Multiple sequence alignment - TraesCS2B01G620700

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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 TraesCS2B01G620700 chr2B 100.000 4270 0 0 1 4270 795047709 795051978 0.000000e+00 7886.0
1 TraesCS2B01G620700 chr2B 91.060 302 22 3 1702 2003 523781555 523781259 1.850000e-108 403.0
2 TraesCS2B01G620700 chr2D 88.291 2229 140 55 10 2133 637633432 637635644 0.000000e+00 2558.0
3 TraesCS2B01G620700 chr2D 90.238 799 51 13 3127 3907 637636645 637637434 0.000000e+00 1018.0
4 TraesCS2B01G620700 chr2D 89.731 633 55 5 2403 3026 637636005 637636636 0.000000e+00 800.0
5 TraesCS2B01G620700 chr2D 93.646 362 23 0 3905 4266 637637471 637637832 3.760000e-150 542.0
6 TraesCS2B01G620700 chr2D 90.698 172 16 0 2664 2835 597847725 597847896 3.320000e-56 230.0
7 TraesCS2B01G620700 chr2D 90.116 172 17 0 2664 2835 641893134 641893305 1.550000e-54 224.0
8 TraesCS2B01G620700 chr2D 81.070 243 22 9 2128 2347 637635773 637636014 5.680000e-39 172.0
9 TraesCS2B01G620700 chr2D 95.000 100 5 0 3031 3130 98693500 98693599 1.590000e-34 158.0
10 TraesCS2B01G620700 chr2D 88.889 81 9 0 2924 3004 597847950 597848030 2.720000e-17 100.0
11 TraesCS2B01G620700 chr2D 88.889 81 9 0 2924 3004 641893359 641893439 2.720000e-17 100.0
12 TraesCS2B01G620700 chr2A 87.387 2212 139 57 13 2128 762316479 762314312 0.000000e+00 2410.0
13 TraesCS2B01G620700 chr2A 92.240 915 58 7 2128 3033 762314177 762313267 0.000000e+00 1284.0
14 TraesCS2B01G620700 chr2A 87.905 802 54 10 3127 3907 762313268 762312489 0.000000e+00 904.0
15 TraesCS2B01G620700 chr2A 93.094 362 25 0 3905 4266 762312452 762312091 8.130000e-147 531.0
16 TraesCS2B01G620700 chr2A 80.979 531 51 30 13 533 753815780 753815290 4.030000e-100 375.0
17 TraesCS2B01G620700 chr2A 96.000 100 4 0 3030 3129 68155922 68155823 3.420000e-36 163.0
18 TraesCS2B01G620700 chr1A 84.192 563 58 18 1061 1603 168548093 168548644 6.330000e-143 518.0
19 TraesCS2B01G620700 chr1A 81.947 565 81 15 24 580 96732477 96731926 3.890000e-125 459.0
20 TraesCS2B01G620700 chr1A 91.262 309 21 1 1700 2002 168548664 168548972 2.380000e-112 416.0
21 TraesCS2B01G620700 chr1A 97.872 47 0 1 14 59 561117113 561117067 3.540000e-11 80.5
22 TraesCS2B01G620700 chr5B 86.787 333 44 0 3932 4264 98514186 98513854 5.210000e-99 372.0
23 TraesCS2B01G620700 chr5B 92.174 115 6 3 3028 3140 203503152 203503039 4.420000e-35 159.0
24 TraesCS2B01G620700 chr7D 85.237 359 51 1 3907 4263 575925177 575925535 6.750000e-98 368.0
25 TraesCS2B01G620700 chr7D 89.091 55 6 0 2347 2401 622185366 622185420 7.660000e-08 69.4
26 TraesCS2B01G620700 chr7A 84.551 356 53 1 3907 4260 666794608 666794963 6.790000e-93 351.0
27 TraesCS2B01G620700 chr4A 83.193 357 59 1 3907 4263 735762496 735762141 4.120000e-85 326.0
28 TraesCS2B01G620700 chr4A 82.385 369 59 2 3907 4270 736143954 736143587 2.480000e-82 316.0
29 TraesCS2B01G620700 chr3A 83.384 331 45 8 24 350 572536986 572536662 8.980000e-77 298.0
30 TraesCS2B01G620700 chr1D 84.249 273 36 7 83 354 468126760 468126494 4.240000e-65 259.0
31 TraesCS2B01G620700 chr1D 95.098 102 5 0 3030 3131 485718754 485718653 1.230000e-35 161.0
32 TraesCS2B01G620700 chr1D 92.174 115 6 3 3028 3140 209519397 209519510 4.420000e-35 159.0
33 TraesCS2B01G620700 chr3D 93.805 113 5 2 3023 3134 71512916 71512805 7.340000e-38 169.0
34 TraesCS2B01G620700 chr4D 96.939 98 3 0 3032 3129 13198282 13198379 9.500000e-37 165.0
35 TraesCS2B01G620700 chr3B 95.146 103 4 1 3028 3129 822536275 822536377 1.230000e-35 161.0
36 TraesCS2B01G620700 chrUn 95.098 102 4 1 3028 3128 362465904 362465803 4.420000e-35 159.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G620700 chr2B 795047709 795051978 4269 False 7886.00 7886 100.0000 1 4270 1 chr2B.!!$F1 4269
1 TraesCS2B01G620700 chr2D 637633432 637637832 4400 False 1018.00 2558 88.5952 10 4266 5 chr2D.!!$F3 4256
2 TraesCS2B01G620700 chr2A 762312091 762316479 4388 True 1282.25 2410 90.1565 13 4266 4 chr2A.!!$R3 4253
3 TraesCS2B01G620700 chr1A 168548093 168548972 879 False 467.00 518 87.7270 1061 2002 2 chr1A.!!$F1 941
4 TraesCS2B01G620700 chr1A 96731926 96732477 551 True 459.00 459 81.9470 24 580 1 chr1A.!!$R1 556

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
883 914 1.117749 TCATCTCATCTGAGCCCGGG 61.118 60.0 19.09 19.09 41.80 5.73 F
1153 1245 0.032678 CTCATCTCTAATGGCGGCGT 59.967 55.0 9.37 0.00 0.00 5.68 F
1364 1471 0.035630 ACCTGCATCTCCTCTTGCAC 60.036 55.0 0.00 0.00 43.54 4.57 F
1366 1473 0.035725 CTGCATCTCCTCTTGCACCA 60.036 55.0 0.00 0.00 43.54 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2380 2850 0.309302 TTGTTTGGAACATCACCGCG 59.691 50.000 0.00 0.0 41.79 6.46 R
2973 3456 0.178068 TCTCTGGCCTAACAATCGCC 59.822 55.000 3.32 0.0 43.32 5.54 R
3208 3694 1.000274 GAAAGTCGCCAACCTGCAAAT 60.000 47.619 0.00 0.0 0.00 2.32 R
3344 3830 4.236527 TCTCACTAGGTACAGATGAGCA 57.763 45.455 9.57 0.0 37.34 4.26 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
170 175 8.159344 AGCTTAGGATAATGCATTTCAAGTAC 57.841 34.615 18.75 2.10 0.00 2.73
183 188 7.148255 TGCATTTCAAGTACGAATGAATTAGCT 60.148 33.333 18.96 0.00 35.63 3.32
184 189 8.335356 GCATTTCAAGTACGAATGAATTAGCTA 58.665 33.333 14.32 0.00 35.63 3.32
206 213 7.501559 AGCTATATGACAAAGCTGAATGTGAAT 59.498 33.333 8.94 2.50 44.67 2.57
224 231 3.006859 TGAATCAACTGACGATGGTGACT 59.993 43.478 0.00 0.00 0.00 3.41
361 377 1.823041 CCTCCTCGTCGTAGTCCCC 60.823 68.421 0.00 0.00 0.00 4.81
364 380 2.758089 CCTCGTCGTAGTCCCCGTG 61.758 68.421 0.00 0.00 0.00 4.94
385 401 2.202492 CGCCTCGTCCTCGAACTG 60.202 66.667 0.00 0.00 45.61 3.16
802 833 2.757099 GTTAGCGGGTCGGGAGGA 60.757 66.667 0.00 0.00 0.00 3.71
853 884 2.868583 CAGATATTTGCTCCAGTGGACG 59.131 50.000 8.12 6.02 0.00 4.79
857 888 3.573772 TTGCTCCAGTGGACGCTCG 62.574 63.158 24.73 11.67 30.89 5.03
883 914 1.117749 TCATCTCATCTGAGCCCGGG 61.118 60.000 19.09 19.09 41.80 5.73
1009 1067 1.215647 GCCGGAGACATGTCGAAGT 59.784 57.895 19.85 2.34 34.09 3.01
1092 1150 3.471244 CTCCGACATCCGCGTCTCC 62.471 68.421 4.92 0.00 36.84 3.71
1153 1245 0.032678 CTCATCTCTAATGGCGGCGT 59.967 55.000 9.37 0.00 0.00 5.68
1205 1302 2.435059 GTGGAGGCGCTCAAGGAC 60.435 66.667 7.64 0.00 31.08 3.85
1363 1470 0.035725 CACCTGCATCTCCTCTTGCA 60.036 55.000 0.00 0.00 46.03 4.08
1364 1471 0.035630 ACCTGCATCTCCTCTTGCAC 60.036 55.000 0.00 0.00 43.54 4.57
1366 1473 0.035725 CTGCATCTCCTCTTGCACCA 60.036 55.000 0.00 0.00 43.54 4.17
1367 1474 0.321919 TGCATCTCCTCTTGCACCAC 60.322 55.000 0.00 0.00 43.54 4.16
1374 1481 0.674895 CCTCTTGCACCACCTACTGC 60.675 60.000 0.00 0.00 0.00 4.40
1384 1491 4.624125 GCACCACCTACTGCTATCTTTCTT 60.624 45.833 0.00 0.00 0.00 2.52
1387 1494 6.096987 CACCACCTACTGCTATCTTTCTTCTA 59.903 42.308 0.00 0.00 0.00 2.10
1391 1498 7.067615 CACCTACTGCTATCTTTCTTCTACTGA 59.932 40.741 0.00 0.00 0.00 3.41
1396 1503 8.972127 ACTGCTATCTTTCTTCTACTGATGTTA 58.028 33.333 0.00 0.00 0.00 2.41
1527 1634 1.002142 CCATATCGGACGAAGCGTACA 60.002 52.381 0.00 0.00 41.29 2.90
1532 1639 0.854062 CGGACGAAGCGTACAACAAA 59.146 50.000 2.92 0.00 41.29 2.83
1550 1657 0.390472 AACTCGGCAGTAAGCTCAGC 60.390 55.000 0.00 0.00 44.79 4.26
1654 1791 9.700831 ATTCCTTAAAAATTGCATACCTCTAGT 57.299 29.630 0.00 0.00 0.00 2.57
1655 1792 8.506168 TCCTTAAAAATTGCATACCTCTAGTG 57.494 34.615 0.00 0.00 0.00 2.74
1672 1826 8.091449 ACCTCTAGTGAAAGATAGTTCAGTTTG 58.909 37.037 0.94 0.00 40.73 2.93
1673 1827 7.064016 CCTCTAGTGAAAGATAGTTCAGTTTGC 59.936 40.741 0.94 0.00 40.73 3.68
1725 1879 7.270757 ACATCTAAACTTGTGTGCAATTGTA 57.729 32.000 7.40 0.00 33.65 2.41
1768 1922 5.236478 TCAAAGAGAAGATGGTGTCGAAAAC 59.764 40.000 0.00 0.00 0.00 2.43
1805 1959 0.329261 AGCAAGTAAGCTGCCCATGA 59.671 50.000 0.00 0.00 44.66 3.07
1841 1995 3.576078 TCCTTTCAAGGCTTCAACAGA 57.424 42.857 0.00 0.00 46.06 3.41
1907 2075 2.307496 TGGAGGAATTGTGTGCCAAT 57.693 45.000 0.00 0.00 45.81 3.16
1985 2159 8.460285 ACATGCTATGGAATGGAATATTGCCAT 61.460 37.037 4.35 8.67 40.24 4.40
2043 2218 2.039746 TGCCTACCTTGCATACACTGTT 59.960 45.455 0.00 0.00 32.85 3.16
2074 2249 8.207521 TCCAAGGCAAAGTTTTCTAATTTTTG 57.792 30.769 0.00 0.00 0.00 2.44
2098 2276 4.755411 TGTCTACCTTGCTGCATAGTAAC 58.245 43.478 1.84 9.59 0.00 2.50
2118 2296 1.613255 CGGTTTAGCACCCCATCACTT 60.613 52.381 0.00 0.00 43.83 3.16
2121 2299 2.198827 TTAGCACCCCATCACTTGTG 57.801 50.000 0.00 0.00 0.00 3.33
2138 2585 2.695561 TGGAGCTACCATTGGCTGA 58.304 52.632 1.54 0.00 44.64 4.26
2144 2591 4.829492 GGAGCTACCATTGGCTGAATATTT 59.171 41.667 1.54 0.00 39.05 1.40
2323 2793 2.808906 AAAGCACACTAGGAATCCCC 57.191 50.000 0.00 0.00 0.00 4.81
2324 2794 1.668826 AAGCACACTAGGAATCCCCA 58.331 50.000 0.00 0.00 37.41 4.96
2325 2795 0.912486 AGCACACTAGGAATCCCCAC 59.088 55.000 0.00 0.00 37.41 4.61
2326 2796 0.912486 GCACACTAGGAATCCCCACT 59.088 55.000 0.00 0.00 37.41 4.00
2327 2797 1.134371 GCACACTAGGAATCCCCACTC 60.134 57.143 0.00 0.00 37.41 3.51
2328 2798 2.187958 CACACTAGGAATCCCCACTCA 58.812 52.381 0.00 0.00 37.41 3.41
2329 2799 2.774234 CACACTAGGAATCCCCACTCAT 59.226 50.000 0.00 0.00 37.41 2.90
2330 2800 2.774234 ACACTAGGAATCCCCACTCATG 59.226 50.000 0.00 0.00 37.41 3.07
2331 2801 3.041211 CACTAGGAATCCCCACTCATGA 58.959 50.000 0.00 0.00 37.41 3.07
2334 2804 4.728860 ACTAGGAATCCCCACTCATGAAAT 59.271 41.667 0.00 0.00 37.41 2.17
2343 2813 5.103558 TCCCCACTCATGAAATATGACCATT 60.104 40.000 0.00 0.00 0.00 3.16
2524 2998 8.671384 ACATGCGTATGTAGTAAATATTGGTT 57.329 30.769 18.03 0.00 45.45 3.67
2601 3079 1.532868 CTTTCTTCTTCTGTGGCGTGG 59.467 52.381 0.00 0.00 0.00 4.94
2675 3153 6.770286 ACATTTATGTCATAGGTGGGAGAT 57.230 37.500 9.85 0.00 35.87 2.75
2687 3165 4.366267 AGGTGGGAGATAGATGTGAAGTT 58.634 43.478 0.00 0.00 0.00 2.66
2725 3203 1.408422 GGCACAGTGAAATTCGTTGC 58.592 50.000 4.15 0.00 0.00 4.17
2762 3240 1.182385 GGCGTGGATTTTGGGTTGGA 61.182 55.000 0.00 0.00 0.00 3.53
2822 3300 8.408601 GGCATGTATGTTCATTCTCAAACTATT 58.591 33.333 0.00 0.00 0.00 1.73
2857 3335 5.459982 TTATACCCAGTGCCCAAGTTATT 57.540 39.130 0.00 0.00 0.00 1.40
2862 3340 3.627237 CCCAGTGCCCAAGTTATTATGGT 60.627 47.826 0.00 0.00 34.79 3.55
2878 3356 9.257651 GTTATTATGGTTTCTTGCGACTAGTAT 57.742 33.333 0.00 0.00 0.00 2.12
2879 3357 9.826574 TTATTATGGTTTCTTGCGACTAGTATT 57.173 29.630 0.00 0.00 0.00 1.89
2900 3378 4.286297 TGACATACCCTTGGAGAAACAG 57.714 45.455 0.00 0.00 0.00 3.16
2911 3394 5.067674 CCTTGGAGAAACAGTTCATTTGACA 59.932 40.000 0.00 0.00 36.09 3.58
2913 3396 6.713762 TGGAGAAACAGTTCATTTGACATT 57.286 33.333 0.00 0.00 36.09 2.71
2940 3423 2.151049 CTTGCTGCAGGGTGAAAGGC 62.151 60.000 17.12 0.00 0.00 4.35
3013 3496 8.687242 CAGAGAAAGTGAAGGTAGATACATACA 58.313 37.037 0.00 0.00 0.00 2.29
3026 3512 8.901793 GGTAGATACATACATACCTTACCTAGC 58.098 40.741 0.00 0.00 35.75 3.42
3031 3517 9.992442 ATACATACATACCTTACCTAGCAGTAT 57.008 33.333 0.00 0.00 0.00 2.12
3033 3519 9.240734 ACATACATACCTTACCTAGCAGTATAC 57.759 37.037 0.00 0.00 0.00 1.47
3034 3520 9.463902 CATACATACCTTACCTAGCAGTATACT 57.536 37.037 0.00 0.00 0.00 2.12
3035 3521 7.999450 ACATACCTTACCTAGCAGTATACTC 57.001 40.000 1.26 0.00 0.00 2.59
3036 3522 6.947158 ACATACCTTACCTAGCAGTATACTCC 59.053 42.308 1.26 0.00 0.00 3.85
3037 3523 4.738685 ACCTTACCTAGCAGTATACTCCC 58.261 47.826 1.26 0.00 0.00 4.30
3038 3524 4.419537 ACCTTACCTAGCAGTATACTCCCT 59.580 45.833 1.26 5.20 0.00 4.20
3039 3525 5.011586 CCTTACCTAGCAGTATACTCCCTC 58.988 50.000 1.26 0.00 0.00 4.30
3040 3526 3.529216 ACCTAGCAGTATACTCCCTCC 57.471 52.381 1.26 0.00 0.00 4.30
3041 3527 2.789992 ACCTAGCAGTATACTCCCTCCA 59.210 50.000 1.26 0.00 0.00 3.86
3042 3528 3.403051 ACCTAGCAGTATACTCCCTCCAT 59.597 47.826 1.26 0.00 0.00 3.41
3043 3529 4.020543 CCTAGCAGTATACTCCCTCCATC 58.979 52.174 1.26 0.00 0.00 3.51
3044 3530 2.896039 AGCAGTATACTCCCTCCATCC 58.104 52.381 1.26 0.00 0.00 3.51
3045 3531 1.903183 GCAGTATACTCCCTCCATCCC 59.097 57.143 1.26 0.00 0.00 3.85
3046 3532 2.760025 GCAGTATACTCCCTCCATCCCA 60.760 54.545 1.26 0.00 0.00 4.37
3047 3533 3.587498 CAGTATACTCCCTCCATCCCAA 58.413 50.000 1.26 0.00 0.00 4.12
3048 3534 3.973973 CAGTATACTCCCTCCATCCCAAA 59.026 47.826 1.26 0.00 0.00 3.28
3049 3535 4.412199 CAGTATACTCCCTCCATCCCAAAA 59.588 45.833 1.26 0.00 0.00 2.44
3050 3536 5.073691 CAGTATACTCCCTCCATCCCAAAAT 59.926 44.000 1.26 0.00 0.00 1.82
3051 3537 6.272324 CAGTATACTCCCTCCATCCCAAAATA 59.728 42.308 1.26 0.00 0.00 1.40
3052 3538 6.855061 AGTATACTCCCTCCATCCCAAAATAA 59.145 38.462 0.00 0.00 0.00 1.40
3053 3539 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
3054 3540 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
3055 3541 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
3056 3542 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
3057 3543 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
3058 3544 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
3059 3545 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
3060 3546 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
3061 3547 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
3062 3548 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
3063 3549 5.711976 CCATCCCAAAATAAGTGTCTCAACT 59.288 40.000 0.00 0.00 0.00 3.16
3064 3550 6.209391 CCATCCCAAAATAAGTGTCTCAACTT 59.791 38.462 0.00 0.00 42.89 2.66
3065 3551 7.255942 CCATCCCAAAATAAGTGTCTCAACTTT 60.256 37.037 0.00 0.00 40.77 2.66
3066 3552 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
3067 3553 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3068 3554 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3069 3555 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3070 3556 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3071 3557 9.438291 CAAAATAAGTGTCTCAACTTTGTACTG 57.562 33.333 0.00 0.00 40.77 2.74
3072 3558 8.958119 AAATAAGTGTCTCAACTTTGTACTGA 57.042 30.769 0.00 0.00 40.77 3.41
3073 3559 7.948278 ATAAGTGTCTCAACTTTGTACTGAC 57.052 36.000 0.00 0.00 40.77 3.51
3074 3560 5.599999 AGTGTCTCAACTTTGTACTGACT 57.400 39.130 0.00 0.00 0.00 3.41
3075 3561 5.593010 AGTGTCTCAACTTTGTACTGACTC 58.407 41.667 0.00 0.00 0.00 3.36
3076 3562 5.361285 AGTGTCTCAACTTTGTACTGACTCT 59.639 40.000 0.00 0.00 0.00 3.24
3077 3563 6.546403 AGTGTCTCAACTTTGTACTGACTCTA 59.454 38.462 0.00 0.00 0.00 2.43
3078 3564 6.858993 GTGTCTCAACTTTGTACTGACTCTAG 59.141 42.308 0.00 0.00 0.00 2.43
3079 3565 6.546403 TGTCTCAACTTTGTACTGACTCTAGT 59.454 38.462 0.00 0.00 34.71 2.57
3080 3566 6.858993 GTCTCAACTTTGTACTGACTCTAGTG 59.141 42.308 0.00 0.00 32.19 2.74
3081 3567 5.529791 TCAACTTTGTACTGACTCTAGTGC 58.470 41.667 0.00 0.00 34.39 4.40
3082 3568 5.068591 TCAACTTTGTACTGACTCTAGTGCA 59.931 40.000 0.00 0.00 40.72 4.57
3083 3569 5.531122 ACTTTGTACTGACTCTAGTGCAA 57.469 39.130 5.52 5.52 46.65 4.08
3086 3572 5.531122 TTGTACTGACTCTAGTGCAAAGT 57.469 39.130 6.91 0.00 45.80 2.66
3087 3573 5.531122 TGTACTGACTCTAGTGCAAAGTT 57.469 39.130 0.00 0.00 39.75 2.66
3088 3574 5.289595 TGTACTGACTCTAGTGCAAAGTTG 58.710 41.667 0.00 0.00 39.75 3.16
3089 3575 4.408182 ACTGACTCTAGTGCAAAGTTGT 57.592 40.909 0.00 0.00 0.00 3.32
3090 3576 5.531122 ACTGACTCTAGTGCAAAGTTGTA 57.469 39.130 0.00 0.00 0.00 2.41
3091 3577 5.290386 ACTGACTCTAGTGCAAAGTTGTAC 58.710 41.667 4.30 4.30 42.99 2.90
3102 3588 7.486802 GTGCAAAGTTGTACTAAGGTTAAGA 57.513 36.000 5.17 0.00 40.10 2.10
3103 3589 7.350467 GTGCAAAGTTGTACTAAGGTTAAGAC 58.650 38.462 5.17 0.00 40.10 3.01
3104 3590 7.011669 GTGCAAAGTTGTACTAAGGTTAAGACA 59.988 37.037 5.17 0.00 40.10 3.41
3105 3591 7.011669 TGCAAAGTTGTACTAAGGTTAAGACAC 59.988 37.037 0.00 0.00 0.00 3.67
3106 3592 7.226128 GCAAAGTTGTACTAAGGTTAAGACACT 59.774 37.037 0.00 0.00 0.00 3.55
3107 3593 9.106070 CAAAGTTGTACTAAGGTTAAGACACTT 57.894 33.333 0.00 0.00 0.00 3.16
3115 3601 8.631480 ACTAAGGTTAAGACACTTATTTTGGG 57.369 34.615 0.00 0.00 0.00 4.12
3116 3602 8.442374 ACTAAGGTTAAGACACTTATTTTGGGA 58.558 33.333 0.00 0.00 0.00 4.37
3117 3603 7.520451 AAGGTTAAGACACTTATTTTGGGAC 57.480 36.000 0.00 0.00 0.00 4.46
3118 3604 5.704053 AGGTTAAGACACTTATTTTGGGACG 59.296 40.000 0.00 0.00 0.00 4.79
3119 3605 5.106436 GGTTAAGACACTTATTTTGGGACGG 60.106 44.000 0.00 0.00 0.00 4.79
3120 3606 4.360951 AAGACACTTATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
3121 3607 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
3122 3608 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3123 3609 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3124 3610 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3125 3611 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3156 3642 7.870509 TCATTGCTTCTTATAACATTCAGCT 57.129 32.000 0.00 0.00 0.00 4.24
3180 3666 4.667262 TCATGCATCCGGTTAAAAATTCG 58.333 39.130 0.00 0.00 0.00 3.34
3181 3667 4.396478 TCATGCATCCGGTTAAAAATTCGA 59.604 37.500 0.00 0.00 0.00 3.71
3208 3694 5.008613 GTGGAAGTGTTATTGAGCAGTTTCA 59.991 40.000 0.00 0.00 32.76 2.69
3297 3783 6.539173 AGTTTATGTACTTTGGTGTGGATCA 58.461 36.000 0.00 0.00 0.00 2.92
3344 3830 6.211184 TGCCAAATTCATTTGTTATGGAGTCT 59.789 34.615 10.63 0.00 44.21 3.24
3391 3877 3.534554 TGAACATGCATGTACTGGCTAG 58.465 45.455 31.55 2.09 40.80 3.42
3392 3878 3.055167 TGAACATGCATGTACTGGCTAGT 60.055 43.478 31.55 13.47 40.80 2.57
3407 3893 5.354234 ACTGGCTAGTGTATTTGTTATGCAC 59.646 40.000 0.13 0.00 35.34 4.57
3408 3894 5.496556 TGGCTAGTGTATTTGTTATGCACT 58.503 37.500 12.03 12.03 44.82 4.40
3411 3897 7.608376 TGGCTAGTGTATTTGTTATGCACTTTA 59.392 33.333 12.49 0.00 41.10 1.85
3474 3960 7.027874 TGGAGATTAGTTTGGGTTCAAGTAT 57.972 36.000 0.00 0.00 33.98 2.12
3529 4018 4.179579 GACCAAGATTGCGGGCGC 62.180 66.667 0.00 0.00 42.35 6.53
3587 4077 2.737252 CCAGAAGTACCTGAAAACTCGC 59.263 50.000 1.10 0.00 36.29 5.03
3634 4124 6.480763 TGGAATCAAAGCAGTAACCTGATTA 58.519 36.000 0.00 0.00 46.14 1.75
3672 4162 7.099764 TCTTGAACTTTAGCTATCTGAACCAG 58.900 38.462 0.00 0.00 0.00 4.00
3683 4173 5.355350 GCTATCTGAACCAGTGTAGCAATTT 59.645 40.000 19.04 0.00 41.44 1.82
3728 4218 2.162408 CGGCAAGGAGAACTGAAAATCC 59.838 50.000 0.00 0.00 0.00 3.01
3750 4240 0.183014 TAGGAGTAGGAGCCACTCGG 59.817 60.000 10.73 0.00 42.79 4.63
3769 4259 2.292267 GGTACAGTCTTGATGCCATGG 58.708 52.381 7.63 7.63 0.00 3.66
3785 4275 3.349022 CCATGGAAAATTGCAGCCAAAT 58.651 40.909 5.56 0.00 34.05 2.32
3808 4299 9.921637 AAATTTATTTCTACGAGGATTGCAAAA 57.078 25.926 1.71 0.00 0.00 2.44
3829 4320 9.937175 GCAAAATAAACTACTTATGCTTCTAGG 57.063 33.333 0.00 0.00 30.24 3.02
3870 4379 5.913137 AACAGAAAACAGGAATTGTCACA 57.087 34.783 0.00 0.00 39.73 3.58
3877 4386 6.907206 AAACAGGAATTGTCACAAAACATG 57.093 33.333 0.00 2.42 39.73 3.21
3879 4388 3.742369 CAGGAATTGTCACAAAACATGCC 59.258 43.478 0.00 0.00 0.00 4.40
3927 4475 4.273724 CACTTCATTGCTCATCCAGATCAG 59.726 45.833 0.00 0.00 0.00 2.90
3951 4499 2.476185 GGTTGCTCGAAATCCATGAACG 60.476 50.000 0.00 0.00 0.00 3.95
3952 4500 1.368641 TGCTCGAAATCCATGAACGG 58.631 50.000 0.00 0.00 0.00 4.44
3965 4513 1.227556 GAACGGGCATATGAGCGGT 60.228 57.895 6.97 0.00 34.64 5.68
4035 4583 0.322456 TTCTGTGCCTTGGGGAATCG 60.322 55.000 0.00 0.00 33.58 3.34
4038 4586 2.106683 GTGCCTTGGGGAATCGTCG 61.107 63.158 0.00 0.00 33.58 5.12
4055 4603 0.390340 TCGCAGCAAGCTAGACCAAG 60.390 55.000 0.00 0.00 42.61 3.61
4070 4618 7.442656 GCTAGACCAAGCTTAAACATAGGATA 58.557 38.462 0.00 0.00 39.50 2.59
4115 4663 0.035739 GGGTTTCCGCTGTAGGTTGA 59.964 55.000 0.00 0.00 0.00 3.18
4266 4814 3.425892 CGTAGCTATATACGTCACCAGCC 60.426 52.174 0.00 0.00 42.73 4.85
4267 4815 2.594131 AGCTATATACGTCACCAGCCA 58.406 47.619 0.00 0.00 0.00 4.75
4268 4816 3.165875 AGCTATATACGTCACCAGCCAT 58.834 45.455 0.00 0.00 0.00 4.40
4269 4817 3.056536 AGCTATATACGTCACCAGCCATG 60.057 47.826 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.899661 ACATGTAATTAACCACACTGTGTATAT 57.100 29.630 13.89 5.06 0.00 0.86
5 6 9.373603 GACATGTAATTAACCACACTGTGTATA 57.626 33.333 13.89 4.79 0.00 1.47
6 7 7.064134 CGACATGTAATTAACCACACTGTGTAT 59.936 37.037 13.89 5.77 0.00 2.29
8 9 5.178623 CGACATGTAATTAACCACACTGTGT 59.821 40.000 7.80 7.80 0.00 3.72
10 11 5.407387 GTCGACATGTAATTAACCACACTGT 59.593 40.000 11.55 1.40 0.00 3.55
20 21 1.481363 TGCCCGGTCGACATGTAATTA 59.519 47.619 18.91 0.00 0.00 1.40
117 118 4.593597 GCAAATTTGTGCAGATTGATGG 57.406 40.909 19.03 0.00 44.29 3.51
142 143 6.872628 TGAAATGCATTATCCTAAGCTCAG 57.127 37.500 13.39 0.00 0.00 3.35
170 175 8.715998 AGCTTTGTCATATAGCTAATTCATTCG 58.284 33.333 0.00 0.00 43.08 3.34
183 188 8.735692 TGATTCACATTCAGCTTTGTCATATA 57.264 30.769 0.00 0.00 0.00 0.86
184 189 7.634671 TGATTCACATTCAGCTTTGTCATAT 57.365 32.000 0.00 0.00 0.00 1.78
206 213 3.676049 GCATAGTCACCATCGTCAGTTGA 60.676 47.826 0.00 0.00 0.00 3.18
336 343 0.979709 TACGACGAGGAGGAGGAGGA 60.980 60.000 0.00 0.00 0.00 3.71
377 393 2.492090 CGGGAGGAGCAGTTCGAG 59.508 66.667 0.00 0.00 0.00 4.04
545 564 3.319198 GGCGAAGACCAGGGTCCA 61.319 66.667 14.67 0.00 45.59 4.02
724 755 4.962836 GGATGGGGATGGCGGCTG 62.963 72.222 11.43 0.00 0.00 4.85
802 833 5.124776 CACTCTGTTATCTCCTCGTCTTCTT 59.875 44.000 0.00 0.00 0.00 2.52
853 884 4.959596 GAGATGAGGCCCGCGAGC 62.960 72.222 8.23 5.53 0.00 5.03
857 888 1.301558 CAGATGAGATGAGGCCCGC 60.302 63.158 0.00 0.00 0.00 6.13
895 926 4.228567 GGCTCTAGGTGGGCTCGC 62.229 72.222 0.00 0.00 0.00 5.03
960 1009 1.441311 GACTCTCTGGCCTGCTAGC 59.559 63.158 8.10 8.10 0.00 3.42
968 1017 2.179517 CCACGACGACTCTCTGGC 59.820 66.667 0.00 0.00 0.00 4.85
1165 1257 3.819920 TCTGCGAGCAGAGCGGAG 61.820 66.667 22.28 0.00 46.80 4.63
1205 1302 1.151668 CCGTCTTCTTCCACAGCTTG 58.848 55.000 0.00 0.00 0.00 4.01
1363 1470 5.026790 AGAAGAAAGATAGCAGTAGGTGGT 58.973 41.667 0.00 0.00 40.92 4.16
1364 1471 5.606348 AGAAGAAAGATAGCAGTAGGTGG 57.394 43.478 0.00 0.00 0.00 4.61
1366 1473 7.120051 TCAGTAGAAGAAAGATAGCAGTAGGT 58.880 38.462 0.00 0.00 0.00 3.08
1367 1474 7.575414 TCAGTAGAAGAAAGATAGCAGTAGG 57.425 40.000 0.00 0.00 0.00 3.18
1384 1491 6.384015 ACCACCATCAATCTAACATCAGTAGA 59.616 38.462 0.00 0.00 0.00 2.59
1387 1494 5.190528 AGACCACCATCAATCTAACATCAGT 59.809 40.000 0.00 0.00 0.00 3.41
1391 1498 4.080129 AGCAGACCACCATCAATCTAACAT 60.080 41.667 0.00 0.00 0.00 2.71
1396 1503 2.093075 CAGAGCAGACCACCATCAATCT 60.093 50.000 0.00 0.00 0.00 2.40
1399 1506 1.351076 TCAGAGCAGACCACCATCAA 58.649 50.000 0.00 0.00 0.00 2.57
1527 1634 2.143925 GAGCTTACTGCCGAGTTTGTT 58.856 47.619 0.00 0.00 44.23 2.83
1532 1639 1.216710 GCTGAGCTTACTGCCGAGT 59.783 57.895 0.00 0.00 44.23 4.18
1579 1686 4.019231 AGAATTCTACAAGGGGTCCAAGTC 60.019 45.833 6.06 0.00 0.00 3.01
1581 1691 4.019321 TGAGAATTCTACAAGGGGTCCAAG 60.019 45.833 8.25 0.00 0.00 3.61
1637 1767 9.553064 CTATCTTTCACTAGAGGTATGCAATTT 57.447 33.333 0.00 0.00 0.00 1.82
1638 1768 8.709308 ACTATCTTTCACTAGAGGTATGCAATT 58.291 33.333 0.00 0.00 0.00 2.32
1654 1791 6.899393 AATGGCAAACTGAACTATCTTTCA 57.101 33.333 0.00 0.00 34.30 2.69
1655 1792 6.089954 GCAAATGGCAAACTGAACTATCTTTC 59.910 38.462 0.00 0.00 43.97 2.62
1672 1826 1.470098 AGTGAGTCGATTGCAAATGGC 59.530 47.619 1.71 0.00 45.13 4.40
1673 1827 3.395858 GAGTGAGTCGATTGCAAATGG 57.604 47.619 1.71 0.00 0.00 3.16
1768 1922 2.567169 TGCTTATCATCCGATACAGGGG 59.433 50.000 0.00 0.00 33.74 4.79
1805 1959 5.694995 TGAAAGGAACAAAGAAGTCCAGAT 58.305 37.500 0.00 0.00 0.00 2.90
1841 1995 5.104485 AGGACAAGAAACAGAGTAAACAGGT 60.104 40.000 0.00 0.00 0.00 4.00
1907 2075 6.899393 AAAGCAAATGAACTGACCTTGATA 57.101 33.333 0.00 0.00 0.00 2.15
1985 2159 5.126067 GGGCTTTAACATCAGCAGATTAGA 58.874 41.667 0.00 0.00 37.81 2.10
2065 2240 6.363357 GCAGCAAGGTAGACAACAAAAATTAG 59.637 38.462 0.00 0.00 0.00 1.73
2066 2241 6.183360 TGCAGCAAGGTAGACAACAAAAATTA 60.183 34.615 0.00 0.00 0.00 1.40
2074 2249 3.600388 ACTATGCAGCAAGGTAGACAAC 58.400 45.455 0.00 0.00 0.00 3.32
2082 2257 2.024176 ACCGTTACTATGCAGCAAGG 57.976 50.000 0.00 0.00 0.00 3.61
2121 2299 2.355010 ATTCAGCCAATGGTAGCTCC 57.645 50.000 0.00 0.00 37.18 4.70
2138 2585 7.876068 TGACTGTAGACGGAAGAACAAAATATT 59.124 33.333 0.00 0.00 0.00 1.28
2144 2591 4.866508 ATGACTGTAGACGGAAGAACAA 57.133 40.909 0.00 0.00 0.00 2.83
2323 2793 9.459640 GAATTGAATGGTCATATTTCATGAGTG 57.540 33.333 0.00 0.00 32.48 3.51
2324 2794 9.192642 TGAATTGAATGGTCATATTTCATGAGT 57.807 29.630 0.00 0.00 32.48 3.41
2343 2813 6.465948 CCCACCTGAATTTTCATTGAATTGA 58.534 36.000 0.00 0.00 36.46 2.57
2352 2822 3.895041 GAGTTTCCCCACCTGAATTTTCA 59.105 43.478 0.00 0.00 35.57 2.69
2354 2824 3.641436 GTGAGTTTCCCCACCTGAATTTT 59.359 43.478 0.00 0.00 0.00 1.82
2380 2850 0.309302 TTGTTTGGAACATCACCGCG 59.691 50.000 0.00 0.00 41.79 6.46
2504 2978 9.321562 ACCAAGAACCAATATTTACTACATACG 57.678 33.333 0.00 0.00 0.00 3.06
2524 2998 4.469657 AGCAAAGAATAACCACACCAAGA 58.530 39.130 0.00 0.00 0.00 3.02
2601 3079 7.433680 AGACAAAACAGGTGTAATTTCCATTC 58.566 34.615 0.00 0.00 0.00 2.67
2637 3115 8.626526 TGACATAAATGTTCATCTTGGATCATG 58.373 33.333 0.00 0.00 41.95 3.07
2675 3153 2.906389 ACCTGGCTCAACTTCACATCTA 59.094 45.455 0.00 0.00 0.00 1.98
2687 3165 2.752358 CTCTTGGCACCTGGCTCA 59.248 61.111 0.00 0.00 44.01 4.26
2711 3189 2.362077 AGCTTTGGCAACGAATTTCACT 59.638 40.909 8.03 0.00 39.89 3.41
2725 3203 1.538687 CCCAAGGGCTTCAGCTTTGG 61.539 60.000 20.03 20.03 45.87 3.28
2762 3240 1.208052 AGTGGCTCATCGTATTGCACT 59.792 47.619 0.00 0.00 0.00 4.40
2822 3300 6.039270 GCACTGGGTATAAATTTATCACTGCA 59.961 38.462 13.95 3.38 0.00 4.41
2862 3340 6.755141 GGTATGTCAATACTAGTCGCAAGAAA 59.245 38.462 0.00 0.00 42.84 2.52
2878 3356 4.104102 ACTGTTTCTCCAAGGGTATGTCAA 59.896 41.667 0.00 0.00 0.00 3.18
2879 3357 3.650942 ACTGTTTCTCCAAGGGTATGTCA 59.349 43.478 0.00 0.00 0.00 3.58
2900 3378 4.379652 AGCACCCAAAATGTCAAATGAAC 58.620 39.130 0.00 0.00 0.00 3.18
2940 3423 2.437343 GCACTCGAAGAAGCGGACG 61.437 63.158 0.00 0.00 34.09 4.79
2973 3456 0.178068 TCTCTGGCCTAACAATCGCC 59.822 55.000 3.32 0.00 43.32 5.54
3013 3496 6.277522 AGGGAGTATACTGCTAGGTAAGGTAT 59.722 42.308 21.90 0.00 34.50 2.73
3026 3512 3.260269 TGGGATGGAGGGAGTATACTG 57.740 52.381 10.90 0.00 0.00 2.74
3031 3517 5.043762 ACTTATTTTGGGATGGAGGGAGTA 58.956 41.667 0.00 0.00 0.00 2.59
3032 3518 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
3033 3519 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
3034 3520 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
3035 3521 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
3036 3522 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
3037 3523 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
3038 3524 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
3039 3525 5.711976 AGTTGAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
3040 3526 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
3041 3527 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
3042 3528 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
3043 3529 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
3044 3530 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3045 3531 9.438291 CAGTACAAAGTTGAGACACTTATTTTG 57.562 33.333 0.00 0.00 35.87 2.44
3046 3532 9.391006 TCAGTACAAAGTTGAGACACTTATTTT 57.609 29.630 0.00 0.00 35.87 1.82
3047 3533 8.827677 GTCAGTACAAAGTTGAGACACTTATTT 58.172 33.333 0.00 0.00 35.87 1.40
3048 3534 8.204836 AGTCAGTACAAAGTTGAGACACTTATT 58.795 33.333 0.00 0.00 35.87 1.40
3049 3535 7.727181 AGTCAGTACAAAGTTGAGACACTTAT 58.273 34.615 0.00 0.00 35.87 1.73
3050 3536 7.068348 AGAGTCAGTACAAAGTTGAGACACTTA 59.932 37.037 0.00 0.00 35.87 2.24
3051 3537 5.978814 AGTCAGTACAAAGTTGAGACACTT 58.021 37.500 0.00 0.00 38.74 3.16
3052 3538 5.361285 AGAGTCAGTACAAAGTTGAGACACT 59.639 40.000 0.00 2.55 0.00 3.55
3053 3539 5.593010 AGAGTCAGTACAAAGTTGAGACAC 58.407 41.667 0.00 0.58 0.00 3.67
3054 3540 5.854010 AGAGTCAGTACAAAGTTGAGACA 57.146 39.130 0.00 0.00 0.00 3.41
3055 3541 6.858993 CACTAGAGTCAGTACAAAGTTGAGAC 59.141 42.308 0.00 1.34 0.00 3.36
3056 3542 6.515200 GCACTAGAGTCAGTACAAAGTTGAGA 60.515 42.308 0.00 0.00 0.00 3.27
3057 3543 5.631512 GCACTAGAGTCAGTACAAAGTTGAG 59.368 44.000 0.00 0.00 0.00 3.02
3058 3544 5.068591 TGCACTAGAGTCAGTACAAAGTTGA 59.931 40.000 0.00 0.00 0.00 3.18
3059 3545 5.289595 TGCACTAGAGTCAGTACAAAGTTG 58.710 41.667 0.00 0.00 0.00 3.16
3060 3546 5.531122 TGCACTAGAGTCAGTACAAAGTT 57.469 39.130 0.00 0.00 0.00 2.66
3061 3547 5.531122 TTGCACTAGAGTCAGTACAAAGT 57.469 39.130 0.00 0.00 30.58 2.66
3062 3548 6.459257 CTTTGCACTAGAGTCAGTACAAAG 57.541 41.667 21.20 21.20 46.00 2.77
3063 3549 5.914033 ACTTTGCACTAGAGTCAGTACAAA 58.086 37.500 14.81 14.81 38.74 2.83
3064 3550 5.531122 ACTTTGCACTAGAGTCAGTACAA 57.469 39.130 0.00 0.00 31.43 2.41
3065 3551 5.163447 ACAACTTTGCACTAGAGTCAGTACA 60.163 40.000 0.00 0.00 0.00 2.90
3066 3552 5.290386 ACAACTTTGCACTAGAGTCAGTAC 58.710 41.667 0.00 0.00 0.00 2.73
3067 3553 5.531122 ACAACTTTGCACTAGAGTCAGTA 57.469 39.130 0.00 0.00 0.00 2.74
3068 3554 4.408182 ACAACTTTGCACTAGAGTCAGT 57.592 40.909 0.00 0.00 0.00 3.41
3069 3555 5.533482 AGTACAACTTTGCACTAGAGTCAG 58.467 41.667 0.00 0.00 33.18 3.51
3070 3556 5.531122 AGTACAACTTTGCACTAGAGTCA 57.469 39.130 0.00 0.00 33.18 3.41
3071 3557 6.586844 CCTTAGTACAACTTTGCACTAGAGTC 59.413 42.308 0.00 0.00 38.06 3.36
3072 3558 6.041751 ACCTTAGTACAACTTTGCACTAGAGT 59.958 38.462 0.00 2.80 38.06 3.24
3073 3559 6.456501 ACCTTAGTACAACTTTGCACTAGAG 58.543 40.000 0.00 0.00 38.06 2.43
3074 3560 6.415206 ACCTTAGTACAACTTTGCACTAGA 57.585 37.500 0.00 0.00 38.06 2.43
3075 3561 8.597662 TTAACCTTAGTACAACTTTGCACTAG 57.402 34.615 0.00 0.00 38.06 2.57
3076 3562 8.423349 TCTTAACCTTAGTACAACTTTGCACTA 58.577 33.333 0.00 0.00 36.29 2.74
3077 3563 7.226128 GTCTTAACCTTAGTACAACTTTGCACT 59.774 37.037 0.00 0.65 38.32 4.40
3078 3564 7.011669 TGTCTTAACCTTAGTACAACTTTGCAC 59.988 37.037 0.00 0.00 0.00 4.57
3079 3565 7.011669 GTGTCTTAACCTTAGTACAACTTTGCA 59.988 37.037 0.00 0.00 0.00 4.08
3080 3566 7.226128 AGTGTCTTAACCTTAGTACAACTTTGC 59.774 37.037 0.00 0.00 0.00 3.68
3081 3567 8.658499 AGTGTCTTAACCTTAGTACAACTTTG 57.342 34.615 0.00 0.00 0.00 2.77
3089 3575 9.729281 CCCAAAATAAGTGTCTTAACCTTAGTA 57.271 33.333 0.00 0.00 0.00 1.82
3090 3576 8.442374 TCCCAAAATAAGTGTCTTAACCTTAGT 58.558 33.333 0.00 0.00 0.00 2.24
3091 3577 8.727910 GTCCCAAAATAAGTGTCTTAACCTTAG 58.272 37.037 0.00 0.00 0.00 2.18
3092 3578 7.388500 CGTCCCAAAATAAGTGTCTTAACCTTA 59.612 37.037 0.00 0.00 0.00 2.69
3093 3579 6.206048 CGTCCCAAAATAAGTGTCTTAACCTT 59.794 38.462 0.00 0.00 0.00 3.50
3094 3580 5.704053 CGTCCCAAAATAAGTGTCTTAACCT 59.296 40.000 0.00 0.00 0.00 3.50
3095 3581 5.106436 CCGTCCCAAAATAAGTGTCTTAACC 60.106 44.000 0.00 0.00 0.00 2.85
3096 3582 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
3097 3583 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
3098 3584 5.484715 CTCCGTCCCAAAATAAGTGTCTTA 58.515 41.667 0.00 0.00 0.00 2.10
3099 3585 4.324267 CTCCGTCCCAAAATAAGTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
3100 3586 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3101 3587 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3102 3588 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3103 3589 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3104 3590 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3105 3591 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3106 3592 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3107 3593 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3108 3594 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3109 3595 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3110 3596 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3111 3597 1.961133 AAATACTCCCTCCGTCCCAA 58.039 50.000 0.00 0.00 0.00 4.12
3112 3598 1.961133 AAAATACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
3113 3599 2.237893 TGAAAAATACTCCCTCCGTCCC 59.762 50.000 0.00 0.00 0.00 4.46
3114 3600 3.622166 TGAAAAATACTCCCTCCGTCC 57.378 47.619 0.00 0.00 0.00 4.79
3115 3601 4.201920 GCAATGAAAAATACTCCCTCCGTC 60.202 45.833 0.00 0.00 0.00 4.79
3116 3602 3.694566 GCAATGAAAAATACTCCCTCCGT 59.305 43.478 0.00 0.00 0.00 4.69
3117 3603 3.947834 AGCAATGAAAAATACTCCCTCCG 59.052 43.478 0.00 0.00 0.00 4.63
3118 3604 5.654209 AGAAGCAATGAAAAATACTCCCTCC 59.346 40.000 0.00 0.00 0.00 4.30
3119 3605 6.765915 AGAAGCAATGAAAAATACTCCCTC 57.234 37.500 0.00 0.00 0.00 4.30
3120 3606 8.829373 ATAAGAAGCAATGAAAAATACTCCCT 57.171 30.769 0.00 0.00 0.00 4.20
3156 3642 5.574830 CGAATTTTTAACCGGATGCATGAAA 59.425 36.000 9.46 0.00 0.00 2.69
3180 3666 4.569943 TGCTCAATAACACTTCCACTCTC 58.430 43.478 0.00 0.00 0.00 3.20
3181 3667 4.040952 ACTGCTCAATAACACTTCCACTCT 59.959 41.667 0.00 0.00 0.00 3.24
3208 3694 1.000274 GAAAGTCGCCAACCTGCAAAT 60.000 47.619 0.00 0.00 0.00 2.32
3297 3783 5.679638 GCACAAGTTGAAGAGACACCAAAAT 60.680 40.000 10.54 0.00 0.00 1.82
3344 3830 4.236527 TCTCACTAGGTACAGATGAGCA 57.763 45.455 9.57 0.00 37.34 4.26
3407 3893 5.694995 TCCCCTTCCTTTGCTGATATAAAG 58.305 41.667 0.00 0.00 34.49 1.85
3408 3894 5.725551 TCCCCTTCCTTTGCTGATATAAA 57.274 39.130 0.00 0.00 0.00 1.40
3411 3897 3.986134 AGATCCCCTTCCTTTGCTGATAT 59.014 43.478 0.00 0.00 0.00 1.63
3474 3960 4.280436 TGAGCTTTTTAGTCATCCCGAA 57.720 40.909 0.00 0.00 0.00 4.30
3529 4018 7.433708 TGGCATCAAGTTTATATACCGATTG 57.566 36.000 0.00 0.00 0.00 2.67
3533 4022 6.429692 TCCAATGGCATCAAGTTTATATACCG 59.570 38.462 0.00 0.00 0.00 4.02
3577 4067 1.378531 AACAGTGCTGCGAGTTTTCA 58.621 45.000 0.00 0.00 0.00 2.69
3587 4077 3.983344 GTGGCTAATGAAAAACAGTGCTG 59.017 43.478 0.00 0.00 0.00 4.41
3634 4124 6.560253 AAAGTTCAAGATAATGCTTGTCGT 57.440 33.333 0.00 0.00 44.30 4.34
3683 4173 9.542462 CCGTTGTATCATCTTTAGAATTTCCTA 57.458 33.333 0.00 0.00 0.00 2.94
3728 4218 0.466555 AGTGGCTCCTACTCCTAGCG 60.467 60.000 0.00 0.00 37.11 4.26
3750 4240 3.266510 TCCATGGCATCAAGACTGTAC 57.733 47.619 6.96 0.00 0.00 2.90
3769 4259 9.759259 GTAGAAATAAATTTGGCTGCAATTTTC 57.241 29.630 13.64 7.65 35.78 2.29
3864 4373 0.466372 TCCCGGCATGTTTTGTGACA 60.466 50.000 0.00 0.00 0.00 3.58
3870 4379 0.035739 AGTACGTCCCGGCATGTTTT 59.964 50.000 0.00 0.00 0.00 2.43
3877 4386 0.737367 GGTTACAAGTACGTCCCGGC 60.737 60.000 0.00 0.00 0.00 6.13
3879 4388 1.000385 TGTGGTTACAAGTACGTCCCG 60.000 52.381 0.00 0.00 32.88 5.14
3885 4394 2.414138 GTGGCGATGTGGTTACAAGTAC 59.586 50.000 0.00 0.00 40.84 2.73
3887 4396 1.071699 AGTGGCGATGTGGTTACAAGT 59.928 47.619 0.00 0.00 40.84 3.16
3927 4475 1.376609 ATGGATTTCGAGCAACCGCC 61.377 55.000 0.00 0.00 39.83 6.13
3951 4499 2.203195 TGCACCGCTCATATGCCC 60.203 61.111 0.00 0.00 38.63 5.36
3952 4500 2.885676 CGTGCACCGCTCATATGCC 61.886 63.158 12.15 0.00 38.63 4.40
3965 4513 2.179764 GCCATAAAGAAGGCGTGCA 58.820 52.632 0.00 0.00 41.70 4.57
3984 4532 3.182967 CGATGTAGTCAAGGAGCTGAAC 58.817 50.000 0.00 0.00 0.00 3.18
4038 4586 1.799383 GCTTGGTCTAGCTTGCTGC 59.201 57.895 5.26 0.00 43.29 5.25
4073 4621 8.150945 ACCCGCAACATATCATAGATATATTCC 58.849 37.037 0.00 0.00 0.00 3.01
4080 4628 5.003804 GGAAACCCGCAACATATCATAGAT 58.996 41.667 0.00 0.00 0.00 1.98
4115 4663 6.325028 TCTGCTGGAAGTATTAGATGCTAGTT 59.675 38.462 0.00 0.00 35.30 2.24


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

AutoCloner maintained by Alex Coulton.