.07
3335 3454 8.660435 AGTAGCATATAGGTGTATGGTGATTTT 58.340 33.333 8.26 0.00 41.43 1.82
3337 3456 7.454694 TCAGTAGCATATAGGTGTATGGTGATT 59.545 37.037 8.26 0.00 41.43 2.57
3341 3460 6.209589 CAGTCAGTAGCATATAGGTGTATGGT 59.790 42.308 4.22 4.22 43.17 3.55
3342 3461 6.434340 TCAGTCAGTAGCATATAGGTGTATGG 59.566 42.308 0.00 0.00 33.61 2.74
3345 3464 7.462590 AGATCAGTCAGTAGCATATAGGTGTA 58.537 38.462 0.00 0.00 0.00 2.90
3346 3465 6.310941 AGATCAGTCAGTAGCATATAGGTGT 58.689 40.000 0.00 0.00 0.00 4.16
3347 3466 6.127758 GGAGATCAGTCAGTAGCATATAGGTG 60.128 46.154 0.00 0.00 0.00 4.00
3348 3467 5.949354 GGAGATCAGTCAGTAGCATATAGGT 59.051 44.000 0.00 0.00 0.00 3.08
3349 3468 5.359576 GGGAGATCAGTCAGTAGCATATAGG 59.640 48.000 0.00 0.00 0.00 2.57
3350 3469 5.948758 TGGGAGATCAGTCAGTAGCATATAG 59.051 44.000 0.00 0.00 0.00 1.31
3351 3470 5.712446 GTGGGAGATCAGTCAGTAGCATATA 59.288 44.000 0.00 0.00 0.00 0.86
3352 3471 4.526262 GTGGGAGATCAGTCAGTAGCATAT 59.474 45.833 0.00 0.00 0.00 1.78
3353 3472 3.891977 GTGGGAGATCAGTCAGTAGCATA 59.108 47.826 0.00 0.00 0.00 3.14
3356 3475 2.100584 CAGTGGGAGATCAGTCAGTAGC 59.899 54.545 0.00 0.00 0.00 3.58
3357 3476 2.692557 CCAGTGGGAGATCAGTCAGTAG 59.307 54.545 0.00 0.00 35.59 2.57
3358 3477 2.311841 TCCAGTGGGAGATCAGTCAGTA 59.688 50.000 9.92 0.00 38.64 2.74
3359 3478 1.077828 TCCAGTGGGAGATCAGTCAGT 59.922 52.381 9.92 0.00 38.64 3.41
3360 3479 1.857965 TCCAGTGGGAGATCAGTCAG 58.142 55.000 9.92 0.00 38.64 3.51
3361 3480 2.325661 TTCCAGTGGGAGATCAGTCA 57.674 50.000 9.92 0.00 46.01 3.41
3362 3481 2.569404 ACTTTCCAGTGGGAGATCAGTC 59.431 50.000 9.92 0.00 46.01 3.51
3363 3482 2.304180 CACTTTCCAGTGGGAGATCAGT 59.696 50.000 9.92 0.00 46.10 3.41
3364 3483 2.983229 CACTTTCCAGTGGGAGATCAG 58.017 52.381 9.92 0.00 46.10 2.90
3374 3494 3.772025 CAGGTAGGAGATCACTTTCCAGT 59.228 47.826 0.00 0.00 35.88 4.00
3381 3501 4.323569 TCTGAACAGGTAGGAGATCACT 57.676 45.455 0.00 0.00 0.00 3.41
3395 3515 2.031258 TTCGCAACCAGTTCTGAACA 57.969 45.000 21.50 0.00 0.00 3.18
3401 3521 2.870411 ACACTAGTTTCGCAACCAGTTC 59.130 45.455 0.00 0.00 33.09 3.01
3409 3529 2.683968 CTAAGCCACACTAGTTTCGCA 58.316 47.619 1.46 0.00 0.00 5.10
3410 3530 1.393883 GCTAAGCCACACTAGTTTCGC 59.606 52.381 0.00 0.00 0.00 4.70
3411 3531 2.668457 CAGCTAAGCCACACTAGTTTCG 59.332 50.000 0.00 0.00 0.00 3.46
3413 3533 3.071023 TCACAGCTAAGCCACACTAGTTT 59.929 43.478 0.00 0.00 0.00 2.66
3414 3534 2.632996 TCACAGCTAAGCCACACTAGTT 59.367 45.455 0.00 0.00 0.00 2.24
3415 3535 2.232452 CTCACAGCTAAGCCACACTAGT 59.768 50.000 0.00 0.00 0.00 2.57
3416 3536 2.886081 CTCACAGCTAAGCCACACTAG 58.114 52.381 0.00 0.00 0.00 2.57
3417 3537 1.066858 GCTCACAGCTAAGCCACACTA 60.067 52.381 4.06 0.00 38.45 2.74
3418 3538 0.321122 GCTCACAGCTAAGCCACACT 60.321 55.000 4.06 0.00 38.45 3.55
3419 3539 2.166270 GCTCACAGCTAAGCCACAC 58.834 57.895 4.06 0.00 38.45 3.82
3420 3540 4.701663 GCTCACAGCTAAGCCACA 57.298 55.556 4.06 0.00 38.45 4.17
3467 3748 3.617284 AGAACAAAACCGAACAAGGAGT 58.383 40.909 0.00 0.00 34.73 3.85
3478 3759 6.040504 ACCTGGAGTATTTCAAGAACAAAACC 59.959 38.462 0.00 0.00 0.00 3.27
3483 3764 7.921786 CATTACCTGGAGTATTTCAAGAACA 57.078 36.000 0.00 0.00 0.00 3.18
3499 3780 4.923893 TCGTACGTATGAACCATTACCTG 58.076 43.478 15.05 0.00 0.00 4.00
3500 3781 4.037208 CCTCGTACGTATGAACCATTACCT 59.963 45.833 17.76 0.00 0.00 3.08
3502 3783 5.173774 TCCTCGTACGTATGAACCATTAC 57.826 43.478 17.76 0.00 0.00 1.89
3503 3784 6.039605 TCAATCCTCGTACGTATGAACCATTA 59.960 38.462 17.76 1.52 0.00 1.90
3504 3785 4.931661 ATCCTCGTACGTATGAACCATT 57.068 40.909 17.76 0.31 0.00 3.16
3505 3786 4.340097 TCAATCCTCGTACGTATGAACCAT 59.660 41.667 17.76 7.71 0.00 3.55
3508 3789 5.575957 TCTTCAATCCTCGTACGTATGAAC 58.424 41.667 17.76 0.00 0.00 3.18
3567 3848 9.668497 GGAGTTTATGTTCTTTTGTCTAGGTAT 57.332 33.333 0.00 0.00 0.00 2.73
3568 3849 8.098912 GGGAGTTTATGTTCTTTTGTCTAGGTA 58.901 37.037 0.00 0.00 0.00 3.08
3569 3850 6.940867 GGGAGTTTATGTTCTTTTGTCTAGGT 59.059 38.462 0.00 0.00 0.00 3.08
3570 3851 6.940298 TGGGAGTTTATGTTCTTTTGTCTAGG 59.060 38.462 0.00 0.00 0.00 3.02
3571 3852 7.979444 TGGGAGTTTATGTTCTTTTGTCTAG 57.021 36.000 0.00 0.00 0.00 2.43
3572 3853 8.754991 TTTGGGAGTTTATGTTCTTTTGTCTA 57.245 30.769 0.00 0.00 0.00 2.59
3599 4101 6.673106 TGTGCAACATTGTACGTCAAATATT 58.327 32.000 8.09 0.00 45.67 1.28
3601 4103 5.674933 TGTGCAACATTGTACGTCAAATA 57.325 34.783 8.09 0.00 45.67 1.40
3602 4104 4.560136 TGTGCAACATTGTACGTCAAAT 57.440 36.364 8.09 0.00 45.67 2.32
3639 4141 8.758633 TTGTAACTTTGTAGCATCTCTAGAAC 57.241 34.615 0.00 0.00 31.19 3.01


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

AutoCloner maintained by Alex Coulton.