Multiple sequence alignment - TraesCS2B01G334900

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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 TraesCS2B01G334900 chr2B 100.000 4309 0 0 1 4309 478194794 478190486 0.000000e+00 7958.0
1 TraesCS2B01G334900 chr2B 83.955 268 41 2 3803 4070 90663257 90662992 5.530000e-64 255.0
2 TraesCS2B01G334900 chr2D 89.077 2243 132 58 1861 4061 404126583 404124412 0.000000e+00 2680.0
3 TraesCS2B01G334900 chr2D 90.205 1899 96 46 1 1859 404128483 404126635 0.000000e+00 2394.0
4 TraesCS2B01G334900 chr2D 85.263 285 30 9 3788 4070 57273038 57272764 2.540000e-72 283.0
5 TraesCS2B01G334900 chr2D 87.671 219 23 4 3804 4020 607641497 607641281 7.150000e-63 252.0
6 TraesCS2B01G334900 chr2A 92.962 1222 59 14 653 1856 542557902 542556690 0.000000e+00 1755.0
7 TraesCS2B01G334900 chr2A 92.222 1080 51 16 2600 3665 542555810 542554750 0.000000e+00 1498.0
8 TraesCS2B01G334900 chr2A 92.978 712 32 10 1861 2567 542556633 542555935 0.000000e+00 1022.0
9 TraesCS2B01G334900 chr2A 84.600 487 38 17 3754 4235 542554469 542554015 2.360000e-122 449.0
10 TraesCS2B01G334900 chr2A 81.272 283 46 6 3788 4070 58465565 58465290 5.610000e-54 222.0
11 TraesCS2B01G334900 chr6D 89.498 219 19 4 3804 4020 434444155 434443939 1.530000e-69 274.0
12 TraesCS2B01G334900 chr6D 88.732 213 22 2 3819 4030 429353488 429353699 4.270000e-65 259.0
13 TraesCS2B01G334900 chr6D 87.671 219 23 4 3804 4020 434450350 434450134 7.150000e-63 252.0
14 TraesCS2B01G334900 chr5B 85.333 75 10 1 2617 2690 9580148 9580222 4.620000e-10 76.8
15 TraesCS2B01G334900 chr5B 85.333 75 10 1 2617 2690 326960110 326960184 4.620000e-10 76.8


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 TraesCS2B01G334900 chr2B 478190486 478194794 4308 True 7958 7958 100.0000 1 4309 1 chr2B.!!$R2 4308
1 TraesCS2B01G334900 chr2D 404124412 404128483 4071 True 2537 2680 89.6410 1 4061 2 chr2D.!!$R3 4060
2 TraesCS2B01G334900 chr2A 542554015 542557902 3887 True 1181 1755 90.6905 653 4235 4 chr2A.!!$R2 3582

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
108 111 0.107654 GGAGAATTGGAGGACGGTGG 60.108 60.000 0.0 0.0 0.00 4.61 F
297 312 0.838122 ATCCATCCTAAGGGCTCCCG 60.838 60.000 0.0 0.0 41.95 5.14 F
1426 1459 1.066143 GCGATGAGGTCAAGGAGGAAA 60.066 52.381 0.0 0.0 0.00 3.13 F
1858 1902 0.314935 AAACCCGCTGCTTGAACATG 59.685 50.000 0.0 0.0 0.00 3.21 F
3155 3362 0.174389 CTCTGCTGCGTACACTGGAT 59.826 55.000 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1826 1.004560 TCACGGCAGCTTCCTTCTG 60.005 57.895 0.00 0.00 34.79 3.02 R
1815 1853 1.411977 CCACCACAATTCACAAAGGCA 59.588 47.619 0.00 0.00 0.00 4.75 R
2437 2540 0.178975 AAAAACCAGGACCGGCATCA 60.179 50.000 0.00 0.00 0.00 3.07 R
3249 3456 0.455295 CCACTGCTCGAGTTCTCGTC 60.455 60.000 15.13 13.56 29.75 4.20 R
4206 4666 0.030092 TTGGATACCTCCCCTCCCAG 60.030 60.000 0.00 0.00 41.29 4.45 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
75 78 6.003326 GGAAATTTTGGACAAAATGGACCAT 58.997 36.000 20.08 0.00 46.76 3.55
95 98 5.786121 CATACATATGGGGAAGGGAGAAT 57.214 43.478 7.80 0.00 0.00 2.40
105 108 0.912486 AAGGGAGAATTGGAGGACGG 59.088 55.000 0.00 0.00 0.00 4.79
106 109 0.252742 AGGGAGAATTGGAGGACGGT 60.253 55.000 0.00 0.00 0.00 4.83
108 111 0.107654 GGAGAATTGGAGGACGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
129 132 3.396260 TGGACGTCCACTTTTTAGAGG 57.604 47.619 33.23 0.00 42.01 3.69
136 139 4.579869 GTCCACTTTTTAGAGGCAGATGA 58.420 43.478 0.00 0.00 0.00 2.92
156 159 8.890718 CAGATGATATTTATCCATGGACATGTC 58.109 37.037 18.99 17.91 37.11 3.06
157 160 8.051535 AGATGATATTTATCCATGGACATGTCC 58.948 37.037 33.97 33.97 39.77 4.02
158 161 7.089106 TGATATTTATCCATGGACATGTCCA 57.911 36.000 41.86 41.86 46.08 4.02
160 163 7.421147 TGATATTTATCCATGGACATGTCCACA 60.421 37.037 42.55 30.49 45.49 4.17
172 175 4.637276 ACATGTCCACAAACATACGAAGA 58.363 39.130 0.00 0.00 37.78 2.87
175 178 4.699637 TGTCCACAAACATACGAAGACTT 58.300 39.130 0.00 0.00 0.00 3.01
177 180 5.924254 TGTCCACAAACATACGAAGACTTAG 59.076 40.000 0.00 0.00 0.00 2.18
208 211 2.024080 TGCCCTTTGAGATGCCCTTATT 60.024 45.455 0.00 0.00 0.00 1.40
211 214 4.038042 GCCCTTTGAGATGCCCTTATTAAC 59.962 45.833 0.00 0.00 0.00 2.01
245 248 6.790285 ATGAAATTTGCAGCGAAAAATCTT 57.210 29.167 0.00 0.00 0.00 2.40
296 311 1.074566 CAATCCATCCTAAGGGCTCCC 59.925 57.143 0.00 0.00 0.00 4.30
297 312 0.838122 ATCCATCCTAAGGGCTCCCG 60.838 60.000 0.00 0.00 41.95 5.14
298 313 2.427753 CATCCTAAGGGCTCCCGC 59.572 66.667 0.00 0.00 41.95 6.13
318 333 2.867472 CGTGACCCACCAAATCGC 59.133 61.111 0.00 0.00 0.00 4.58
359 374 1.683385 GCCCAGACAATATTTGCCCTC 59.317 52.381 0.00 0.00 0.00 4.30
388 403 2.866156 AGTCATCAATATTGCGGACACG 59.134 45.455 26.84 2.61 44.63 4.49
389 404 2.863740 GTCATCAATATTGCGGACACGA 59.136 45.455 23.28 3.85 44.60 4.35
390 405 3.060272 GTCATCAATATTGCGGACACGAG 60.060 47.826 23.28 0.00 44.60 4.18
391 406 1.286501 TCAATATTGCGGACACGAGC 58.713 50.000 10.76 0.00 44.60 5.03
396 411 4.999212 TGCGGACACGAGCAAATA 57.001 50.000 0.00 0.00 44.60 1.40
398 413 1.732941 TGCGGACACGAGCAAATATT 58.267 45.000 0.00 0.00 44.60 1.28
399 414 2.080693 TGCGGACACGAGCAAATATTT 58.919 42.857 0.00 0.00 44.60 1.40
415 430 8.751335 AGCAAATATTTAAAATCGCATAAACCG 58.249 29.630 0.00 0.00 0.00 4.44
427 442 3.622163 CGCATAAACCGGTACCAAACATA 59.378 43.478 8.00 0.00 0.00 2.29
428 443 4.260456 CGCATAAACCGGTACCAAACATAG 60.260 45.833 8.00 0.00 0.00 2.23
429 444 4.637091 GCATAAACCGGTACCAAACATAGT 59.363 41.667 8.00 0.00 0.00 2.12
430 445 5.816777 GCATAAACCGGTACCAAACATAGTA 59.183 40.000 8.00 0.00 0.00 1.82
431 446 6.238184 GCATAAACCGGTACCAAACATAGTAC 60.238 42.308 8.00 0.00 38.49 2.73
432 447 4.888326 AACCGGTACCAAACATAGTACA 57.112 40.909 8.00 0.00 40.51 2.90
453 471 4.697352 ACATAGTGATTTGGAGAAGTGCAC 59.303 41.667 9.40 9.40 0.00 4.57
476 494 1.134250 TGCAGACACACCAACTTAGCA 60.134 47.619 0.00 0.00 0.00 3.49
488 507 4.227300 ACCAACTTAGCATTAGACCCATCA 59.773 41.667 0.00 0.00 0.00 3.07
609 633 5.456921 ACACCCAATTCTATCTGTCCATT 57.543 39.130 0.00 0.00 0.00 3.16
610 634 5.831103 ACACCCAATTCTATCTGTCCATTT 58.169 37.500 0.00 0.00 0.00 2.32
611 635 6.969043 ACACCCAATTCTATCTGTCCATTTA 58.031 36.000 0.00 0.00 0.00 1.40
612 636 7.056635 ACACCCAATTCTATCTGTCCATTTAG 58.943 38.462 0.00 0.00 0.00 1.85
613 637 7.056635 CACCCAATTCTATCTGTCCATTTAGT 58.943 38.462 0.00 0.00 0.00 2.24
614 638 8.210946 CACCCAATTCTATCTGTCCATTTAGTA 58.789 37.037 0.00 0.00 0.00 1.82
616 640 9.224267 CCCAATTCTATCTGTCCATTTAGTATG 57.776 37.037 0.00 0.00 0.00 2.39
617 641 9.224267 CCAATTCTATCTGTCCATTTAGTATGG 57.776 37.037 0.00 0.00 40.48 2.74
628 652 9.337396 TGTCCATTTAGTATGGTCAATTATGTC 57.663 33.333 3.89 0.00 40.06 3.06
674 698 1.218316 GTGGACCGCCTAGGAGTTG 59.782 63.158 14.75 0.00 45.00 3.16
714 740 4.615949 CAGTTTACTGATCTGATCTCCCG 58.384 47.826 17.82 7.11 46.59 5.14
810 841 2.181021 GCGTCGATCCGTTGGAGT 59.819 61.111 0.00 0.00 34.05 3.85
981 1012 2.051345 CAAACACGGCGAGTTGGC 60.051 61.111 22.61 0.00 40.44 4.52
1211 1244 2.040464 AGGGTGGCGGATGGAGAT 60.040 61.111 0.00 0.00 0.00 2.75
1361 1394 4.187056 GGAGACGGAAAAGGCGAG 57.813 61.111 0.00 0.00 0.00 5.03
1426 1459 1.066143 GCGATGAGGTCAAGGAGGAAA 60.066 52.381 0.00 0.00 0.00 3.13
1674 1707 4.770362 TCCCAGGGCACGATCCGA 62.770 66.667 0.00 0.00 0.00 4.55
1788 1826 4.938226 AGTTCTTGGTTTCATGCTAGTAGC 59.062 41.667 15.56 15.56 42.82 3.58
1814 1852 2.432456 GCTGCCGTGACATGTCGA 60.432 61.111 20.54 7.55 0.00 4.20
1815 1853 1.811266 GCTGCCGTGACATGTCGAT 60.811 57.895 20.54 0.00 0.00 3.59
1816 1854 2.001357 CTGCCGTGACATGTCGATG 58.999 57.895 20.54 14.07 35.49 3.84
1818 1856 2.813179 GCCGTGACATGTCGATGCC 61.813 63.158 20.54 4.69 32.14 4.40
1819 1857 1.153568 CCGTGACATGTCGATGCCT 60.154 57.895 20.54 0.00 32.14 4.75
1835 1877 1.411977 TGCCTTTGTGAATTGTGGTGG 59.588 47.619 0.00 0.00 0.00 4.61
1856 1900 0.820871 AAAAACCCGCTGCTTGAACA 59.179 45.000 0.00 0.00 0.00 3.18
1857 1901 1.039856 AAAACCCGCTGCTTGAACAT 58.960 45.000 0.00 0.00 0.00 2.71
1858 1902 0.314935 AAACCCGCTGCTTGAACATG 59.685 50.000 0.00 0.00 0.00 3.21
1901 1997 7.690952 ATTGCCAATTTTGCATCAATAGTTT 57.309 28.000 0.53 0.00 38.76 2.66
1917 2013 7.331026 TCAATAGTTTGGGAGACTCATAGTTG 58.669 38.462 4.53 0.00 33.44 3.16
1921 2017 3.199442 TGGGAGACTCATAGTTGGGAA 57.801 47.619 4.53 0.00 0.00 3.97
1933 2029 3.477210 AGTTGGGAACTGTGAGAACTC 57.523 47.619 0.00 0.00 41.01 3.01
1948 2049 8.096621 TGTGAGAACTCATATATTTGGGGTAA 57.903 34.615 7.77 0.00 42.18 2.85
1949 2050 8.723365 TGTGAGAACTCATATATTTGGGGTAAT 58.277 33.333 7.77 0.00 42.18 1.89
2053 2155 1.065926 GTGATCAGGCACCAGTGATGA 60.066 52.381 0.99 5.37 33.43 2.92
2076 2178 8.039603 TGACACTGTGAAATCCATGTTTATAC 57.960 34.615 15.86 0.00 0.00 1.47
2108 2210 1.825474 GTAGGTGGCAGCTCACTTCTA 59.175 52.381 24.23 0.00 37.75 2.10
2110 2212 1.912043 AGGTGGCAGCTCACTTCTATT 59.088 47.619 14.51 0.00 37.75 1.73
2111 2213 3.107601 AGGTGGCAGCTCACTTCTATTA 58.892 45.455 14.51 0.00 37.75 0.98
2112 2214 3.519510 AGGTGGCAGCTCACTTCTATTAA 59.480 43.478 14.51 0.00 37.75 1.40
2164 2266 7.328005 CCTCCTACGTTTTTAGTCTTACAGAAC 59.672 40.741 0.00 0.00 0.00 3.01
2281 2383 4.778213 ATTTGCTACTGAAGGGCATCTA 57.222 40.909 0.00 0.00 35.84 1.98
2329 2432 7.092137 TGATCTGCTATTTTGATTTGACAGG 57.908 36.000 0.00 0.00 0.00 4.00
2595 2799 7.533289 AGAAGATTAGGACTATAACTCTGCC 57.467 40.000 0.00 0.00 0.00 4.85
2596 2800 7.302184 AGAAGATTAGGACTATAACTCTGCCT 58.698 38.462 0.00 0.00 0.00 4.75
2597 2801 6.909550 AGATTAGGACTATAACTCTGCCTG 57.090 41.667 0.00 0.00 0.00 4.85
2598 2802 6.377912 AGATTAGGACTATAACTCTGCCTGT 58.622 40.000 0.00 0.00 0.00 4.00
2618 2822 6.989169 GCCTGTGATACTTCTCTATGACATTT 59.011 38.462 0.00 0.00 0.00 2.32
2651 2855 2.566833 TGCTCTGTTATGTGCCAGTT 57.433 45.000 0.00 0.00 0.00 3.16
2685 2889 6.310711 GGTACTACATCTTTTCTTTCCTGTCG 59.689 42.308 0.00 0.00 0.00 4.35
2727 2931 5.104374 CCTAATTTACCATTGCTGCAACTG 58.896 41.667 18.51 15.70 0.00 3.16
2730 2934 5.720371 ATTTACCATTGCTGCAACTGTTA 57.280 34.783 18.51 8.77 0.00 2.41
2907 3111 2.484264 GTGTTGGACATCAGTTACTGCC 59.516 50.000 7.61 3.70 0.00 4.85
2991 3198 1.613630 AGGAACATGCCTCCGGAGT 60.614 57.895 29.25 10.39 38.08 3.85
2993 3200 1.153349 GAACATGCCTCCGGAGTCC 60.153 63.158 29.25 19.70 0.00 3.85
3155 3362 0.174389 CTCTGCTGCGTACACTGGAT 59.826 55.000 0.00 0.00 0.00 3.41
3194 3401 2.034879 CAGGCTTGACGGCGACATT 61.035 57.895 16.62 0.00 44.22 2.71
3249 3456 0.886490 GCCATGGGAGCCTGATTACG 60.886 60.000 15.13 0.00 0.00 3.18
3293 3500 3.545624 GCGATTACGACTACGATGACACT 60.546 47.826 0.00 0.00 42.66 3.55
3350 3559 0.677288 GGCTAAACGGCTGGGTTTTT 59.323 50.000 0.00 0.00 40.41 1.94
3351 3560 1.604438 GGCTAAACGGCTGGGTTTTTG 60.604 52.381 0.00 0.00 40.41 2.44
3388 3597 2.827921 CTGCAGGCTTCCTTTTGGTTAT 59.172 45.455 5.57 0.00 41.38 1.89
3389 3598 3.238597 TGCAGGCTTCCTTTTGGTTATT 58.761 40.909 0.00 0.00 41.38 1.40
3458 3669 2.543777 TTTTAGCTTGGCGTCTGTCT 57.456 45.000 0.00 0.00 0.00 3.41
3520 3758 5.841957 GGATTGATCCTGCAATGTTACTT 57.158 39.130 2.72 0.00 43.73 2.24
3521 3759 6.212888 GGATTGATCCTGCAATGTTACTTT 57.787 37.500 2.72 0.00 43.73 2.66
3522 3760 6.038356 GGATTGATCCTGCAATGTTACTTTG 58.962 40.000 6.61 6.61 43.73 2.77
3523 3761 5.389859 TTGATCCTGCAATGTTACTTTGG 57.610 39.130 11.92 0.00 0.00 3.28
3524 3762 4.661222 TGATCCTGCAATGTTACTTTGGA 58.339 39.130 11.92 8.66 0.00 3.53
3525 3763 5.076182 TGATCCTGCAATGTTACTTTGGAA 58.924 37.500 11.92 0.00 0.00 3.53
3526 3764 5.538053 TGATCCTGCAATGTTACTTTGGAAA 59.462 36.000 11.92 2.52 0.00 3.13
3527 3765 5.452078 TCCTGCAATGTTACTTTGGAAAG 57.548 39.130 11.92 0.00 41.73 2.62
3528 3766 5.136828 TCCTGCAATGTTACTTTGGAAAGA 58.863 37.500 11.92 6.86 39.31 2.52
3529 3767 5.241506 TCCTGCAATGTTACTTTGGAAAGAG 59.758 40.000 11.92 0.00 39.31 2.85
3530 3768 5.241506 CCTGCAATGTTACTTTGGAAAGAGA 59.758 40.000 11.92 0.00 39.31 3.10
3531 3769 6.239008 CCTGCAATGTTACTTTGGAAAGAGAA 60.239 38.462 11.92 0.00 39.31 2.87
3532 3770 6.503524 TGCAATGTTACTTTGGAAAGAGAAC 58.496 36.000 11.92 9.48 39.31 3.01
3533 3771 5.625311 GCAATGTTACTTTGGAAAGAGAACG 59.375 40.000 11.92 0.00 37.77 3.95
3534 3772 6.725246 CAATGTTACTTTGGAAAGAGAACGT 58.275 36.000 6.13 7.92 37.77 3.99
3535 3773 5.728351 TGTTACTTTGGAAAGAGAACGTG 57.272 39.130 6.13 0.00 37.77 4.49
3536 3774 5.180271 TGTTACTTTGGAAAGAGAACGTGT 58.820 37.500 6.13 0.00 37.77 4.49
3537 3775 5.292589 TGTTACTTTGGAAAGAGAACGTGTC 59.707 40.000 6.13 0.00 37.77 3.67
3538 3776 4.138487 ACTTTGGAAAGAGAACGTGTCT 57.862 40.909 6.13 0.00 39.31 3.41
3539 3777 4.514401 ACTTTGGAAAGAGAACGTGTCTT 58.486 39.130 6.13 7.46 39.31 3.01
3540 3778 4.941873 ACTTTGGAAAGAGAACGTGTCTTT 59.058 37.500 20.58 20.58 45.05 2.52
3541 3779 4.875544 TTGGAAAGAGAACGTGTCTTTG 57.124 40.909 23.84 0.00 42.95 2.77
3542 3780 3.869065 TGGAAAGAGAACGTGTCTTTGT 58.131 40.909 23.84 7.59 42.95 2.83
3580 3820 1.434696 GGGATTTGGCATGTGCTCG 59.565 57.895 4.84 0.00 41.70 5.03
3582 3822 1.378531 GGATTTGGCATGTGCTCGTA 58.621 50.000 4.84 0.00 41.70 3.43
3605 3848 7.481798 CGTAATTGTTCCTGAATGCTACTTTTC 59.518 37.037 0.00 0.00 0.00 2.29
3672 4081 0.251077 AGGTGCTGCTTTTCTGGAGG 60.251 55.000 0.00 0.00 0.00 4.30
3697 4106 6.143919 GCCAAATGTTTAAGAGCAAGTGTTAC 59.856 38.462 0.00 0.00 0.00 2.50
3698 4107 6.640907 CCAAATGTTTAAGAGCAAGTGTTACC 59.359 38.462 0.00 0.00 0.00 2.85
3709 4118 4.833380 AGCAAGTGTTACCAGAAGACTAGA 59.167 41.667 0.00 0.00 0.00 2.43
3711 4120 6.014156 AGCAAGTGTTACCAGAAGACTAGAAT 60.014 38.462 0.00 0.00 0.00 2.40
3713 4122 7.489757 GCAAGTGTTACCAGAAGACTAGAATAG 59.510 40.741 0.00 0.00 46.50 1.73
3714 4123 8.740906 CAAGTGTTACCAGAAGACTAGAATAGA 58.259 37.037 0.00 0.00 42.77 1.98
3716 4125 8.110908 AGTGTTACCAGAAGACTAGAATAGAGT 58.889 37.037 0.00 0.00 42.77 3.24
3727 4136 9.908747 AAGACTAGAATAGAGTAAGCTCAGTTA 57.091 33.333 0.00 0.00 42.77 2.24
3728 4137 9.908747 AGACTAGAATAGAGTAAGCTCAGTTAA 57.091 33.333 0.00 0.00 42.77 2.01
3784 4241 5.662211 AATTCATGAACAAAAAGCAGCAC 57.338 34.783 11.07 0.00 0.00 4.40
3789 4246 7.155655 TCATGAACAAAAAGCAGCACATATA 57.844 32.000 0.00 0.00 0.00 0.86
3882 4340 1.100510 TTATGACGTCCACTCTCCCG 58.899 55.000 14.12 0.00 0.00 5.14
3901 4359 0.255890 GCTTGGGGAGATGGTAAGCA 59.744 55.000 0.00 0.00 42.35 3.91
3904 4362 1.668826 TGGGGAGATGGTAAGCAAGT 58.331 50.000 0.00 0.00 0.00 3.16
3946 4404 1.056700 ACCACTAGCCTAGGCCATGG 61.057 60.000 32.43 32.43 43.17 3.66
3991 4449 4.498241 CCCGTCCAGGTAAGTAAGTTTAC 58.502 47.826 0.00 0.00 38.74 2.01
3992 4450 4.168760 CCGTCCAGGTAAGTAAGTTTACG 58.831 47.826 0.00 0.00 34.97 3.18
3995 4453 3.515104 TCCAGGTAAGTAAGTTTACGGGG 59.485 47.826 0.00 0.00 38.65 5.73
4001 4459 0.671472 GTAAGTTTACGGGGCGCACT 60.671 55.000 10.74 0.00 0.00 4.40
4005 4463 1.153329 TTTACGGGGCGCACTATGG 60.153 57.895 10.74 0.00 0.00 2.74
4010 4468 2.124736 GGGCGCACTATGGCTTGA 60.125 61.111 10.83 0.00 0.00 3.02
4031 4489 1.263356 TATATAGCACAGTCCCCGGC 58.737 55.000 0.00 0.00 0.00 6.13
4086 4544 8.197988 CTAAACAAGTTTAGCGACCTAATGAT 57.802 34.615 16.95 0.00 43.52 2.45
4095 4555 7.703058 TTAGCGACCTAATGATCTGATGATA 57.297 36.000 0.00 0.00 32.19 2.15
4104 4564 9.080915 CCTAATGATCTGATGATATGTAACGTG 57.919 37.037 0.00 0.00 32.19 4.49
4105 4565 7.895975 AATGATCTGATGATATGTAACGTGG 57.104 36.000 0.00 0.00 32.19 4.94
4106 4566 6.405278 TGATCTGATGATATGTAACGTGGT 57.595 37.500 0.00 0.00 32.19 4.16
4107 4567 6.215845 TGATCTGATGATATGTAACGTGGTG 58.784 40.000 0.00 0.00 32.19 4.17
4108 4568 4.368315 TCTGATGATATGTAACGTGGTGC 58.632 43.478 0.00 0.00 0.00 5.01
4109 4569 4.099419 TCTGATGATATGTAACGTGGTGCT 59.901 41.667 0.00 0.00 0.00 4.40
4110 4570 5.300792 TCTGATGATATGTAACGTGGTGCTA 59.699 40.000 0.00 0.00 0.00 3.49
4111 4571 5.286438 TGATGATATGTAACGTGGTGCTAC 58.714 41.667 0.00 0.00 0.00 3.58
4112 4572 4.049546 TGATATGTAACGTGGTGCTACC 57.950 45.455 0.00 0.00 39.22 3.18
4120 4580 3.238497 TGGTGCTACCACTGGCGT 61.238 61.111 4.16 0.00 44.79 5.68
4121 4581 2.742372 GGTGCTACCACTGGCGTG 60.742 66.667 0.00 3.06 41.75 5.34
4122 4582 2.030562 GTGCTACCACTGGCGTGT 59.969 61.111 0.00 0.00 39.55 4.49
4123 4583 1.597027 GTGCTACCACTGGCGTGTT 60.597 57.895 0.00 0.00 39.55 3.32
4124 4584 0.320073 GTGCTACCACTGGCGTGTTA 60.320 55.000 0.00 0.00 39.55 2.41
4125 4585 0.320073 TGCTACCACTGGCGTGTTAC 60.320 55.000 0.00 0.00 39.55 2.50
4126 4586 1.017701 GCTACCACTGGCGTGTTACC 61.018 60.000 0.00 0.00 39.55 2.85
4127 4587 0.319083 CTACCACTGGCGTGTTACCA 59.681 55.000 0.00 0.00 39.55 3.25
4128 4588 0.033781 TACCACTGGCGTGTTACCAC 59.966 55.000 0.00 0.00 39.55 4.16
4129 4589 1.964373 CCACTGGCGTGTTACCACC 60.964 63.158 8.28 0.00 39.55 4.61
4166 4626 0.542702 CCCAAACATGGGCCTTCAGT 60.543 55.000 4.53 0.00 42.99 3.41
4167 4627 1.341080 CCAAACATGGGCCTTCAGTT 58.659 50.000 4.53 1.17 0.00 3.16
4169 4629 1.001181 CAAACATGGGCCTTCAGTTGG 59.999 52.381 4.53 0.00 0.00 3.77
4203 4663 0.944311 CTCCAACTGTCCAACCGTCG 60.944 60.000 0.00 0.00 0.00 5.12
4206 4666 1.068585 AACTGTCCAACCGTCGTCC 59.931 57.895 0.00 0.00 0.00 4.79
4207 4667 1.397390 AACTGTCCAACCGTCGTCCT 61.397 55.000 0.00 0.00 0.00 3.85
4209 4669 2.048503 GTCCAACCGTCGTCCTGG 60.049 66.667 0.00 0.00 0.00 4.45
4210 4670 3.307906 TCCAACCGTCGTCCTGGG 61.308 66.667 0.00 0.00 0.00 4.45
4211 4671 3.307906 CCAACCGTCGTCCTGGGA 61.308 66.667 0.00 0.00 0.00 4.37
4212 4672 2.261671 CAACCGTCGTCCTGGGAG 59.738 66.667 0.00 0.00 0.00 4.30
4235 4695 4.001618 GGAGGTATCCAATCAGAGAAGC 57.998 50.000 0.00 0.00 45.87 3.86
4236 4696 3.553922 GGAGGTATCCAATCAGAGAAGCG 60.554 52.174 0.00 0.00 45.87 4.68
4237 4697 2.366916 AGGTATCCAATCAGAGAAGCGG 59.633 50.000 0.00 0.00 0.00 5.52
4238 4698 2.139118 GTATCCAATCAGAGAAGCGGC 58.861 52.381 0.00 0.00 0.00 6.53
4239 4699 0.543277 ATCCAATCAGAGAAGCGGCA 59.457 50.000 1.45 0.00 0.00 5.69
4240 4700 0.107993 TCCAATCAGAGAAGCGGCAG 60.108 55.000 1.45 0.00 0.00 4.85
4241 4701 0.107993 CCAATCAGAGAAGCGGCAGA 60.108 55.000 1.45 0.00 0.00 4.26
4242 4702 1.288350 CAATCAGAGAAGCGGCAGAG 58.712 55.000 1.45 0.00 0.00 3.35
4243 4703 0.177604 AATCAGAGAAGCGGCAGAGG 59.822 55.000 1.45 0.00 0.00 3.69
4244 4704 2.308968 ATCAGAGAAGCGGCAGAGGC 62.309 60.000 1.45 0.00 40.13 4.70
4245 4705 2.999648 AGAGAAGCGGCAGAGGCA 61.000 61.111 1.45 0.00 43.71 4.75
4246 4706 2.046892 GAGAAGCGGCAGAGGCAA 60.047 61.111 1.45 0.00 43.71 4.52
4247 4707 1.672356 GAGAAGCGGCAGAGGCAAA 60.672 57.895 1.45 0.00 43.71 3.68
4248 4708 1.916697 GAGAAGCGGCAGAGGCAAAC 61.917 60.000 1.45 0.00 43.71 2.93
4249 4709 2.982744 GAAGCGGCAGAGGCAAACC 61.983 63.158 1.45 0.00 43.71 3.27
4252 4712 3.365265 CGGCAGAGGCAAACCCAC 61.365 66.667 0.00 0.00 43.71 4.61
4253 4713 2.203480 GGCAGAGGCAAACCCACA 60.203 61.111 0.00 0.00 43.71 4.17
4254 4714 2.564721 GGCAGAGGCAAACCCACAC 61.565 63.158 0.00 0.00 43.71 3.82
4255 4715 2.908073 GCAGAGGCAAACCCACACG 61.908 63.158 0.00 0.00 40.72 4.49
4256 4716 2.594592 AGAGGCAAACCCACACGC 60.595 61.111 0.00 0.00 36.11 5.34
4257 4717 2.904866 GAGGCAAACCCACACGCA 60.905 61.111 0.00 0.00 36.11 5.24
4258 4718 3.194272 GAGGCAAACCCACACGCAC 62.194 63.158 0.00 0.00 36.11 5.34
4259 4719 4.622456 GGCAAACCCACACGCACG 62.622 66.667 0.00 0.00 0.00 5.34
4261 4721 4.622456 CAAACCCACACGCACGCC 62.622 66.667 0.00 0.00 0.00 5.68
4266 4726 4.444024 CCACACGCACGCCGATTG 62.444 66.667 2.93 0.06 41.02 2.67
4267 4727 4.444024 CACACGCACGCCGATTGG 62.444 66.667 2.93 0.00 41.02 3.16
4273 4733 2.745884 CACGCCGATTGGGAGCAA 60.746 61.111 0.00 0.00 39.59 3.91
4274 4734 2.436646 ACGCCGATTGGGAGCAAG 60.437 61.111 0.00 0.00 39.59 4.01
4275 4735 2.436646 CGCCGATTGGGAGCAAGT 60.437 61.111 0.00 0.00 38.47 3.16
4276 4736 2.753966 CGCCGATTGGGAGCAAGTG 61.754 63.158 0.00 0.00 38.47 3.16
4277 4737 1.377202 GCCGATTGGGAGCAAGTGA 60.377 57.895 0.00 0.00 38.47 3.41
4278 4738 1.372087 GCCGATTGGGAGCAAGTGAG 61.372 60.000 0.00 0.00 38.47 3.51
4279 4739 0.745845 CCGATTGGGAGCAAGTGAGG 60.746 60.000 0.00 0.00 38.47 3.86
4280 4740 0.745845 CGATTGGGAGCAAGTGAGGG 60.746 60.000 0.00 0.00 0.00 4.30
4281 4741 0.394899 GATTGGGAGCAAGTGAGGGG 60.395 60.000 0.00 0.00 0.00 4.79
4282 4742 0.846427 ATTGGGAGCAAGTGAGGGGA 60.846 55.000 0.00 0.00 0.00 4.81
4283 4743 1.492133 TTGGGAGCAAGTGAGGGGAG 61.492 60.000 0.00 0.00 0.00 4.30
4284 4744 2.674220 GGGAGCAAGTGAGGGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
4285 4745 2.674220 GGAGCAAGTGAGGGGAGGG 61.674 68.421 0.00 0.00 0.00 4.30
4286 4746 2.612115 AGCAAGTGAGGGGAGGGG 60.612 66.667 0.00 0.00 0.00 4.79
4287 4747 4.432741 GCAAGTGAGGGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
4288 4748 2.935481 CAAGTGAGGGGAGGGGCA 60.935 66.667 0.00 0.00 0.00 5.36
4289 4749 2.612115 AAGTGAGGGGAGGGGCAG 60.612 66.667 0.00 0.00 0.00 4.85
4290 4750 4.748798 AGTGAGGGGAGGGGCAGG 62.749 72.222 0.00 0.00 0.00 4.85
4297 4757 4.828296 GGAGGGGCAGGCATGGTG 62.828 72.222 0.00 0.00 0.00 4.17
4298 4758 3.731728 GAGGGGCAGGCATGGTGA 61.732 66.667 0.00 0.00 0.00 4.02
4299 4759 3.025599 AGGGGCAGGCATGGTGAT 61.026 61.111 0.00 0.00 0.00 3.06
4300 4760 2.836360 GGGGCAGGCATGGTGATG 60.836 66.667 0.00 0.00 0.00 3.07
4301 4761 2.043652 GGGCAGGCATGGTGATGT 60.044 61.111 0.00 0.00 31.50 3.06
4302 4762 2.420568 GGGCAGGCATGGTGATGTG 61.421 63.158 0.00 0.00 31.50 3.21
4303 4763 2.420568 GGCAGGCATGGTGATGTGG 61.421 63.158 0.00 0.00 31.50 4.17
4304 4764 2.420568 GCAGGCATGGTGATGTGGG 61.421 63.158 0.00 0.00 31.50 4.61
4305 4765 1.000521 CAGGCATGGTGATGTGGGT 60.001 57.895 0.00 0.00 31.50 4.51
4306 4766 1.000521 AGGCATGGTGATGTGGGTG 60.001 57.895 0.00 0.00 31.50 4.61
4307 4767 1.304381 GGCATGGTGATGTGGGTGT 60.304 57.895 0.00 0.00 31.50 4.16
4308 4768 0.899717 GGCATGGTGATGTGGGTGTT 60.900 55.000 0.00 0.00 31.50 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 45 8.688747 TTTTGTCCAAAATTTCCAATATTGCT 57.311 26.923 10.11 0.00 35.57 3.91
43 46 9.344309 CATTTTGTCCAAAATTTCCAATATTGC 57.656 29.630 13.79 0.00 45.67 3.56
44 47 9.843334 CCATTTTGTCCAAAATTTCCAATATTG 57.157 29.630 13.79 8.58 45.67 1.90
45 48 9.804977 TCCATTTTGTCCAAAATTTCCAATATT 57.195 25.926 13.79 0.00 45.67 1.28
46 49 9.230122 GTCCATTTTGTCCAAAATTTCCAATAT 57.770 29.630 13.79 0.00 45.67 1.28
47 50 7.663493 GGTCCATTTTGTCCAAAATTTCCAATA 59.337 33.333 13.79 0.00 45.67 1.90
48 51 6.489700 GGTCCATTTTGTCCAAAATTTCCAAT 59.510 34.615 13.79 0.00 45.67 3.16
49 52 5.825151 GGTCCATTTTGTCCAAAATTTCCAA 59.175 36.000 13.79 0.00 45.67 3.53
50 53 5.104360 TGGTCCATTTTGTCCAAAATTTCCA 60.104 36.000 13.79 16.65 45.67 3.53
75 78 4.353788 CCAATTCTCCCTTCCCCATATGTA 59.646 45.833 1.24 0.00 0.00 2.29
85 88 1.134371 CCGTCCTCCAATTCTCCCTTC 60.134 57.143 0.00 0.00 0.00 3.46
95 98 2.122769 TCCACCACCGTCCTCCAA 60.123 61.111 0.00 0.00 0.00 3.53
115 118 4.908601 TCATCTGCCTCTAAAAAGTGGA 57.091 40.909 0.00 0.00 0.00 4.02
129 132 7.338703 ACATGTCCATGGATAAATATCATCTGC 59.661 37.037 19.62 0.00 42.91 4.26
156 159 7.596749 AATCTAAGTCTTCGTATGTTTGTGG 57.403 36.000 0.00 0.00 0.00 4.17
168 171 7.631717 AGGGCAATGTTAAATCTAAGTCTTC 57.368 36.000 0.00 0.00 0.00 2.87
172 175 7.669722 TCTCAAAGGGCAATGTTAAATCTAAGT 59.330 33.333 0.00 0.00 0.00 2.24
175 178 7.416664 GCATCTCAAAGGGCAATGTTAAATCTA 60.417 37.037 0.00 0.00 0.00 1.98
177 180 5.521372 GCATCTCAAAGGGCAATGTTAAATC 59.479 40.000 0.00 0.00 0.00 2.17
211 214 6.951530 CGCTGCAAATTTCATTGTAAATGAAG 59.048 34.615 13.43 5.72 38.98 3.02
276 279 1.074566 GGGAGCCCTTAGGATGGATTG 59.925 57.143 0.00 0.00 33.47 2.67
297 312 2.200170 GATTTGGTGGGTCACGCTGC 62.200 60.000 0.00 0.00 34.83 5.25
298 313 1.875963 GATTTGGTGGGTCACGCTG 59.124 57.895 0.00 0.00 34.83 5.18
305 320 6.538945 AATATTAAAAGCGATTTGGTGGGT 57.461 33.333 0.00 0.00 32.27 4.51
318 333 4.226761 GCCGCCGATCCAAATATTAAAAG 58.773 43.478 0.00 0.00 0.00 2.27
335 350 0.385390 CAAATATTGTCTGGGCCGCC 59.615 55.000 0.00 0.00 0.00 6.13
359 374 4.260907 CGCAATATTGATGACTCCTGTTGG 60.261 45.833 19.73 0.00 0.00 3.77
377 392 1.732941 TATTTGCTCGTGTCCGCAAT 58.267 45.000 0.00 0.00 44.60 3.56
389 404 8.751335 CGGTTTATGCGATTTTAAATATTTGCT 58.249 29.630 11.05 0.00 0.00 3.91
390 405 8.001549 CCGGTTTATGCGATTTTAAATATTTGC 58.998 33.333 11.05 5.11 0.00 3.68
391 406 9.026074 ACCGGTTTATGCGATTTTAAATATTTG 57.974 29.630 11.05 0.00 0.00 2.32
396 411 6.095160 TGGTACCGGTTTATGCGATTTTAAAT 59.905 34.615 15.04 0.00 0.00 1.40
398 413 4.940046 TGGTACCGGTTTATGCGATTTTAA 59.060 37.500 15.04 0.00 0.00 1.52
399 414 4.511527 TGGTACCGGTTTATGCGATTTTA 58.488 39.130 15.04 0.00 0.00 1.52
415 430 9.609346 AAATCACTATGTACTATGTTTGGTACC 57.391 33.333 4.43 4.43 38.62 3.34
427 442 6.109359 GCACTTCTCCAAATCACTATGTACT 58.891 40.000 0.00 0.00 0.00 2.73
428 443 5.874810 TGCACTTCTCCAAATCACTATGTAC 59.125 40.000 0.00 0.00 0.00 2.90
429 444 5.874810 GTGCACTTCTCCAAATCACTATGTA 59.125 40.000 10.32 0.00 0.00 2.29
430 445 4.697352 GTGCACTTCTCCAAATCACTATGT 59.303 41.667 10.32 0.00 0.00 2.29
431 446 4.696877 TGTGCACTTCTCCAAATCACTATG 59.303 41.667 19.41 0.00 0.00 2.23
432 447 4.910195 TGTGCACTTCTCCAAATCACTAT 58.090 39.130 19.41 0.00 0.00 2.12
453 471 3.610114 GCTAAGTTGGTGTGTCTGCAATG 60.610 47.826 0.00 0.00 0.00 2.82
459 477 5.238583 GTCTAATGCTAAGTTGGTGTGTCT 58.761 41.667 0.00 0.00 0.00 3.41
476 494 6.271585 AGATGGATTTGTGATGGGTCTAAT 57.728 37.500 0.00 0.00 0.00 1.73
488 507 5.406163 AGAAAGGGGAAAAGATGGATTTGT 58.594 37.500 0.00 0.00 0.00 2.83
518 542 4.420206 TGTCCAATGAAGAGGAGAGAGAA 58.580 43.478 0.00 0.00 33.85 2.87
520 544 4.815533 TTGTCCAATGAAGAGGAGAGAG 57.184 45.455 0.00 0.00 33.85 3.20
590 614 9.224267 CATACTAAATGGACAGATAGAATTGGG 57.776 37.037 0.00 0.00 0.00 4.12
592 616 9.784531 ACCATACTAAATGGACAGATAGAATTG 57.215 33.333 10.90 0.00 41.64 2.32
609 633 9.693739 ATTTGTGGACATAATTGACCATACTAA 57.306 29.630 0.82 0.00 46.76 2.24
611 635 9.866655 ATATTTGTGGACATAATTGACCATACT 57.133 29.630 0.82 0.00 46.76 2.12
628 652 6.817765 ACAGACACCAGTAAATATTTGTGG 57.182 37.500 21.50 21.50 33.89 4.17
640 664 1.283613 TCCACCAAAACAGACACCAGT 59.716 47.619 0.00 0.00 0.00 4.00
641 665 1.676006 GTCCACCAAAACAGACACCAG 59.324 52.381 0.00 0.00 0.00 4.00
674 698 1.896465 CTGAGTATAGGTGGGCTAGGC 59.104 57.143 8.00 8.00 0.00 3.93
810 841 1.513373 GATGTGCGACGCGTGTCTA 60.513 57.895 25.28 12.49 43.21 2.59
891 922 0.744874 GCACATCCGGCTCACTAGTA 59.255 55.000 0.00 0.00 0.00 1.82
892 923 1.517832 GCACATCCGGCTCACTAGT 59.482 57.895 0.00 0.00 0.00 2.57
893 924 1.589993 CGCACATCCGGCTCACTAG 60.590 63.158 0.00 0.00 0.00 2.57
999 1032 1.677552 AGGGTTCCGACGCTTCATT 59.322 52.632 0.00 0.00 45.75 2.57
1211 1244 2.354729 CCACCATTTCCGCCTCCA 59.645 61.111 0.00 0.00 0.00 3.86
1395 1428 3.432051 CTCATCGCCCCTCACGTCC 62.432 68.421 0.00 0.00 0.00 4.79
1426 1459 1.136305 CGTCCACCTCCAATCGTACAT 59.864 52.381 0.00 0.00 0.00 2.29
1754 1787 1.350019 ACCAAGAACTACCTTTCGGGG 59.650 52.381 0.00 0.00 40.03 5.73
1758 1791 5.241728 AGCATGAAACCAAGAACTACCTTTC 59.758 40.000 0.00 0.00 0.00 2.62
1765 1798 4.938226 GCTACTAGCATGAAACCAAGAACT 59.062 41.667 0.00 0.00 41.89 3.01
1788 1826 1.004560 TCACGGCAGCTTCCTTCTG 60.005 57.895 0.00 0.00 34.79 3.02
1814 1852 2.037511 CCACCACAATTCACAAAGGCAT 59.962 45.455 0.00 0.00 0.00 4.40
1815 1853 1.411977 CCACCACAATTCACAAAGGCA 59.588 47.619 0.00 0.00 0.00 4.75
1816 1854 1.686052 TCCACCACAATTCACAAAGGC 59.314 47.619 0.00 0.00 0.00 4.35
1842 1886 1.503542 GACATGTTCAAGCAGCGGG 59.496 57.895 0.00 0.00 0.00 6.13
1845 1889 1.733912 TCATCGACATGTTCAAGCAGC 59.266 47.619 0.00 0.00 0.00 5.25
1856 1900 6.238211 GCAATTTTACTAGCAGTCATCGACAT 60.238 38.462 0.00 0.00 34.60 3.06
1857 1901 5.063438 GCAATTTTACTAGCAGTCATCGACA 59.937 40.000 0.00 0.00 34.60 4.35
1858 1902 5.493735 GCAATTTTACTAGCAGTCATCGAC 58.506 41.667 0.00 0.00 0.00 4.20
1901 1997 2.838202 GTTCCCAACTATGAGTCTCCCA 59.162 50.000 0.00 0.00 0.00 4.37
1917 2013 7.227512 CCAAATATATGAGTTCTCACAGTTCCC 59.772 40.741 4.58 0.00 0.00 3.97
1921 2017 6.158695 ACCCCAAATATATGAGTTCTCACAGT 59.841 38.462 4.58 0.00 0.00 3.55
2053 2155 6.876789 TCGTATAAACATGGATTTCACAGTGT 59.123 34.615 0.00 0.00 0.00 3.55
2076 2178 3.275143 TGCCACCTACAAATGGTTATCG 58.725 45.455 0.00 0.00 38.34 2.92
2164 2266 2.662006 TGGCTCTGAACTCTGATTCG 57.338 50.000 0.00 0.00 0.00 3.34
2281 2383 3.865011 TGTTCACATTTGCACACAAGT 57.135 38.095 0.00 0.00 37.04 3.16
2419 2522 4.333926 GCATCATCTGAAACTAGTGGTTCC 59.666 45.833 0.00 0.00 37.12 3.62
2437 2540 0.178975 AAAAACCAGGACCGGCATCA 60.179 50.000 0.00 0.00 0.00 3.07
2488 2591 8.948631 TCAAGAAATAGATTAGCTAGTTGGTG 57.051 34.615 0.00 0.00 37.50 4.17
2590 2794 5.300539 GTCATAGAGAAGTATCACAGGCAGA 59.699 44.000 0.00 0.00 0.00 4.26
2591 2795 5.068329 TGTCATAGAGAAGTATCACAGGCAG 59.932 44.000 0.00 0.00 0.00 4.85
2592 2796 4.956075 TGTCATAGAGAAGTATCACAGGCA 59.044 41.667 0.00 0.00 0.00 4.75
2593 2797 5.521906 TGTCATAGAGAAGTATCACAGGC 57.478 43.478 0.00 0.00 0.00 4.85
2594 2798 8.824781 CAAAATGTCATAGAGAAGTATCACAGG 58.175 37.037 0.00 0.00 0.00 4.00
2595 2799 9.376075 ACAAAATGTCATAGAGAAGTATCACAG 57.624 33.333 0.00 0.00 0.00 3.66
2596 2800 9.154847 CACAAAATGTCATAGAGAAGTATCACA 57.845 33.333 0.00 0.00 0.00 3.58
2597 2801 9.155975 ACACAAAATGTCATAGAGAAGTATCAC 57.844 33.333 0.00 0.00 36.54 3.06
2618 2822 3.156293 ACAGAGCAATGGCATTACACAA 58.844 40.909 13.23 0.00 44.61 3.33
2651 2855 5.410355 AAAGATGTAGTACCGTTAAGCCA 57.590 39.130 0.00 0.00 0.00 4.75
2764 2968 7.031372 CAGTGGAAATTAACCATCACAATCAG 58.969 38.462 7.41 0.00 39.69 2.90
2907 3111 2.266554 GCCTCTCGATGTGACTTTCAG 58.733 52.381 0.00 0.00 0.00 3.02
2993 3200 3.451894 GCATCGTTGCCTTGGGGG 61.452 66.667 7.24 0.00 43.38 5.40
3006 3213 1.740025 GACCACTTTAGGTGCTGCATC 59.260 52.381 5.27 4.79 43.38 3.91
3026 3233 4.821589 GCCAGGGCCTCGTCTTCG 62.822 72.222 0.95 0.00 35.14 3.79
3155 3362 4.842574 TGACATTCAAGCTGCCAAGTATA 58.157 39.130 0.00 0.00 0.00 1.47
3249 3456 0.455295 CCACTGCTCGAGTTCTCGTC 60.455 60.000 15.13 13.56 29.75 4.20
3293 3500 3.681417 CACAGAGTCAATCATCGCTTTCA 59.319 43.478 0.00 0.00 0.00 2.69
3350 3559 4.042062 CCTGCAGTTTCTGATATATCCCCA 59.958 45.833 13.81 0.00 32.44 4.96
3351 3560 4.583871 CCTGCAGTTTCTGATATATCCCC 58.416 47.826 13.81 0.00 32.44 4.81
3389 3598 9.979578 ACAGTAAGCATTTCAAATTGATGTTTA 57.020 25.926 0.00 0.00 0.00 2.01
3458 3669 6.108687 CACATACAGAGCAATTACCTCAGAA 58.891 40.000 7.73 0.00 0.00 3.02
3516 3754 5.272283 AGACACGTTCTCTTTCCAAAGTA 57.728 39.130 0.00 0.00 37.31 2.24
3517 3755 4.138487 AGACACGTTCTCTTTCCAAAGT 57.862 40.909 0.00 0.00 37.31 2.66
3518 3756 5.163754 ACAAAGACACGTTCTCTTTCCAAAG 60.164 40.000 12.96 6.61 36.09 2.77
3519 3757 4.698304 ACAAAGACACGTTCTCTTTCCAAA 59.302 37.500 12.96 0.00 36.09 3.28
3520 3758 4.094294 CACAAAGACACGTTCTCTTTCCAA 59.906 41.667 12.96 0.00 36.09 3.53
3521 3759 3.621268 CACAAAGACACGTTCTCTTTCCA 59.379 43.478 12.96 0.00 36.09 3.53
3522 3760 3.621715 ACACAAAGACACGTTCTCTTTCC 59.378 43.478 12.96 0.00 36.09 3.13
3523 3761 4.859629 ACACAAAGACACGTTCTCTTTC 57.140 40.909 12.96 0.00 36.09 2.62
3524 3762 4.935808 AGAACACAAAGACACGTTCTCTTT 59.064 37.500 10.84 10.84 43.43 2.52
3525 3763 4.330074 CAGAACACAAAGACACGTTCTCTT 59.670 41.667 0.00 0.19 44.69 2.85
3526 3764 3.865745 CAGAACACAAAGACACGTTCTCT 59.134 43.478 0.00 0.00 44.69 3.10
3527 3765 3.001330 CCAGAACACAAAGACACGTTCTC 59.999 47.826 0.00 0.00 44.69 2.87
3528 3766 2.936498 CCAGAACACAAAGACACGTTCT 59.064 45.455 0.00 0.00 46.80 3.01
3529 3767 2.933906 TCCAGAACACAAAGACACGTTC 59.066 45.455 0.00 0.00 38.40 3.95
3530 3768 2.936498 CTCCAGAACACAAAGACACGTT 59.064 45.455 0.00 0.00 0.00 3.99
3531 3769 2.093658 ACTCCAGAACACAAAGACACGT 60.094 45.455 0.00 0.00 0.00 4.49
3532 3770 2.550978 ACTCCAGAACACAAAGACACG 58.449 47.619 0.00 0.00 0.00 4.49
3533 3771 6.260050 TCAATAACTCCAGAACACAAAGACAC 59.740 38.462 0.00 0.00 0.00 3.67
3534 3772 6.260050 GTCAATAACTCCAGAACACAAAGACA 59.740 38.462 0.00 0.00 0.00 3.41
3535 3773 6.483640 AGTCAATAACTCCAGAACACAAAGAC 59.516 38.462 0.00 0.00 30.02 3.01
3536 3774 6.483307 CAGTCAATAACTCCAGAACACAAAGA 59.517 38.462 0.00 0.00 35.45 2.52
3537 3775 6.293626 CCAGTCAATAACTCCAGAACACAAAG 60.294 42.308 0.00 0.00 35.45 2.77
3538 3776 5.530915 CCAGTCAATAACTCCAGAACACAAA 59.469 40.000 0.00 0.00 35.45 2.83
3539 3777 5.063204 CCAGTCAATAACTCCAGAACACAA 58.937 41.667 0.00 0.00 35.45 3.33
3540 3778 4.504864 CCCAGTCAATAACTCCAGAACACA 60.505 45.833 0.00 0.00 35.45 3.72
3541 3779 4.003648 CCCAGTCAATAACTCCAGAACAC 58.996 47.826 0.00 0.00 35.45 3.32
3542 3780 3.009033 CCCCAGTCAATAACTCCAGAACA 59.991 47.826 0.00 0.00 35.45 3.18
3580 3820 7.755373 GGAAAAGTAGCATTCAGGAACAATTAC 59.245 37.037 0.00 0.00 0.00 1.89
3582 3822 6.494835 AGGAAAAGTAGCATTCAGGAACAATT 59.505 34.615 0.00 0.00 0.00 2.32
3605 3848 9.063615 ACATTTTTACTCCTACAAACACTAAGG 57.936 33.333 0.00 0.00 0.00 2.69
3672 4081 4.620982 ACACTTGCTCTTAAACATTTGGC 58.379 39.130 0.00 0.00 0.00 4.52
3697 4106 7.500892 TGAGCTTACTCTATTCTAGTCTTCTGG 59.499 40.741 0.00 0.00 43.85 3.86
3698 4107 8.445275 TGAGCTTACTCTATTCTAGTCTTCTG 57.555 38.462 0.00 0.00 43.85 3.02
3757 4166 9.656040 TGCTGCTTTTTGTTCATGAATTATTAT 57.344 25.926 12.12 0.00 0.00 1.28
3758 4167 8.924691 GTGCTGCTTTTTGTTCATGAATTATTA 58.075 29.630 12.12 0.00 0.00 0.98
3759 4168 7.441760 TGTGCTGCTTTTTGTTCATGAATTATT 59.558 29.630 12.12 0.00 0.00 1.40
3882 4340 0.255890 TGCTTACCATCTCCCCAAGC 59.744 55.000 0.00 0.00 41.51 4.01
3901 4359 0.467844 TGCACTTGGTGGATGCACTT 60.468 50.000 17.44 0.00 44.17 3.16
3946 4404 2.162208 TCGATGGCTGATCAACAAAAGC 59.838 45.455 0.00 0.00 34.86 3.51
3949 4407 2.083774 GGTCGATGGCTGATCAACAAA 58.916 47.619 0.00 0.00 0.00 2.83
3991 4449 4.856801 AAGCCATAGTGCGCCCCG 62.857 66.667 4.18 0.00 36.02 5.73
3992 4450 2.965716 ATCAAGCCATAGTGCGCCCC 62.966 60.000 4.18 0.00 36.02 5.80
3995 4453 5.277058 GCTATATAATCAAGCCATAGTGCGC 60.277 44.000 0.00 0.00 36.02 6.09
4001 4459 7.331026 GGACTGTGCTATATAATCAAGCCATA 58.669 38.462 0.00 0.00 35.33 2.74
4005 4463 4.938226 GGGGACTGTGCTATATAATCAAGC 59.062 45.833 0.00 0.00 36.77 4.01
4010 4468 2.236395 GCCGGGGACTGTGCTATATAAT 59.764 50.000 2.18 0.00 0.00 1.28
4042 4500 1.745115 TACCACATCGCTTGCCTGC 60.745 57.895 0.00 0.00 0.00 4.85
4083 4541 6.215845 CACCACGTTACATATCATCAGATCA 58.784 40.000 0.00 0.00 35.67 2.92
4086 4544 4.099419 AGCACCACGTTACATATCATCAGA 59.901 41.667 0.00 0.00 0.00 3.27
4104 4564 2.742372 CACGCCAGTGGTAGCACC 60.742 66.667 20.99 5.64 44.34 5.01
4121 4581 3.638592 ATGGCAGCCCGGTGGTAAC 62.639 63.158 9.64 0.00 0.00 2.50
4122 4582 3.334891 ATGGCAGCCCGGTGGTAA 61.335 61.111 9.64 0.00 0.00 2.85
4123 4583 4.108299 CATGGCAGCCCGGTGGTA 62.108 66.667 9.64 0.00 0.00 3.25
4126 4586 3.443045 GAACATGGCAGCCCGGTG 61.443 66.667 9.64 8.01 0.00 4.94
4149 4609 1.001181 CCAACTGAAGGCCCATGTTTG 59.999 52.381 0.00 0.00 0.00 2.93
4150 4610 1.341080 CCAACTGAAGGCCCATGTTT 58.659 50.000 0.00 0.00 0.00 2.83
4169 4629 2.360475 GAGGACAACTGGCTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
4184 4644 0.944311 CGACGGTTGGACAGTTGGAG 60.944 60.000 0.00 0.00 0.00 3.86
4203 4663 0.472161 GATACCTCCCCTCCCAGGAC 60.472 65.000 0.00 0.00 37.67 3.85
4206 4666 0.030092 TTGGATACCTCCCCTCCCAG 60.030 60.000 0.00 0.00 41.29 4.45
4207 4667 0.653397 ATTGGATACCTCCCCTCCCA 59.347 55.000 0.00 0.00 41.29 4.37
4209 4669 1.981495 CTGATTGGATACCTCCCCTCC 59.019 57.143 0.00 0.00 41.29 4.30
4210 4670 2.903135 CTCTGATTGGATACCTCCCCTC 59.097 54.545 0.00 0.00 41.29 4.30
4211 4671 2.524440 TCTCTGATTGGATACCTCCCCT 59.476 50.000 0.00 0.00 41.29 4.79
4212 4672 2.977808 TCTCTGATTGGATACCTCCCC 58.022 52.381 0.00 0.00 41.29 4.81
4235 4695 3.365265 GTGGGTTTGCCTCTGCCG 61.365 66.667 0.00 0.00 36.33 5.69
4236 4696 2.203480 TGTGGGTTTGCCTCTGCC 60.203 61.111 0.00 0.00 36.33 4.85
4237 4697 2.908073 CGTGTGGGTTTGCCTCTGC 61.908 63.158 0.00 0.00 38.26 4.26
4238 4698 2.908073 GCGTGTGGGTTTGCCTCTG 61.908 63.158 0.00 0.00 34.45 3.35
4239 4699 2.594592 GCGTGTGGGTTTGCCTCT 60.595 61.111 0.00 0.00 34.45 3.69
4240 4700 2.904866 TGCGTGTGGGTTTGCCTC 60.905 61.111 0.00 0.00 34.45 4.70
4241 4701 3.216292 GTGCGTGTGGGTTTGCCT 61.216 61.111 0.00 0.00 34.45 4.75
4242 4702 4.622456 CGTGCGTGTGGGTTTGCC 62.622 66.667 0.00 0.00 0.00 4.52
4244 4704 4.622456 GGCGTGCGTGTGGGTTTG 62.622 66.667 0.00 0.00 0.00 2.93
4249 4709 4.444024 CAATCGGCGTGCGTGTGG 62.444 66.667 6.85 0.00 0.00 4.17
4250 4710 4.444024 CCAATCGGCGTGCGTGTG 62.444 66.667 6.85 0.00 0.00 3.82
4256 4716 2.745884 TTGCTCCCAATCGGCGTG 60.746 61.111 6.85 0.00 0.00 5.34
4257 4717 2.436646 CTTGCTCCCAATCGGCGT 60.437 61.111 6.85 0.00 0.00 5.68
4258 4718 2.436646 ACTTGCTCCCAATCGGCG 60.437 61.111 0.00 0.00 0.00 6.46
4259 4719 1.372087 CTCACTTGCTCCCAATCGGC 61.372 60.000 0.00 0.00 0.00 5.54
4260 4720 0.745845 CCTCACTTGCTCCCAATCGG 60.746 60.000 0.00 0.00 0.00 4.18
4261 4721 0.745845 CCCTCACTTGCTCCCAATCG 60.746 60.000 0.00 0.00 0.00 3.34
4262 4722 0.394899 CCCCTCACTTGCTCCCAATC 60.395 60.000 0.00 0.00 0.00 2.67
4263 4723 0.846427 TCCCCTCACTTGCTCCCAAT 60.846 55.000 0.00 0.00 0.00 3.16
4264 4724 1.463214 TCCCCTCACTTGCTCCCAA 60.463 57.895 0.00 0.00 0.00 4.12
4265 4725 1.920325 CTCCCCTCACTTGCTCCCA 60.920 63.158 0.00 0.00 0.00 4.37
4266 4726 2.674220 CCTCCCCTCACTTGCTCCC 61.674 68.421 0.00 0.00 0.00 4.30
4267 4727 2.674220 CCCTCCCCTCACTTGCTCC 61.674 68.421 0.00 0.00 0.00 4.70
4268 4728 2.674220 CCCCTCCCCTCACTTGCTC 61.674 68.421 0.00 0.00 0.00 4.26
4269 4729 2.612115 CCCCTCCCCTCACTTGCT 60.612 66.667 0.00 0.00 0.00 3.91
4270 4730 4.432741 GCCCCTCCCCTCACTTGC 62.433 72.222 0.00 0.00 0.00 4.01
4271 4731 2.935481 TGCCCCTCCCCTCACTTG 60.935 66.667 0.00 0.00 0.00 3.16
4272 4732 2.612115 CTGCCCCTCCCCTCACTT 60.612 66.667 0.00 0.00 0.00 3.16
4273 4733 4.748798 CCTGCCCCTCCCCTCACT 62.749 72.222 0.00 0.00 0.00 3.41
4280 4740 4.828296 CACCATGCCTGCCCCTCC 62.828 72.222 0.00 0.00 0.00 4.30
4281 4741 3.065787 ATCACCATGCCTGCCCCTC 62.066 63.158 0.00 0.00 0.00 4.30
4282 4742 3.025599 ATCACCATGCCTGCCCCT 61.026 61.111 0.00 0.00 0.00 4.79
4283 4743 2.836360 CATCACCATGCCTGCCCC 60.836 66.667 0.00 0.00 0.00 5.80
4284 4744 2.043652 ACATCACCATGCCTGCCC 60.044 61.111 0.00 0.00 32.57 5.36
4285 4745 2.420568 CCACATCACCATGCCTGCC 61.421 63.158 0.00 0.00 32.57 4.85
4286 4746 2.420568 CCCACATCACCATGCCTGC 61.421 63.158 0.00 0.00 32.57 4.85
4287 4747 1.000521 ACCCACATCACCATGCCTG 60.001 57.895 0.00 0.00 32.57 4.85
4288 4748 1.000521 CACCCACATCACCATGCCT 60.001 57.895 0.00 0.00 32.57 4.75
4289 4749 0.899717 AACACCCACATCACCATGCC 60.900 55.000 0.00 0.00 32.57 4.40
4290 4750 2.657297 AACACCCACATCACCATGC 58.343 52.632 0.00 0.00 32.57 4.06


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

AutoCloner maintained by Alex Coulton.