Multiple sequence alignment - TraesCS6A01G197700

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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 TraesCS6A01G197700 chr6A 100.000 4273 0 0 1 4273 298561304 298565576 0.000000e+00 7891.0
1 TraesCS6A01G197700 chr6A 96.183 262 10 0 1374 1635 76520938 76520677 3.050000e-116 429.0
2 TraesCS6A01G197700 chr6A 94.565 92 5 0 1766 1857 180667599 180667690 4.450000e-30 143.0
3 TraesCS6A01G197700 chr6A 94.565 92 5 0 1766 1857 381087509 381087600 4.450000e-30 143.0
4 TraesCS6A01G197700 chr6D 96.754 1941 36 13 1896 3811 219091357 219089419 0.000000e+00 3210.0
5 TraesCS6A01G197700 chr6D 94.729 1385 59 5 1 1376 219093130 219091751 0.000000e+00 2141.0
6 TraesCS6A01G197700 chr6D 91.684 469 27 7 3809 4273 219089345 219088885 1.300000e-179 640.0
7 TraesCS6A01G197700 chr6D 95.865 266 10 1 1370 1635 388990618 388990882 3.050000e-116 429.0
8 TraesCS6A01G197700 chr6D 86.449 214 29 0 3811 4024 186544660 186544873 7.140000e-58 235.0
9 TraesCS6A01G197700 chr6D 97.778 135 0 1 1633 1764 219091753 219091619 3.320000e-56 230.0
10 TraesCS6A01G197700 chr6D 85.581 215 30 1 3809 4023 60026875 60026662 1.550000e-54 224.0
11 TraesCS6A01G197700 chr6D 84.651 215 33 0 3809 4023 226378913 226379127 9.310000e-52 215.0
12 TraesCS6A01G197700 chr6D 86.735 196 19 3 3812 4007 11692564 11692752 1.200000e-50 211.0
13 TraesCS6A01G197700 chr6D 84.579 214 29 3 3809 4021 200816046 200815836 4.330000e-50 209.0
14 TraesCS6A01G197700 chr6D 84.332 217 30 3 3809 4023 400124143 400124357 4.330000e-50 209.0
15 TraesCS6A01G197700 chr6D 84.653 202 31 0 3809 4010 262897146 262897347 7.240000e-48 202.0
16 TraesCS6A01G197700 chr6D 84.158 202 32 0 3809 4010 130426425 130426224 3.370000e-46 196.0
17 TraesCS6A01G197700 chr6D 82.379 227 35 5 3809 4031 68249429 68249204 4.360000e-45 193.0
18 TraesCS6A01G197700 chr6D 96.053 76 3 0 1829 1904 219091614 219091539 1.610000e-24 124.0
19 TraesCS6A01G197700 chr6B 95.439 1732 46 11 2101 3807 306798848 306800571 0.000000e+00 2730.0
20 TraesCS6A01G197700 chr6B 88.548 978 47 28 437 1376 306797324 306798274 0.000000e+00 1125.0
21 TraesCS6A01G197700 chr6B 92.827 474 21 8 1633 2103 306798272 306798735 0.000000e+00 675.0
22 TraesCS6A01G197700 chr6B 87.500 440 35 5 3 441 306796871 306797291 1.380000e-134 490.0
23 TraesCS6A01G197700 chr6B 82.143 448 51 19 3814 4233 306800735 306801181 1.460000e-94 357.0
24 TraesCS6A01G197700 chr4D 89.947 378 35 2 1 375 163790496 163790119 6.420000e-133 484.0
25 TraesCS6A01G197700 chr4D 87.879 198 24 0 3809 4006 446220305 446220502 2.570000e-57 233.0
26 TraesCS6A01G197700 chr4D 100.000 29 0 0 437 465 163788455 163788427 2.000000e-03 54.7
27 TraesCS6A01G197700 chr2D 96.604 265 9 0 1370 1634 204112948 204112684 1.410000e-119 440.0
28 TraesCS6A01G197700 chr2D 92.157 102 7 1 1766 1866 382198159 382198260 4.450000e-30 143.0
29 TraesCS6A01G197700 chr3D 95.539 269 12 0 1367 1635 586578928 586579196 8.490000e-117 431.0
30 TraesCS6A01G197700 chr3D 95.539 269 9 3 1373 1639 168354629 168354896 1.100000e-115 427.0
31 TraesCS6A01G197700 chr3D 87.097 217 28 0 3809 4025 110402685 110402901 3.300000e-61 246.0
32 TraesCS6A01G197700 chr3D 85.581 215 29 2 3809 4023 250129179 250129391 1.550000e-54 224.0
33 TraesCS6A01G197700 chr3D 98.734 79 1 0 1140 1218 24745358 24745436 1.600000e-29 141.0
34 TraesCS6A01G197700 chr3D 98.551 69 1 0 1150 1218 306007134 306007202 5.800000e-24 122.0
35 TraesCS6A01G197700 chrUn 96.183 262 10 0 1374 1635 108799237 108799498 3.050000e-116 429.0
36 TraesCS6A01G197700 chrUn 95.506 267 11 1 1368 1634 68758073 68758338 3.950000e-115 425.0
37 TraesCS6A01G197700 chrUn 97.436 78 2 0 1141 1218 389316159 389316236 2.680000e-27 134.0
38 TraesCS6A01G197700 chrUn 98.667 75 1 0 1144 1218 389367731 389367657 2.680000e-27 134.0
39 TraesCS6A01G197700 chr7D 95.849 265 10 1 1374 1637 101582739 101583003 1.100000e-115 427.0
40 TraesCS6A01G197700 chr7D 88.372 215 24 1 3809 4023 432329230 432329443 1.520000e-64 257.0
41 TraesCS6A01G197700 chr7D 87.736 212 26 0 3812 4023 254340125 254340336 9.180000e-62 248.0
42 TraesCS6A01G197700 chr7D 86.222 225 28 2 3809 4033 545310558 545310337 1.540000e-59 241.0
43 TraesCS6A01G197700 chr7D 80.165 242 37 9 3194 3432 369172939 369172706 2.040000e-38 171.0
44 TraesCS6A01G197700 chr7D 92.157 102 7 1 1760 1860 393617428 393617327 4.450000e-30 143.0
45 TraesCS6A01G197700 chr4A 94.585 277 14 1 1373 1648 688909919 688909643 1.100000e-115 427.0
46 TraesCS6A01G197700 chr4A 98.667 75 1 0 1144 1218 605364661 605364587 2.680000e-27 134.0
47 TraesCS6A01G197700 chr5D 88.837 215 24 0 3809 4023 449668365 449668579 9.110000e-67 265.0
48 TraesCS6A01G197700 chr5D 86.977 215 28 0 3809 4023 69208925 69209139 4.270000e-60 243.0
49 TraesCS6A01G197700 chr4B 88.889 216 21 3 3809 4023 333980316 333980103 3.280000e-66 263.0
50 TraesCS6A01G197700 chr4B 86.977 215 28 0 3809 4023 426500552 426500766 4.270000e-60 243.0
51 TraesCS6A01G197700 chr5A 87.156 218 27 1 3809 4026 559734579 559734363 3.300000e-61 246.0
52 TraesCS6A01G197700 chr5B 86.239 218 26 4 3809 4024 19957420 19957205 2.570000e-57 233.0
53 TraesCS6A01G197700 chr1D 86.047 215 30 0 3809 4023 315072378 315072164 9.240000e-57 231.0
54 TraesCS6A01G197700 chr1D 85.253 217 29 2 3809 4023 356833095 356832880 2.000000e-53 220.0
55 TraesCS6A01G197700 chr1D 94.565 92 5 0 1766 1857 225936857 225936948 4.450000e-30 143.0
56 TraesCS6A01G197700 chr1D 94.565 92 5 0 1766 1857 225943947 225944038 4.450000e-30 143.0
57 TraesCS6A01G197700 chr7B 89.524 105 11 0 1766 1870 633235686 633235582 2.680000e-27 134.0
58 TraesCS6A01G197700 chr1A 89.623 106 10 1 1755 1859 550890222 550890117 2.680000e-27 134.0
59 TraesCS6A01G197700 chr1A 89.394 66 4 2 3704 3766 210720886 210720951 3.540000e-11 80.5
60 TraesCS6A01G197700 chr2A 89.394 66 4 2 3704 3766 328923090 328923155 3.540000e-11 80.5
61 TraesCS6A01G197700 chr2A 89.394 66 4 2 3704 3766 328926136 328926201 3.540000e-11 80.5
62 TraesCS6A01G197700 chr3A 90.164 61 4 1 3704 3762 291939650 291939710 1.270000e-10 78.7
63 TraesCS6A01G197700 chr7A 86.364 66 4 4 3704 3766 288829676 288829739 2.760000e-07 67.6
64 TraesCS6A01G197700 chr2B 86.885 61 6 1 3704 3762 360045469 360045409 2.760000e-07 67.6


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 TraesCS6A01G197700 chr6A 298561304 298565576 4272 False 7891.00 7891 100.0000 1 4273 1 chr6A.!!$F2 4272
1 TraesCS6A01G197700 chr6D 219088885 219093130 4245 True 1269.00 3210 95.3996 1 4273 5 chr6D.!!$R5 4272
2 TraesCS6A01G197700 chr6B 306796871 306801181 4310 False 1075.40 2730 89.2914 3 4233 5 chr6B.!!$F1 4230
3 TraesCS6A01G197700 chr4D 163788427 163790496 2069 True 269.35 484 94.9735 1 465 2 chr4D.!!$R1 464

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
336 340 0.041238 ACGGAGATGACCAGGAGGAA 59.959 55.000 0.0 0.0 38.69 3.36 F
891 2535 0.741326 TGTCATCTACTGCTCGCCTC 59.259 55.000 0.0 0.0 0.00 4.70 F
2084 3944 1.069227 GCCTGTTTTCCGCACTTGTAG 60.069 52.381 0.0 0.0 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 4242 0.252789 TAATTCAGGGTCGGGGGTCA 60.253 55.0 0.00 0.0 0.0 4.02 R
2270 4245 2.748209 AAATAATTCAGGGTCGGGGG 57.252 50.0 0.00 0.0 0.0 5.40 R
3483 5479 2.032178 TGATCTGATCGTCACTACTGCG 59.968 50.0 12.65 0.0 0.0 5.18 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
103 106 0.397941 GATCGAGAATGGCATGGGGA 59.602 55.000 0.00 0.00 0.00 4.81
201 204 3.635268 GAGCTGCACCTTGAGGGGG 62.635 68.421 1.02 0.00 39.60 5.40
253 257 0.889306 CGAAGACGGAGGAGTCCTTT 59.111 55.000 14.41 2.49 41.34 3.11
254 258 1.272769 CGAAGACGGAGGAGTCCTTTT 59.727 52.381 14.41 0.00 41.34 2.27
282 286 4.648762 CGAAGCATAGGGATGATAGAGGAT 59.351 45.833 0.00 0.00 34.73 3.24
295 299 1.561643 AGAGGATTGCTCCACGAAGA 58.438 50.000 1.04 0.00 44.79 2.87
304 308 1.203523 GCTCCACGAAGAGATGTGAGT 59.796 52.381 10.06 0.00 38.36 3.41
336 340 0.041238 ACGGAGATGACCAGGAGGAA 59.959 55.000 0.00 0.00 38.69 3.36
342 346 3.706373 GACCAGGAGGAAGCGGCA 61.706 66.667 1.45 0.00 38.69 5.69
393 1963 3.913163 GGAGGAGGATGATATTTGTCCCT 59.087 47.826 0.00 0.00 32.31 4.20
395 1965 4.570926 AGGAGGATGATATTTGTCCCTCA 58.429 43.478 0.00 0.00 41.33 3.86
503 2110 2.556622 GGCAAGGATGAAGAAACGGAAA 59.443 45.455 0.00 0.00 0.00 3.13
525 2132 2.489073 GGGTGAATGAGGTTGTCCTTGT 60.489 50.000 0.00 0.00 45.24 3.16
533 2140 3.072330 TGAGGTTGTCCTTGTCATGCTTA 59.928 43.478 0.00 0.00 45.24 3.09
540 2147 5.555966 TGTCCTTGTCATGCTTATTGTACA 58.444 37.500 0.00 0.00 0.00 2.90
611 2225 2.056223 GGAGTAGCGGCCCACTACA 61.056 63.158 25.04 0.00 42.04 2.74
622 2236 2.027192 GGCCCACTACAGATTCTGTTCA 60.027 50.000 23.53 6.85 42.59 3.18
645 2259 2.624316 TAGCTAACGAAGTGACGTGG 57.376 50.000 0.00 0.00 45.00 4.94
663 2277 1.339631 TGGCACGGGATTAAGTGGAAG 60.340 52.381 0.00 0.00 38.68 3.46
718 2332 9.060347 TGATCTAAAGGCTGAAAATGCTAATAG 57.940 33.333 0.00 0.00 0.00 1.73
740 2381 0.976641 TGAGATGGCTGGAAAGACGT 59.023 50.000 0.00 0.00 0.00 4.34
753 2394 6.456988 GCTGGAAAGACGTTCAGTTATAATGG 60.457 42.308 3.52 0.00 38.06 3.16
807 2451 1.340697 ACCGGTAGGGCCAAATCTTTC 60.341 52.381 4.49 0.00 43.47 2.62
811 2455 3.509967 CGGTAGGGCCAAATCTTTCTTTT 59.490 43.478 6.18 0.00 36.97 2.27
891 2535 0.741326 TGTCATCTACTGCTCGCCTC 59.259 55.000 0.00 0.00 0.00 4.70
923 2567 2.663852 CGAAACAACCGCCCGTCT 60.664 61.111 0.00 0.00 0.00 4.18
977 2621 1.601419 TTCTTCCTACGCCCTCACCG 61.601 60.000 0.00 0.00 0.00 4.94
1225 2869 4.536765 CCTATCCAGGTTGCCTTTTACAT 58.463 43.478 0.00 0.00 37.15 2.29
1261 2905 7.920160 TCAAATCAAAATTCCCCTTATTTGC 57.080 32.000 0.00 0.00 34.45 3.68
1341 2985 6.862711 TTGTACGACAATTCATGGTTTGTA 57.137 33.333 12.30 0.12 36.25 2.41
1363 3008 7.732025 TGTACTTAGATTTCACAACTTCCTGA 58.268 34.615 0.00 0.00 0.00 3.86
1378 3023 9.523168 ACAACTTCCTGATCTAGTATATACTCC 57.477 37.037 18.68 7.84 37.73 3.85
1379 3024 8.962679 CAACTTCCTGATCTAGTATATACTCCC 58.037 40.741 18.68 7.53 37.73 4.30
1380 3025 8.471302 ACTTCCTGATCTAGTATATACTCCCT 57.529 38.462 18.68 4.86 37.73 4.20
1381 3026 8.554011 ACTTCCTGATCTAGTATATACTCCCTC 58.446 40.741 18.68 13.26 37.73 4.30
1382 3027 7.454553 TCCTGATCTAGTATATACTCCCTCC 57.545 44.000 18.68 6.90 37.73 4.30
1383 3028 6.099990 TCCTGATCTAGTATATACTCCCTCCG 59.900 46.154 18.68 9.79 37.73 4.63
1384 3029 6.126710 CCTGATCTAGTATATACTCCCTCCGT 60.127 46.154 18.68 0.45 37.73 4.69
1385 3030 7.268212 TGATCTAGTATATACTCCCTCCGTT 57.732 40.000 18.68 0.00 37.73 4.44
1386 3031 7.696981 TGATCTAGTATATACTCCCTCCGTTT 58.303 38.462 18.68 0.00 37.73 3.60
1387 3032 7.828223 TGATCTAGTATATACTCCCTCCGTTTC 59.172 40.741 18.68 5.66 37.73 2.78
1388 3033 7.327064 TCTAGTATATACTCCCTCCGTTTCT 57.673 40.000 18.68 0.00 37.73 2.52
1389 3034 7.753630 TCTAGTATATACTCCCTCCGTTTCTT 58.246 38.462 18.68 0.00 37.73 2.52
1390 3035 8.223330 TCTAGTATATACTCCCTCCGTTTCTTT 58.777 37.037 18.68 0.00 37.73 2.52
1391 3036 7.672122 AGTATATACTCCCTCCGTTTCTTTT 57.328 36.000 9.71 0.00 0.00 2.27
1392 3037 8.087303 AGTATATACTCCCTCCGTTTCTTTTT 57.913 34.615 9.71 0.00 0.00 1.94
1393 3038 9.205513 AGTATATACTCCCTCCGTTTCTTTTTA 57.794 33.333 9.71 0.00 0.00 1.52
1394 3039 9.473640 GTATATACTCCCTCCGTTTCTTTTTAG 57.526 37.037 5.58 0.00 0.00 1.85
1395 3040 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
1396 3041 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
1397 3042 4.001652 CTCCCTCCGTTTCTTTTTAGTCC 58.998 47.826 0.00 0.00 0.00 3.85
1398 3043 2.740447 CCCTCCGTTTCTTTTTAGTCCG 59.260 50.000 0.00 0.00 0.00 4.79
1399 3044 2.159037 CCTCCGTTTCTTTTTAGTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
1400 3045 2.803956 CTCCGTTTCTTTTTAGTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
1401 3046 3.404899 TCCGTTTCTTTTTAGTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
1402 3047 4.567971 TCCGTTTCTTTTTAGTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
1403 3048 5.180271 TCCGTTTCTTTTTAGTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
1404 3049 6.339730 TCCGTTTCTTTTTAGTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
1405 3050 6.817641 TCCGTTTCTTTTTAGTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
1406 3051 7.010738 TCCGTTTCTTTTTAGTCCGCATATAAG 59.989 37.037 0.00 0.00 0.00 1.73
1407 3052 7.123830 CGTTTCTTTTTAGTCCGCATATAAGG 58.876 38.462 0.00 0.00 0.00 2.69
1408 3053 7.010738 CGTTTCTTTTTAGTCCGCATATAAGGA 59.989 37.037 0.00 0.00 0.00 3.36
1409 3054 8.837389 GTTTCTTTTTAGTCCGCATATAAGGAT 58.163 33.333 2.16 0.00 38.97 3.24
1410 3055 8.974060 TTCTTTTTAGTCCGCATATAAGGATT 57.026 30.769 2.16 1.32 38.97 3.01
1411 3056 8.378172 TCTTTTTAGTCCGCATATAAGGATTG 57.622 34.615 2.16 0.00 38.97 2.67
1412 3057 7.444183 TCTTTTTAGTCCGCATATAAGGATTGG 59.556 37.037 2.16 0.00 38.97 3.16
1413 3058 5.818678 TTAGTCCGCATATAAGGATTGGT 57.181 39.130 2.16 0.00 38.97 3.67
1414 3059 4.273148 AGTCCGCATATAAGGATTGGTC 57.727 45.455 2.16 0.00 38.97 4.02
1415 3060 3.646162 AGTCCGCATATAAGGATTGGTCA 59.354 43.478 2.16 0.00 38.97 4.02
1416 3061 4.102524 AGTCCGCATATAAGGATTGGTCAA 59.897 41.667 2.16 0.00 38.97 3.18
1417 3062 4.819630 GTCCGCATATAAGGATTGGTCAAA 59.180 41.667 2.16 0.00 38.97 2.69
1418 3063 5.049405 GTCCGCATATAAGGATTGGTCAAAG 60.049 44.000 2.16 0.00 38.97 2.77
1419 3064 4.821805 CCGCATATAAGGATTGGTCAAAGT 59.178 41.667 0.00 0.00 0.00 2.66
1420 3065 5.049405 CCGCATATAAGGATTGGTCAAAGTC 60.049 44.000 0.00 0.00 0.00 3.01
1421 3066 5.527214 CGCATATAAGGATTGGTCAAAGTCA 59.473 40.000 0.00 0.00 0.00 3.41
1422 3067 6.038161 CGCATATAAGGATTGGTCAAAGTCAA 59.962 38.462 0.00 0.00 0.00 3.18
1423 3068 7.420800 GCATATAAGGATTGGTCAAAGTCAAG 58.579 38.462 0.00 0.00 0.00 3.02
1424 3069 5.904362 ATAAGGATTGGTCAAAGTCAAGC 57.096 39.130 0.00 0.00 0.00 4.01
1425 3070 3.515602 AGGATTGGTCAAAGTCAAGCT 57.484 42.857 0.00 0.00 30.93 3.74
1426 3071 3.837355 AGGATTGGTCAAAGTCAAGCTT 58.163 40.909 0.00 0.00 39.52 3.74
1443 3088 7.478520 TCAAGCTTTGTAGAGTTTGACTAAC 57.521 36.000 0.00 0.00 40.46 2.34
1445 3090 7.769044 TCAAGCTTTGTAGAGTTTGACTAACTT 59.231 33.333 0.00 0.00 47.00 2.66
1446 3091 8.398665 CAAGCTTTGTAGAGTTTGACTAACTTT 58.601 33.333 0.00 1.31 47.00 2.66
1447 3092 9.609346 AAGCTTTGTAGAGTTTGACTAACTTTA 57.391 29.630 3.78 0.37 47.00 1.85
1448 3093 9.780186 AGCTTTGTAGAGTTTGACTAACTTTAT 57.220 29.630 3.78 0.00 47.00 1.40
1499 3144 7.210718 TGAAATCAATATCATCAGATGCACC 57.789 36.000 5.41 0.00 35.67 5.01
1500 3145 6.773685 TGAAATCAATATCATCAGATGCACCA 59.226 34.615 5.41 0.00 35.67 4.17
1501 3146 7.450323 TGAAATCAATATCATCAGATGCACCAT 59.550 33.333 5.41 0.00 35.67 3.55
1502 3147 6.759497 ATCAATATCATCAGATGCACCATG 57.241 37.500 5.41 1.84 35.67 3.66
1503 3148 5.871834 TCAATATCATCAGATGCACCATGA 58.128 37.500 5.41 4.03 35.67 3.07
1504 3149 6.300703 TCAATATCATCAGATGCACCATGAA 58.699 36.000 5.41 0.00 35.67 2.57
1505 3150 6.773685 TCAATATCATCAGATGCACCATGAAA 59.226 34.615 5.41 0.00 35.67 2.69
1506 3151 4.913335 ATCATCAGATGCACCATGAAAC 57.087 40.909 5.41 0.00 31.91 2.78
1507 3152 2.679336 TCATCAGATGCACCATGAAACG 59.321 45.455 5.41 0.00 0.00 3.60
1508 3153 2.183478 TCAGATGCACCATGAAACGT 57.817 45.000 0.00 0.00 0.00 3.99
1509 3154 3.326836 TCAGATGCACCATGAAACGTA 57.673 42.857 0.00 0.00 0.00 3.57
1510 3155 3.872696 TCAGATGCACCATGAAACGTAT 58.127 40.909 0.00 0.00 0.00 3.06
1511 3156 4.260985 TCAGATGCACCATGAAACGTATT 58.739 39.130 0.00 0.00 0.00 1.89
1512 3157 4.699735 TCAGATGCACCATGAAACGTATTT 59.300 37.500 0.00 0.00 0.00 1.40
1513 3158 5.182950 TCAGATGCACCATGAAACGTATTTT 59.817 36.000 0.00 0.00 0.00 1.82
1514 3159 5.512788 CAGATGCACCATGAAACGTATTTTC 59.487 40.000 0.00 0.00 43.63 2.29
1587 3232 9.442047 AATTTGGTCAAAATTTGTGTAGTTTGA 57.558 25.926 5.56 0.00 44.41 2.69
1594 3239 9.134734 TCAAAATTTGTGTAGTTTGACTTTGAC 57.865 29.630 5.56 0.00 35.60 3.18
1595 3240 8.379902 CAAAATTTGTGTAGTTTGACTTTGACC 58.620 33.333 0.00 0.00 33.70 4.02
1596 3241 6.767524 ATTTGTGTAGTTTGACTTTGACCA 57.232 33.333 0.00 0.00 0.00 4.02
1597 3242 6.576662 TTTGTGTAGTTTGACTTTGACCAA 57.423 33.333 0.00 0.00 0.00 3.67
1598 3243 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
1599 3244 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
1600 3245 7.164230 TGTGTAGTTTGACTTTGACCAAATT 57.836 32.000 0.00 0.00 35.14 1.82
1601 3246 7.607250 TGTGTAGTTTGACTTTGACCAAATTT 58.393 30.769 0.00 0.00 35.14 1.82
1602 3247 8.091449 TGTGTAGTTTGACTTTGACCAAATTTT 58.909 29.630 0.00 0.00 35.14 1.82
1603 3248 9.575783 GTGTAGTTTGACTTTGACCAAATTTTA 57.424 29.630 0.00 0.00 35.14 1.52
1609 3254 8.459521 TTGACTTTGACCAAATTTTATATGCG 57.540 30.769 0.00 0.00 0.00 4.73
1610 3255 7.032580 TGACTTTGACCAAATTTTATATGCGG 58.967 34.615 0.00 0.00 0.00 5.69
1611 3256 7.094162 TGACTTTGACCAAATTTTATATGCGGA 60.094 33.333 0.00 0.00 0.00 5.54
1612 3257 7.257722 ACTTTGACCAAATTTTATATGCGGAG 58.742 34.615 0.00 0.00 0.00 4.63
1613 3258 6.767524 TTGACCAAATTTTATATGCGGAGT 57.232 33.333 0.00 0.00 0.00 3.85
1614 3259 7.867305 TTGACCAAATTTTATATGCGGAGTA 57.133 32.000 0.00 0.00 0.00 2.59
1615 3260 7.867305 TGACCAAATTTTATATGCGGAGTAA 57.133 32.000 0.00 0.00 0.00 2.24
1616 3261 8.282455 TGACCAAATTTTATATGCGGAGTAAA 57.718 30.769 0.00 0.00 0.00 2.01
1617 3262 8.740906 TGACCAAATTTTATATGCGGAGTAAAA 58.259 29.630 10.79 10.79 33.41 1.52
1618 3263 9.575783 GACCAAATTTTATATGCGGAGTAAAAA 57.424 29.630 11.91 5.26 32.84 1.94
1619 3264 9.581099 ACCAAATTTTATATGCGGAGTAAAAAG 57.419 29.630 11.91 7.15 32.84 2.27
1620 3265 9.796120 CCAAATTTTATATGCGGAGTAAAAAGA 57.204 29.630 11.91 0.00 32.84 2.52
1624 3269 8.883789 TTTTATATGCGGAGTAAAAAGAAACG 57.116 30.769 7.31 0.00 0.00 3.60
1625 3270 3.824414 ATGCGGAGTAAAAAGAAACGG 57.176 42.857 0.00 0.00 0.00 4.44
1626 3271 2.836262 TGCGGAGTAAAAAGAAACGGA 58.164 42.857 0.00 0.00 0.00 4.69
1627 3272 2.803956 TGCGGAGTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
1628 3273 2.159037 GCGGAGTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
1629 3274 2.740447 CGGAGTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
1630 3275 3.555586 CGGAGTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
1631 3276 4.001652 GGAGTAAAAAGAAACGGAGGGAG 58.998 47.826 0.00 0.00 0.00 4.30
1774 3443 3.983044 ATGCTTATATTCCTCCGTCCC 57.017 47.619 0.00 0.00 0.00 4.46
1775 3444 2.684943 TGCTTATATTCCTCCGTCCCA 58.315 47.619 0.00 0.00 0.00 4.37
1776 3445 3.042682 TGCTTATATTCCTCCGTCCCAA 58.957 45.455 0.00 0.00 0.00 4.12
1777 3446 3.456644 TGCTTATATTCCTCCGTCCCAAA 59.543 43.478 0.00 0.00 0.00 3.28
1778 3447 4.080243 TGCTTATATTCCTCCGTCCCAAAA 60.080 41.667 0.00 0.00 0.00 2.44
1779 3448 5.070685 GCTTATATTCCTCCGTCCCAAAAT 58.929 41.667 0.00 0.00 0.00 1.82
1780 3449 6.183361 TGCTTATATTCCTCCGTCCCAAAATA 60.183 38.462 0.00 0.00 0.00 1.40
1781 3450 6.713450 GCTTATATTCCTCCGTCCCAAAATAA 59.287 38.462 0.00 0.00 0.00 1.40
1791 3460 5.702209 TCCGTCCCAAAATAAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
1847 3516 4.825085 GGTCAAGACACTTATTTTGGGACA 59.175 41.667 2.29 0.00 0.00 4.02
2073 3933 1.981256 TGGAAGAGGTGCCTGTTTTC 58.019 50.000 2.06 1.25 29.30 2.29
2084 3944 1.069227 GCCTGTTTTCCGCACTTGTAG 60.069 52.381 0.00 0.00 0.00 2.74
2267 4242 3.434299 CGTTTTTGCCTTATACGGTGACT 59.566 43.478 0.00 0.00 0.00 3.41
2270 4245 2.953466 TGCCTTATACGGTGACTGAC 57.047 50.000 0.00 0.00 0.00 3.51
3157 5149 5.876651 ATGGTCTATCATACTTGAGCACA 57.123 39.130 0.00 0.00 39.27 4.57
3301 5293 1.890876 ATTTGACGTGTGCCTGCTTA 58.109 45.000 0.00 0.00 0.00 3.09
3367 5361 3.055094 TGGTAGGGCTTGAATCAGTCTTC 60.055 47.826 0.00 0.00 0.00 2.87
3375 5369 5.050499 GGCTTGAATCAGTCTTCGATGTATG 60.050 44.000 0.00 0.00 0.00 2.39
3483 5479 5.699097 AGAGTTATAGCGAGATGAACCTC 57.301 43.478 0.00 0.00 0.00 3.85
3570 5566 7.215719 TCTTTATTCGATGGATATGTCGAGT 57.784 36.000 0.00 0.00 46.14 4.18
3604 5600 3.724716 CGCATAACACAGACAAACATCCG 60.725 47.826 0.00 0.00 0.00 4.18
3617 5613 0.599204 ACATCCGACACGTCCAACAC 60.599 55.000 0.00 0.00 0.00 3.32
3620 5616 0.806884 TCCGACACGTCCAACACAAC 60.807 55.000 0.00 0.00 0.00 3.32
3777 5782 4.878439 ACTACAACGTGTCTTAGCAATCA 58.122 39.130 0.00 0.00 0.00 2.57
3807 5812 6.535508 GCCAACTCTAAGAAGTTATTGATCGT 59.464 38.462 0.00 0.00 37.38 3.73
4136 6330 2.711547 AGCAAAACTCAACCCTAGGTCT 59.288 45.455 8.29 0.00 33.12 3.85
4246 6440 9.202273 GCTTAAGACGAATATGAAGATGAATCT 57.798 33.333 6.67 0.00 39.22 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.605825 ATCCTTACCCAAGATCCCCA 57.394 50.000 0.00 0.00 33.20 4.96
201 204 3.118920 GCCTACTTCCTCTCCTGTCTTTC 60.119 52.174 0.00 0.00 0.00 2.62
242 246 0.034896 TCGTGGCAAAAGGACTCCTC 59.965 55.000 0.00 0.00 30.89 3.71
253 257 0.546122 ATCCCTATGCTTCGTGGCAA 59.454 50.000 8.79 0.00 45.68 4.52
254 258 0.179048 CATCCCTATGCTTCGTGGCA 60.179 55.000 7.40 7.40 46.63 4.92
282 286 1.618343 TCACATCTCTTCGTGGAGCAA 59.382 47.619 0.00 0.00 33.83 3.91
295 299 3.071023 TCGTTCCCTTTTGACTCACATCT 59.929 43.478 0.00 0.00 0.00 2.90
304 308 1.042229 TCTCCGTCGTTCCCTTTTGA 58.958 50.000 0.00 0.00 0.00 2.69
342 346 2.348888 CGTTCCCGTGGGTAGAGCT 61.349 63.158 4.53 0.00 36.47 4.09
393 1963 0.041238 ACGATCCCCTCTTGACCTGA 59.959 55.000 0.00 0.00 0.00 3.86
395 1965 0.978146 CCACGATCCCCTCTTGACCT 60.978 60.000 0.00 0.00 0.00 3.85
503 2110 1.747444 AGGACAACCTCATTCACCCT 58.253 50.000 0.00 0.00 44.13 4.34
525 2132 5.449862 GCCGGAAAATGTACAATAAGCATGA 60.450 40.000 5.05 0.00 0.00 3.07
533 2140 2.099405 CCCAGCCGGAAAATGTACAAT 58.901 47.619 5.05 0.00 0.00 2.71
540 2147 1.682087 GCTTCTACCCAGCCGGAAAAT 60.682 52.381 5.05 0.00 34.64 1.82
611 2225 5.594725 TCGTTAGCTATCCTGAACAGAATCT 59.405 40.000 3.19 0.00 0.00 2.40
622 2236 3.015327 ACGTCACTTCGTTAGCTATCCT 58.985 45.455 0.00 0.00 41.37 3.24
645 2259 2.007608 GACTTCCACTTAATCCCGTGC 58.992 52.381 0.00 0.00 0.00 5.34
663 2277 2.357952 GGGATGATTTTGGCCGTTAGAC 59.642 50.000 0.00 0.00 0.00 2.59
718 2332 2.626840 GTCTTTCCAGCCATCTCAGTC 58.373 52.381 0.00 0.00 0.00 3.51
807 2451 7.148120 ACAGTGAAGGATGATTCTGCATAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
811 2455 5.104817 TCACAGTGAAGGATGATTCTGCATA 60.105 40.000 0.00 0.00 0.00 3.14
999 2643 3.567797 GCGGCGAGGCAAGACATC 61.568 66.667 12.98 0.00 0.00 3.06
1225 2869 3.438216 TTGATTTGATGTGGAGGCTGA 57.562 42.857 0.00 0.00 0.00 4.26
1261 2905 5.799936 GTCATTCCATCAATTTTGTACACCG 59.200 40.000 0.00 0.00 0.00 4.94
1341 2985 7.684529 AGATCAGGAAGTTGTGAAATCTAAGT 58.315 34.615 0.00 0.00 0.00 2.24
1363 3008 7.931046 AGAAACGGAGGGAGTATATACTAGAT 58.069 38.462 15.42 4.35 36.50 1.98
1373 3018 5.279657 GGACTAAAAAGAAACGGAGGGAGTA 60.280 44.000 0.00 0.00 0.00 2.59
1374 3019 4.504514 GGACTAAAAAGAAACGGAGGGAGT 60.505 45.833 0.00 0.00 0.00 3.85
1375 3020 4.001652 GGACTAAAAAGAAACGGAGGGAG 58.998 47.826 0.00 0.00 0.00 4.30
1376 3021 3.555586 CGGACTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
1377 3022 2.740447 CGGACTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
1378 3023 2.159037 GCGGACTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
1379 3024 2.803956 TGCGGACTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
1380 3025 2.836262 TGCGGACTAAAAAGAAACGGA 58.164 42.857 0.00 0.00 0.00 4.69
1381 3026 3.824414 ATGCGGACTAAAAAGAAACGG 57.176 42.857 0.00 0.00 0.00 4.44
1382 3027 7.010738 TCCTTATATGCGGACTAAAAAGAAACG 59.989 37.037 0.00 0.00 0.00 3.60
1383 3028 8.205131 TCCTTATATGCGGACTAAAAAGAAAC 57.795 34.615 0.00 0.00 0.00 2.78
1384 3029 8.974060 ATCCTTATATGCGGACTAAAAAGAAA 57.026 30.769 0.00 0.00 30.90 2.52
1385 3030 8.836413 CAATCCTTATATGCGGACTAAAAAGAA 58.164 33.333 0.00 0.00 30.90 2.52
1386 3031 7.444183 CCAATCCTTATATGCGGACTAAAAAGA 59.556 37.037 0.00 0.00 30.90 2.52
1387 3032 7.228706 ACCAATCCTTATATGCGGACTAAAAAG 59.771 37.037 0.00 0.00 30.90 2.27
1388 3033 7.057894 ACCAATCCTTATATGCGGACTAAAAA 58.942 34.615 0.00 0.00 30.90 1.94
1389 3034 6.597562 ACCAATCCTTATATGCGGACTAAAA 58.402 36.000 0.00 0.00 30.90 1.52
1390 3035 6.182507 ACCAATCCTTATATGCGGACTAAA 57.817 37.500 0.00 0.00 30.90 1.85
1391 3036 5.305902 TGACCAATCCTTATATGCGGACTAA 59.694 40.000 0.00 0.00 30.90 2.24
1392 3037 4.836175 TGACCAATCCTTATATGCGGACTA 59.164 41.667 0.00 0.00 30.90 2.59
1393 3038 3.646162 TGACCAATCCTTATATGCGGACT 59.354 43.478 0.00 0.00 30.90 3.85
1394 3039 4.002906 TGACCAATCCTTATATGCGGAC 57.997 45.455 0.00 0.00 30.90 4.79
1395 3040 4.698201 TTGACCAATCCTTATATGCGGA 57.302 40.909 0.00 0.00 0.00 5.54
1396 3041 4.821805 ACTTTGACCAATCCTTATATGCGG 59.178 41.667 0.00 0.00 0.00 5.69
1397 3042 5.527214 TGACTTTGACCAATCCTTATATGCG 59.473 40.000 0.00 0.00 0.00 4.73
1398 3043 6.942532 TGACTTTGACCAATCCTTATATGC 57.057 37.500 0.00 0.00 0.00 3.14
1399 3044 7.284034 AGCTTGACTTTGACCAATCCTTATATG 59.716 37.037 0.00 0.00 0.00 1.78
1400 3045 7.349598 AGCTTGACTTTGACCAATCCTTATAT 58.650 34.615 0.00 0.00 0.00 0.86
1401 3046 6.721318 AGCTTGACTTTGACCAATCCTTATA 58.279 36.000 0.00 0.00 0.00 0.98
1402 3047 5.574188 AGCTTGACTTTGACCAATCCTTAT 58.426 37.500 0.00 0.00 0.00 1.73
1403 3048 4.985538 AGCTTGACTTTGACCAATCCTTA 58.014 39.130 0.00 0.00 0.00 2.69
1404 3049 3.837355 AGCTTGACTTTGACCAATCCTT 58.163 40.909 0.00 0.00 0.00 3.36
1405 3050 3.515602 AGCTTGACTTTGACCAATCCT 57.484 42.857 0.00 0.00 0.00 3.24
1406 3051 4.590850 AAAGCTTGACTTTGACCAATCC 57.409 40.909 0.00 0.00 47.00 3.01
1416 3061 6.116126 AGTCAAACTCTACAAAGCTTGACTT 58.884 36.000 13.94 3.16 41.70 3.01
1417 3062 5.675538 AGTCAAACTCTACAAAGCTTGACT 58.324 37.500 13.94 13.94 0.00 3.41
1418 3063 5.993106 AGTCAAACTCTACAAAGCTTGAC 57.007 39.130 0.00 10.63 0.00 3.18
1419 3064 7.272978 AGTTAGTCAAACTCTACAAAGCTTGA 58.727 34.615 0.00 0.00 45.64 3.02
1420 3065 7.484035 AGTTAGTCAAACTCTACAAAGCTTG 57.516 36.000 0.00 0.00 45.64 4.01
1473 3118 8.953313 GGTGCATCTGATGATATTGATTTCATA 58.047 33.333 21.30 0.00 32.84 2.15
1474 3119 7.450323 TGGTGCATCTGATGATATTGATTTCAT 59.550 33.333 21.30 0.00 35.33 2.57
1475 3120 6.773685 TGGTGCATCTGATGATATTGATTTCA 59.226 34.615 21.30 2.85 0.00 2.69
1476 3121 7.210718 TGGTGCATCTGATGATATTGATTTC 57.789 36.000 21.30 0.24 0.00 2.17
1477 3122 7.450323 TCATGGTGCATCTGATGATATTGATTT 59.550 33.333 21.30 0.00 0.00 2.17
1478 3123 6.946009 TCATGGTGCATCTGATGATATTGATT 59.054 34.615 21.30 0.00 0.00 2.57
1479 3124 6.481643 TCATGGTGCATCTGATGATATTGAT 58.518 36.000 21.30 2.33 0.00 2.57
1480 3125 5.871834 TCATGGTGCATCTGATGATATTGA 58.128 37.500 21.30 12.59 0.00 2.57
1481 3126 6.569179 TTCATGGTGCATCTGATGATATTG 57.431 37.500 21.30 10.72 0.00 1.90
1482 3127 6.293790 CGTTTCATGGTGCATCTGATGATATT 60.294 38.462 21.30 0.00 0.00 1.28
1483 3128 5.180680 CGTTTCATGGTGCATCTGATGATAT 59.819 40.000 21.30 6.25 0.00 1.63
1484 3129 4.512571 CGTTTCATGGTGCATCTGATGATA 59.487 41.667 21.30 6.40 0.00 2.15
1485 3130 3.314357 CGTTTCATGGTGCATCTGATGAT 59.686 43.478 21.30 2.92 0.00 2.45
1486 3131 2.679336 CGTTTCATGGTGCATCTGATGA 59.321 45.455 21.30 0.00 0.00 2.92
1487 3132 2.421073 ACGTTTCATGGTGCATCTGATG 59.579 45.455 13.26 13.26 0.00 3.07
1488 3133 2.715046 ACGTTTCATGGTGCATCTGAT 58.285 42.857 0.00 0.00 0.00 2.90
1489 3134 2.183478 ACGTTTCATGGTGCATCTGA 57.817 45.000 0.00 0.00 0.00 3.27
1490 3135 4.621068 AATACGTTTCATGGTGCATCTG 57.379 40.909 0.00 0.00 0.00 2.90
1491 3136 5.640732 GAAAATACGTTTCATGGTGCATCT 58.359 37.500 0.00 0.00 44.42 2.90
1492 3137 5.932021 GAAAATACGTTTCATGGTGCATC 57.068 39.130 0.00 0.00 44.42 3.91
1561 3206 9.442047 TCAAACTACACAAATTTTGACCAAATT 57.558 25.926 15.81 2.10 45.50 1.82
1562 3207 8.878769 GTCAAACTACACAAATTTTGACCAAAT 58.121 29.630 15.81 0.00 46.37 2.32
1563 3208 8.245701 GTCAAACTACACAAATTTTGACCAAA 57.754 30.769 15.81 0.00 46.37 3.28
1564 3209 7.820044 GTCAAACTACACAAATTTTGACCAA 57.180 32.000 15.81 0.00 46.37 3.67
1568 3213 9.134734 GTCAAAGTCAAACTACACAAATTTTGA 57.865 29.630 15.81 0.00 35.98 2.69
1569 3214 8.379902 GGTCAAAGTCAAACTACACAAATTTTG 58.620 33.333 7.59 7.59 0.00 2.44
1570 3215 8.091449 TGGTCAAAGTCAAACTACACAAATTTT 58.909 29.630 0.00 0.00 0.00 1.82
1571 3216 7.607250 TGGTCAAAGTCAAACTACACAAATTT 58.393 30.769 0.00 0.00 0.00 1.82
1572 3217 7.164230 TGGTCAAAGTCAAACTACACAAATT 57.836 32.000 0.00 0.00 0.00 1.82
1573 3218 6.767524 TGGTCAAAGTCAAACTACACAAAT 57.232 33.333 0.00 0.00 0.00 2.32
1574 3219 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
1575 3220 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
1576 3221 6.767524 ATTTGGTCAAAGTCAAACTACACA 57.232 33.333 2.55 0.00 35.97 3.72
1577 3222 8.474006 AAAATTTGGTCAAAGTCAAACTACAC 57.526 30.769 0.00 0.00 35.97 2.90
1583 3228 8.920665 CGCATATAAAATTTGGTCAAAGTCAAA 58.079 29.630 0.00 0.00 37.29 2.69
1584 3229 7.543868 CCGCATATAAAATTTGGTCAAAGTCAA 59.456 33.333 0.00 0.00 33.32 3.18
1585 3230 7.032580 CCGCATATAAAATTTGGTCAAAGTCA 58.967 34.615 0.00 0.00 33.32 3.41
1586 3231 7.254852 TCCGCATATAAAATTTGGTCAAAGTC 58.745 34.615 0.00 0.00 33.32 3.01
1587 3232 7.093945 ACTCCGCATATAAAATTTGGTCAAAGT 60.094 33.333 0.00 0.00 33.32 2.66
1588 3233 7.257722 ACTCCGCATATAAAATTTGGTCAAAG 58.742 34.615 0.00 0.00 33.32 2.77
1589 3234 7.164230 ACTCCGCATATAAAATTTGGTCAAA 57.836 32.000 0.00 0.00 34.46 2.69
1590 3235 6.767524 ACTCCGCATATAAAATTTGGTCAA 57.232 33.333 0.00 0.00 0.00 3.18
1591 3236 7.867305 TTACTCCGCATATAAAATTTGGTCA 57.133 32.000 0.00 0.00 0.00 4.02
1592 3237 9.575783 TTTTTACTCCGCATATAAAATTTGGTC 57.424 29.630 0.00 0.00 30.18 4.02
1593 3238 9.581099 CTTTTTACTCCGCATATAAAATTTGGT 57.419 29.630 0.00 0.00 30.18 3.67
1594 3239 9.796120 TCTTTTTACTCCGCATATAAAATTTGG 57.204 29.630 0.00 0.00 30.18 3.28
1598 3243 9.498307 CGTTTCTTTTTACTCCGCATATAAAAT 57.502 29.630 0.00 0.00 30.18 1.82
1599 3244 7.964011 CCGTTTCTTTTTACTCCGCATATAAAA 59.036 33.333 0.00 0.00 0.00 1.52
1600 3245 7.333921 TCCGTTTCTTTTTACTCCGCATATAAA 59.666 33.333 0.00 0.00 0.00 1.40
1601 3246 6.817641 TCCGTTTCTTTTTACTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
1602 3247 6.339730 TCCGTTTCTTTTTACTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
1603 3248 5.180271 TCCGTTTCTTTTTACTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
1604 3249 4.567971 TCCGTTTCTTTTTACTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
1605 3250 3.404899 TCCGTTTCTTTTTACTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
1606 3251 2.803956 CTCCGTTTCTTTTTACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
1607 3252 2.159037 CCTCCGTTTCTTTTTACTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
1608 3253 2.740447 CCCTCCGTTTCTTTTTACTCCG 59.260 50.000 0.00 0.00 0.00 4.63
1609 3254 4.001652 CTCCCTCCGTTTCTTTTTACTCC 58.998 47.826 0.00 0.00 0.00 3.85
1610 3255 4.639334 ACTCCCTCCGTTTCTTTTTACTC 58.361 43.478 0.00 0.00 0.00 2.59
1611 3256 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
1612 3257 5.299949 TGTACTCCCTCCGTTTCTTTTTAC 58.700 41.667 0.00 0.00 0.00 2.01
1613 3258 5.549742 TGTACTCCCTCCGTTTCTTTTTA 57.450 39.130 0.00 0.00 0.00 1.52
1614 3259 4.426736 TGTACTCCCTCCGTTTCTTTTT 57.573 40.909 0.00 0.00 0.00 1.94
1615 3260 4.141551 ACTTGTACTCCCTCCGTTTCTTTT 60.142 41.667 0.00 0.00 0.00 2.27
1616 3261 3.390311 ACTTGTACTCCCTCCGTTTCTTT 59.610 43.478 0.00 0.00 0.00 2.52
1617 3262 2.970640 ACTTGTACTCCCTCCGTTTCTT 59.029 45.455 0.00 0.00 0.00 2.52
1618 3263 2.606378 ACTTGTACTCCCTCCGTTTCT 58.394 47.619 0.00 0.00 0.00 2.52
1619 3264 3.397849 AACTTGTACTCCCTCCGTTTC 57.602 47.619 0.00 0.00 0.00 2.78
1620 3265 3.851458 AAACTTGTACTCCCTCCGTTT 57.149 42.857 0.00 0.00 0.00 3.60
1621 3266 3.135167 TGAAAACTTGTACTCCCTCCGTT 59.865 43.478 0.00 0.00 0.00 4.44
1622 3267 2.701951 TGAAAACTTGTACTCCCTCCGT 59.298 45.455 0.00 0.00 0.00 4.69
1623 3268 3.396260 TGAAAACTTGTACTCCCTCCG 57.604 47.619 0.00 0.00 0.00 4.63
1624 3269 5.070685 ACATTGAAAACTTGTACTCCCTCC 58.929 41.667 0.00 0.00 0.00 4.30
1625 3270 6.635030 AACATTGAAAACTTGTACTCCCTC 57.365 37.500 0.00 0.00 0.00 4.30
1626 3271 8.706322 ATAAACATTGAAAACTTGTACTCCCT 57.294 30.769 0.00 0.00 0.00 4.20
1627 3272 8.793592 AGATAAACATTGAAAACTTGTACTCCC 58.206 33.333 0.00 0.00 0.00 4.30
1764 3433 2.640826 ACACTTATTTTGGGACGGAGGA 59.359 45.455 0.00 0.00 0.00 3.71
1765 3434 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1768 3437 5.704053 AGTTAAGACACTTATTTTGGGACGG 59.296 40.000 0.00 0.00 0.00 4.79
1769 3438 6.796705 AGTTAAGACACTTATTTTGGGACG 57.203 37.500 0.00 0.00 0.00 4.79
1820 3489 7.229907 GTCCCAAAATAAGTGTCTTGACCTTAA 59.770 37.037 12.27 0.00 0.00 1.85
1824 3493 4.825085 TGTCCCAAAATAAGTGTCTTGACC 59.175 41.667 0.00 0.00 0.00 4.02
1847 3516 6.835029 AGATGTTAGTCTAGTACTCCCTCT 57.165 41.667 0.00 0.00 39.80 3.69
2099 3959 6.898912 AAGCTAAGTACGCTGTTAATTACC 57.101 37.500 0.00 0.00 37.87 2.85
2267 4242 0.252789 TAATTCAGGGTCGGGGGTCA 60.253 55.000 0.00 0.00 0.00 4.02
2270 4245 2.748209 AAATAATTCAGGGTCGGGGG 57.252 50.000 0.00 0.00 0.00 5.40
3157 5149 6.893583 ACAGGCATGAATTAAGATAGACTGT 58.106 36.000 4.84 0.00 0.00 3.55
3301 5293 9.859152 AGCTAGATAGAAAAAGGAAATAGCATT 57.141 29.630 0.00 0.00 36.45 3.56
3367 5361 4.724334 CGCTATAACTCGTAGCATACATCG 59.276 45.833 6.04 0.00 43.24 3.84
3375 5369 4.665281 TCATCTCGCTATAACTCGTAGC 57.335 45.455 0.00 0.00 40.83 3.58
3432 5426 3.679502 ACAGCAAAGAACAACAAAGCAAC 59.320 39.130 0.00 0.00 0.00 4.17
3483 5479 2.032178 TGATCTGATCGTCACTACTGCG 59.968 50.000 12.65 0.00 0.00 5.18
3490 5486 4.607955 TCGGTATTTGATCTGATCGTCAC 58.392 43.478 12.65 7.76 0.00 3.67
3558 5554 2.470821 CGGGTTCAACTCGACATATCC 58.529 52.381 2.75 0.00 46.98 2.59
3570 5566 3.269521 TTATGCGGGCCGGGTTCAA 62.270 57.895 29.48 5.20 0.00 2.69
3604 5600 2.904011 TTTGTTGTGTTGGACGTGTC 57.096 45.000 0.00 0.00 0.00 3.67
3777 5782 9.959721 TCAATAACTTCTTAGAGTTGGCTTAAT 57.040 29.630 0.81 0.00 39.99 1.40
3807 5812 4.537751 TGACACAAATTACAAAGGGGACA 58.462 39.130 0.00 0.00 0.00 4.02
3866 6028 7.277539 CCAACGATATAATTTTTGTTGGCATGT 59.722 33.333 16.06 0.00 46.62 3.21
4006 6169 9.669887 TTTTGTTAGTTACTACCTTTGTCTTGA 57.330 29.630 0.00 0.00 0.00 3.02
4113 6307 2.174854 ACCTAGGGTTGAGTTTTGCTGT 59.825 45.455 14.81 0.00 27.29 4.40
4217 6411 8.716646 TCATCTTCATATTCGTCTTAAGCAAA 57.283 30.769 0.00 0.00 0.00 3.68
4219 6413 8.893219 ATTCATCTTCATATTCGTCTTAAGCA 57.107 30.769 0.00 0.00 0.00 3.91
4246 6440 4.462133 TCGTGAACCTTTCAACCCAATTA 58.538 39.130 0.00 0.00 42.15 1.40


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

AutoCloner maintained by Alex Coulton.