Multiple sequence alignment - TraesCS7D01G372100

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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 TraesCS7D01G372100 chr7D 100.000 3822 0 0 979 4800 481596870 481600691 0.000000e+00 7059.0
1 TraesCS7D01G372100 chr7D 100.000 569 0 0 1 569 481595892 481596460 0.000000e+00 1051.0
2 TraesCS7D01G372100 chr7D 90.018 541 36 8 1950 2487 595750361 595749836 0.000000e+00 684.0
3 TraesCS7D01G372100 chr7D 93.243 148 7 1 108 255 510388670 510388814 1.050000e-51 215.0
4 TraesCS7D01G372100 chr7A 95.906 2003 56 7 1022 3018 548561979 548563961 0.000000e+00 3221.0
5 TraesCS7D01G372100 chr7A 93.431 1781 63 23 3050 4800 548563962 548565718 0.000000e+00 2591.0
6 TraesCS7D01G372100 chr7A 90.306 196 6 3 154 339 548560957 548561149 1.330000e-60 244.0
7 TraesCS7D01G372100 chr7A 91.971 137 10 1 1 136 548536954 548537090 1.760000e-44 191.0
8 TraesCS7D01G372100 chr7A 100.000 28 0 0 983 1010 548561883 548561910 9.000000e-03 52.8
9 TraesCS7D01G372100 chr7B 95.379 1623 59 8 1022 2638 506988953 506990565 0.000000e+00 2567.0
10 TraesCS7D01G372100 chr7B 89.742 1628 114 23 2636 4232 506990689 506992294 0.000000e+00 2032.0
11 TraesCS7D01G372100 chr7B 90.909 484 34 5 4319 4800 506992309 506992784 4.050000e-180 641.0
12 TraesCS7D01G372100 chr7B 88.339 283 21 8 1 283 506988294 506988564 3.580000e-86 329.0
13 TraesCS7D01G372100 chr7B 88.068 176 7 8 278 444 506988683 506988853 3.790000e-46 196.0
14 TraesCS7D01G372100 chr7B 84.615 65 6 4 453 513 594069444 594069380 1.440000e-05 62.1
15 TraesCS7D01G372100 chrUn 89.963 538 38 9 1944 2477 70735940 70736465 0.000000e+00 680.0
16 TraesCS7D01G372100 chr5D 90.377 530 34 9 1950 2477 551104690 551105204 0.000000e+00 680.0
17 TraesCS7D01G372100 chr5D 90.207 531 37 7 1950 2477 481096323 481096841 0.000000e+00 678.0
18 TraesCS7D01G372100 chr5D 82.759 145 15 2 97 231 534873177 534873033 2.350000e-23 121.0
19 TraesCS7D01G372100 chr2B 89.852 542 34 11 1950 2487 742354485 742353961 0.000000e+00 676.0
20 TraesCS7D01G372100 chr2B 89.649 541 37 10 1950 2487 684001185 684000661 0.000000e+00 671.0
21 TraesCS7D01G372100 chr2B 89.464 541 37 11 1950 2487 107746551 107746028 0.000000e+00 665.0
22 TraesCS7D01G372100 chr2B 86.408 103 4 1 92 184 263652095 263651993 2.360000e-18 104.0
23 TraesCS7D01G372100 chr2B 98.276 58 1 0 92 149 699043143 699043086 8.500000e-18 102.0
24 TraesCS7D01G372100 chr2B 92.727 55 3 1 143 196 463850551 463850605 1.430000e-10 78.7
25 TraesCS7D01G372100 chr2D 88.971 136 13 2 97 231 629869022 629869156 2.970000e-37 167.0
26 TraesCS7D01G372100 chr2D 84.564 149 7 6 97 231 558729522 558729668 3.010000e-27 134.0
27 TraesCS7D01G372100 chr2D 87.379 103 3 4 92 184 208843898 208843796 5.080000e-20 110.0
28 TraesCS7D01G372100 chr2D 85.714 112 3 4 97 196 563947310 563947200 6.570000e-19 106.0
29 TraesCS7D01G372100 chr3B 90.551 127 9 1 108 231 804242795 804242669 1.070000e-36 165.0
30 TraesCS7D01G372100 chr1D 96.667 60 2 0 172 231 21910933 21910992 3.060000e-17 100.0
31 TraesCS7D01G372100 chr1D 96.667 60 2 0 172 231 21913044 21912985 3.060000e-17 100.0
32 TraesCS7D01G372100 chr2A 85.437 103 5 1 92 184 261642984 261642882 1.100000e-16 99.0
33 TraesCS7D01G372100 chr1B 79.787 94 15 4 477 568 173133256 173133165 1.120000e-06 65.8


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 TraesCS7D01G372100 chr7D 481595892 481600691 4799 False 4055.0 7059 100.00000 1 4800 2 chr7D.!!$F2 4799
1 TraesCS7D01G372100 chr7D 595749836 595750361 525 True 684.0 684 90.01800 1950 2487 1 chr7D.!!$R1 537
2 TraesCS7D01G372100 chr7A 548560957 548565718 4761 False 1527.2 3221 94.91075 154 4800 4 chr7A.!!$F2 4646
3 TraesCS7D01G372100 chr7B 506988294 506992784 4490 False 1153.0 2567 90.48740 1 4800 5 chr7B.!!$F1 4799
4 TraesCS7D01G372100 chrUn 70735940 70736465 525 False 680.0 680 89.96300 1944 2477 1 chrUn.!!$F1 533
5 TraesCS7D01G372100 chr5D 551104690 551105204 514 False 680.0 680 90.37700 1950 2477 1 chr5D.!!$F2 527
6 TraesCS7D01G372100 chr5D 481096323 481096841 518 False 678.0 678 90.20700 1950 2477 1 chr5D.!!$F1 527
7 TraesCS7D01G372100 chr2B 742353961 742354485 524 True 676.0 676 89.85200 1950 2487 1 chr2B.!!$R5 537
8 TraesCS7D01G372100 chr2B 684000661 684001185 524 True 671.0 671 89.64900 1950 2487 1 chr2B.!!$R3 537
9 TraesCS7D01G372100 chr2B 107746028 107746551 523 True 665.0 665 89.46400 1950 2487 1 chr2B.!!$R1 537

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
502 1294 0.036858 GCCTCTCGATCATAAGCCCC 60.037 60.000 0.00 0.00 0.00 5.80 F
522 1314 0.177836 TACACACTGTGCTGCACTGT 59.822 50.000 31.32 31.32 44.93 3.55 F
539 1331 0.181587 TGTTTCGGCCCTCTCACAAA 59.818 50.000 0.00 0.00 0.00 2.83 F
542 1334 0.250727 TTCGGCCCTCTCACAAAAGG 60.251 55.000 0.00 0.00 0.00 3.11 F
1736 2593 1.754201 GCTGGTCCTGAGGTTTTGGTT 60.754 52.381 0.00 0.00 0.00 3.67 F
3514 4514 0.036010 AGCAGTAGTGGCGCAAGAAT 60.036 50.000 10.83 0.00 43.02 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 2569 0.773644 AAACCTCAGGACCAGCATGT 59.226 50.000 0.00 0.00 0.00 3.21 R
1736 2593 1.275010 TCTCCAAATCGTGCTGCACTA 59.725 47.619 28.04 19.53 31.34 2.74 R
1739 2596 1.603456 TTTCTCCAAATCGTGCTGCA 58.397 45.000 0.00 0.00 0.00 4.41 R
1744 2601 3.129287 CCAAGGGATTTCTCCAAATCGTG 59.871 47.826 2.23 1.38 46.33 4.35 R
3539 4548 1.318576 AGGGAAAACGGCTTTCAGTG 58.681 50.000 12.56 0.00 44.61 3.66 R
4699 5737 2.038952 TGATGGGAACTCTGAACACTGG 59.961 50.000 0.00 0.00 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.313172 CCGACGAGGCTATGCATGC 61.313 63.158 11.82 11.82 0.00 4.06
40 41 2.279186 TATGACATCGCCGCGTGG 60.279 61.111 11.67 11.67 38.77 4.94
51 52 2.811747 CGCGTGGCATTACGTCCA 60.812 61.111 0.00 0.00 45.36 4.02
91 92 3.262420 CTTCCCGAAGTAGTGTTGGATG 58.738 50.000 0.00 0.00 33.87 3.51
125 126 6.746120 ACTTGGAGTAGTAGTAGTTTGTGTG 58.254 40.000 0.00 0.00 0.00 3.82
126 127 6.548622 ACTTGGAGTAGTAGTAGTTTGTGTGA 59.451 38.462 0.00 0.00 0.00 3.58
127 128 7.232941 ACTTGGAGTAGTAGTAGTTTGTGTGAT 59.767 37.037 0.00 0.00 0.00 3.06
128 129 6.920817 TGGAGTAGTAGTAGTTTGTGTGATG 58.079 40.000 0.00 0.00 0.00 3.07
129 130 6.492429 TGGAGTAGTAGTAGTTTGTGTGATGT 59.508 38.462 0.00 0.00 0.00 3.06
130 131 7.666804 TGGAGTAGTAGTAGTTTGTGTGATGTA 59.333 37.037 0.00 0.00 0.00 2.29
132 133 8.632906 AGTAGTAGTAGTTTGTGTGATGTAGT 57.367 34.615 0.00 0.00 0.00 2.73
133 134 9.730705 AGTAGTAGTAGTTTGTGTGATGTAGTA 57.269 33.333 0.00 0.00 0.00 1.82
135 136 8.632906 AGTAGTAGTTTGTGTGATGTAGTAGT 57.367 34.615 0.00 0.00 0.00 2.73
136 137 9.075678 AGTAGTAGTTTGTGTGATGTAGTAGTT 57.924 33.333 0.00 0.00 0.00 2.24
137 138 9.688592 GTAGTAGTTTGTGTGATGTAGTAGTTT 57.311 33.333 0.00 0.00 0.00 2.66
138 139 8.589335 AGTAGTTTGTGTGATGTAGTAGTTTG 57.411 34.615 0.00 0.00 0.00 2.93
139 140 8.418662 AGTAGTTTGTGTGATGTAGTAGTTTGA 58.581 33.333 0.00 0.00 0.00 2.69
140 141 9.037737 GTAGTTTGTGTGATGTAGTAGTTTGAA 57.962 33.333 0.00 0.00 0.00 2.69
141 142 7.916552 AGTTTGTGTGATGTAGTAGTTTGAAC 58.083 34.615 0.00 0.00 0.00 3.18
143 144 9.037737 GTTTGTGTGATGTAGTAGTTTGAACTA 57.962 33.333 0.00 0.00 40.37 2.24
144 145 9.772973 TTTGTGTGATGTAGTAGTTTGAACTAT 57.227 29.630 6.85 0.65 42.88 2.12
145 146 8.757164 TGTGTGATGTAGTAGTTTGAACTATG 57.243 34.615 6.85 0.00 42.88 2.23
146 147 8.364894 TGTGTGATGTAGTAGTTTGAACTATGT 58.635 33.333 6.85 1.61 42.88 2.29
147 148 9.204570 GTGTGATGTAGTAGTTTGAACTATGTT 57.795 33.333 6.85 0.50 42.88 2.71
148 149 9.772973 TGTGATGTAGTAGTTTGAACTATGTTT 57.227 29.630 6.85 0.00 42.88 2.83
264 265 4.290969 GAGCACTAGTTTTTGGAGTTTGC 58.709 43.478 0.00 0.00 0.00 3.68
311 436 9.979578 TTTTACATCTAGCATTTGTTTCATGTT 57.020 25.926 0.00 0.00 0.00 2.71
322 454 7.095857 GCATTTGTTTCATGTTCGTTGGATTAA 60.096 33.333 0.00 0.00 0.00 1.40
417 1209 3.503748 AGCCAACAAGTCTTTACAGCATC 59.496 43.478 0.00 0.00 0.00 3.91
431 1223 1.236869 GCATCCCCCATTCCCCAAT 59.763 57.895 0.00 0.00 0.00 3.16
444 1236 3.847042 TCCCCAATACCTCCGATCTAT 57.153 47.619 0.00 0.00 0.00 1.98
445 1237 3.709587 TCCCCAATACCTCCGATCTATC 58.290 50.000 0.00 0.00 0.00 2.08
446 1238 2.766828 CCCCAATACCTCCGATCTATCC 59.233 54.545 0.00 0.00 0.00 2.59
447 1239 3.566775 CCCCAATACCTCCGATCTATCCT 60.567 52.174 0.00 0.00 0.00 3.24
448 1240 4.097418 CCCAATACCTCCGATCTATCCTT 58.903 47.826 0.00 0.00 0.00 3.36
449 1241 4.160626 CCCAATACCTCCGATCTATCCTTC 59.839 50.000 0.00 0.00 0.00 3.46
450 1242 4.142359 CCAATACCTCCGATCTATCCTTCG 60.142 50.000 0.00 0.00 35.19 3.79
451 1243 2.953284 ACCTCCGATCTATCCTTCGA 57.047 50.000 0.00 0.00 37.55 3.71
452 1244 3.225177 ACCTCCGATCTATCCTTCGAA 57.775 47.619 0.00 0.00 37.55 3.71
453 1245 3.563223 ACCTCCGATCTATCCTTCGAAA 58.437 45.455 0.00 0.00 37.55 3.46
454 1246 3.570550 ACCTCCGATCTATCCTTCGAAAG 59.429 47.826 0.00 0.00 37.55 2.62
455 1247 3.821600 CCTCCGATCTATCCTTCGAAAGA 59.178 47.826 0.00 0.00 37.55 2.52
456 1248 4.461081 CCTCCGATCTATCCTTCGAAAGAT 59.539 45.833 13.54 13.54 41.60 2.40
457 1249 5.047660 CCTCCGATCTATCCTTCGAAAGATT 60.048 44.000 14.20 0.00 41.60 2.40
458 1250 6.406692 TCCGATCTATCCTTCGAAAGATTT 57.593 37.500 14.20 1.18 41.60 2.17
459 1251 6.216569 TCCGATCTATCCTTCGAAAGATTTG 58.783 40.000 14.20 8.40 41.60 2.32
460 1252 6.040504 TCCGATCTATCCTTCGAAAGATTTGA 59.959 38.462 14.20 12.76 41.60 2.69
461 1253 6.144724 CCGATCTATCCTTCGAAAGATTTGAC 59.855 42.308 14.20 4.66 41.60 3.18
462 1254 6.129326 CGATCTATCCTTCGAAAGATTTGACG 60.129 42.308 14.20 11.42 41.60 4.35
463 1255 6.203808 TCTATCCTTCGAAAGATTTGACGA 57.796 37.500 14.20 2.53 41.60 4.20
464 1256 6.806751 TCTATCCTTCGAAAGATTTGACGAT 58.193 36.000 14.20 1.59 41.60 3.73
465 1257 7.937649 TCTATCCTTCGAAAGATTTGACGATA 58.062 34.615 14.20 0.00 41.60 2.92
466 1258 8.410912 TCTATCCTTCGAAAGATTTGACGATAA 58.589 33.333 14.20 0.00 41.60 1.75
467 1259 6.642683 TCCTTCGAAAGATTTGACGATAAC 57.357 37.500 0.00 0.00 41.60 1.89
468 1260 5.579511 TCCTTCGAAAGATTTGACGATAACC 59.420 40.000 0.00 0.00 41.60 2.85
469 1261 5.220605 CCTTCGAAAGATTTGACGATAACCC 60.221 44.000 0.00 0.00 41.60 4.11
470 1262 4.186159 TCGAAAGATTTGACGATAACCCC 58.814 43.478 0.00 0.00 33.31 4.95
471 1263 3.311596 CGAAAGATTTGACGATAACCCCC 59.688 47.826 0.00 0.00 0.00 5.40
486 1278 4.089839 CCCCCTATTGGTCTGCCT 57.910 61.111 0.00 0.00 35.27 4.75
487 1279 1.839894 CCCCCTATTGGTCTGCCTC 59.160 63.158 0.00 0.00 35.27 4.70
488 1280 0.695803 CCCCCTATTGGTCTGCCTCT 60.696 60.000 0.00 0.00 35.27 3.69
489 1281 0.761802 CCCCTATTGGTCTGCCTCTC 59.238 60.000 0.00 0.00 35.27 3.20
490 1282 0.390860 CCCTATTGGTCTGCCTCTCG 59.609 60.000 0.00 0.00 35.27 4.04
491 1283 1.403814 CCTATTGGTCTGCCTCTCGA 58.596 55.000 0.00 0.00 35.27 4.04
492 1284 1.967066 CCTATTGGTCTGCCTCTCGAT 59.033 52.381 0.00 0.00 35.27 3.59
493 1285 2.029470 CCTATTGGTCTGCCTCTCGATC 60.029 54.545 0.00 0.00 35.27 3.69
494 1286 1.489481 ATTGGTCTGCCTCTCGATCA 58.511 50.000 0.00 0.00 35.27 2.92
495 1287 1.489481 TTGGTCTGCCTCTCGATCAT 58.511 50.000 0.00 0.00 35.27 2.45
496 1288 2.364972 TGGTCTGCCTCTCGATCATA 57.635 50.000 0.00 0.00 35.27 2.15
497 1289 2.666317 TGGTCTGCCTCTCGATCATAA 58.334 47.619 0.00 0.00 35.27 1.90
498 1290 2.625314 TGGTCTGCCTCTCGATCATAAG 59.375 50.000 0.00 0.00 35.27 1.73
499 1291 2.609244 GGTCTGCCTCTCGATCATAAGC 60.609 54.545 0.00 0.00 0.00 3.09
500 1292 1.615883 TCTGCCTCTCGATCATAAGCC 59.384 52.381 0.00 0.00 0.00 4.35
501 1293 0.681733 TGCCTCTCGATCATAAGCCC 59.318 55.000 0.00 0.00 0.00 5.19
502 1294 0.036858 GCCTCTCGATCATAAGCCCC 60.037 60.000 0.00 0.00 0.00 5.80
503 1295 1.638529 CCTCTCGATCATAAGCCCCT 58.361 55.000 0.00 0.00 0.00 4.79
504 1296 2.808919 CCTCTCGATCATAAGCCCCTA 58.191 52.381 0.00 0.00 0.00 3.53
505 1297 2.494073 CCTCTCGATCATAAGCCCCTAC 59.506 54.545 0.00 0.00 0.00 3.18
506 1298 3.157881 CTCTCGATCATAAGCCCCTACA 58.842 50.000 0.00 0.00 0.00 2.74
507 1299 2.891580 TCTCGATCATAAGCCCCTACAC 59.108 50.000 0.00 0.00 0.00 2.90
508 1300 2.628178 CTCGATCATAAGCCCCTACACA 59.372 50.000 0.00 0.00 0.00 3.72
509 1301 2.364324 TCGATCATAAGCCCCTACACAC 59.636 50.000 0.00 0.00 0.00 3.82
510 1302 2.365617 CGATCATAAGCCCCTACACACT 59.634 50.000 0.00 0.00 0.00 3.55
511 1303 3.733337 GATCATAAGCCCCTACACACTG 58.267 50.000 0.00 0.00 0.00 3.66
512 1304 2.546899 TCATAAGCCCCTACACACTGT 58.453 47.619 0.00 0.00 0.00 3.55
513 1305 2.236146 TCATAAGCCCCTACACACTGTG 59.764 50.000 7.68 7.68 39.75 3.66
514 1306 0.323629 TAAGCCCCTACACACTGTGC 59.676 55.000 9.20 0.00 36.98 4.57
515 1307 1.418908 AAGCCCCTACACACTGTGCT 61.419 55.000 9.20 0.00 36.98 4.40
516 1308 1.672356 GCCCCTACACACTGTGCTG 60.672 63.158 9.20 8.11 36.98 4.41
517 1309 1.672356 CCCCTACACACTGTGCTGC 60.672 63.158 9.20 0.00 36.98 5.25
518 1310 1.071299 CCCTACACACTGTGCTGCA 59.929 57.895 9.20 0.00 36.98 4.41
519 1311 1.230635 CCCTACACACTGTGCTGCAC 61.231 60.000 25.15 25.15 36.98 4.57
520 1312 0.250038 CCTACACACTGTGCTGCACT 60.250 55.000 30.43 13.90 36.98 4.40
521 1313 0.863799 CTACACACTGTGCTGCACTG 59.136 55.000 30.16 30.16 36.98 3.66
522 1314 0.177836 TACACACTGTGCTGCACTGT 59.822 50.000 31.32 31.32 44.93 3.55
523 1315 0.677731 ACACACTGTGCTGCACTGTT 60.678 50.000 33.44 23.77 42.28 3.16
524 1316 0.452987 CACACTGTGCTGCACTGTTT 59.547 50.000 33.44 27.22 42.28 2.83
525 1317 0.734889 ACACTGTGCTGCACTGTTTC 59.265 50.000 33.44 10.24 42.28 2.78
526 1318 0.316442 CACTGTGCTGCACTGTTTCG 60.316 55.000 33.44 22.39 42.28 3.46
527 1319 1.280746 CTGTGCTGCACTGTTTCGG 59.719 57.895 30.43 7.19 35.11 4.30
528 1320 2.050985 GTGCTGCACTGTTTCGGC 60.051 61.111 24.68 4.24 35.26 5.54
529 1321 3.286751 TGCTGCACTGTTTCGGCC 61.287 61.111 0.00 0.00 33.81 6.13
530 1322 4.043200 GCTGCACTGTTTCGGCCC 62.043 66.667 0.00 0.00 0.00 5.80
531 1323 2.281761 CTGCACTGTTTCGGCCCT 60.282 61.111 0.00 0.00 0.00 5.19
532 1324 2.281484 TGCACTGTTTCGGCCCTC 60.281 61.111 0.00 0.00 0.00 4.30
533 1325 2.032681 GCACTGTTTCGGCCCTCT 59.967 61.111 0.00 0.00 0.00 3.69
534 1326 2.035442 GCACTGTTTCGGCCCTCTC 61.035 63.158 0.00 0.00 0.00 3.20
535 1327 1.371183 CACTGTTTCGGCCCTCTCA 59.629 57.895 0.00 0.00 0.00 3.27
536 1328 0.951040 CACTGTTTCGGCCCTCTCAC 60.951 60.000 0.00 0.00 0.00 3.51
537 1329 1.371183 CTGTTTCGGCCCTCTCACA 59.629 57.895 0.00 0.00 0.00 3.58
538 1330 0.250295 CTGTTTCGGCCCTCTCACAA 60.250 55.000 0.00 0.00 0.00 3.33
539 1331 0.181587 TGTTTCGGCCCTCTCACAAA 59.818 50.000 0.00 0.00 0.00 2.83
540 1332 1.314730 GTTTCGGCCCTCTCACAAAA 58.685 50.000 0.00 0.00 0.00 2.44
541 1333 1.266989 GTTTCGGCCCTCTCACAAAAG 59.733 52.381 0.00 0.00 0.00 2.27
542 1334 0.250727 TTCGGCCCTCTCACAAAAGG 60.251 55.000 0.00 0.00 0.00 3.11
547 1339 3.753787 CCTCTCACAAAAGGGGCTT 57.246 52.632 0.00 0.00 27.74 4.35
548 1340 2.879103 CCTCTCACAAAAGGGGCTTA 57.121 50.000 0.00 0.00 27.74 3.09
549 1341 3.154827 CCTCTCACAAAAGGGGCTTAA 57.845 47.619 0.00 0.00 27.74 1.85
550 1342 3.084786 CCTCTCACAAAAGGGGCTTAAG 58.915 50.000 0.00 0.00 27.74 1.85
551 1343 3.244911 CCTCTCACAAAAGGGGCTTAAGA 60.245 47.826 6.67 0.00 27.74 2.10
552 1344 4.568592 CCTCTCACAAAAGGGGCTTAAGAT 60.569 45.833 6.67 0.00 27.74 2.40
553 1345 4.589908 TCTCACAAAAGGGGCTTAAGATC 58.410 43.478 6.67 0.00 0.00 2.75
554 1346 4.042809 TCTCACAAAAGGGGCTTAAGATCA 59.957 41.667 6.67 0.00 0.00 2.92
555 1347 4.735369 TCACAAAAGGGGCTTAAGATCAA 58.265 39.130 6.67 0.00 0.00 2.57
556 1348 5.144100 TCACAAAAGGGGCTTAAGATCAAA 58.856 37.500 6.67 0.00 0.00 2.69
557 1349 5.243730 TCACAAAAGGGGCTTAAGATCAAAG 59.756 40.000 6.67 0.00 0.00 2.77
558 1350 4.528206 ACAAAAGGGGCTTAAGATCAAAGG 59.472 41.667 6.67 0.00 0.00 3.11
559 1351 2.443958 AGGGGCTTAAGATCAAAGGC 57.556 50.000 19.88 19.88 45.93 4.35
564 1356 2.685388 GGCTTAAGATCAAAGGCAGACC 59.315 50.000 21.92 7.30 45.93 3.85
565 1357 3.347216 GCTTAAGATCAAAGGCAGACCA 58.653 45.455 6.67 0.00 39.06 4.02
566 1358 3.758554 GCTTAAGATCAAAGGCAGACCAA 59.241 43.478 6.67 0.00 39.06 3.67
567 1359 4.379918 GCTTAAGATCAAAGGCAGACCAAC 60.380 45.833 6.67 0.00 39.06 3.77
568 1360 2.957402 AGATCAAAGGCAGACCAACA 57.043 45.000 0.00 0.00 39.06 3.33
1012 1804 3.965888 GCTTCCATGGAGAAGGTGT 57.034 52.632 15.53 0.00 42.94 4.16
1016 1808 2.325661 TCCATGGAGAAGGTGTCAGA 57.674 50.000 11.44 0.00 0.00 3.27
1311 2163 2.969443 ACATTTCGCTTTCAGGTTCG 57.031 45.000 0.00 0.00 0.00 3.95
1427 2282 5.869579 TGGAAGTTGAAGCAGAATCTAGTT 58.130 37.500 0.00 0.00 0.00 2.24
1511 2366 8.736244 ACGGGTTTTAATCTAGTAAACTACGTA 58.264 33.333 19.26 0.00 40.13 3.57
1574 2429 3.330267 CGGTTCTTCTAGCAAGCTCTTT 58.670 45.455 0.00 0.00 0.00 2.52
1618 2475 7.998753 GTATACTACCATGGTGTTCAGTTAC 57.001 40.000 28.17 19.43 0.00 2.50
1736 2593 1.754201 GCTGGTCCTGAGGTTTTGGTT 60.754 52.381 0.00 0.00 0.00 3.67
1739 2596 2.781174 TGGTCCTGAGGTTTTGGTTAGT 59.219 45.455 0.00 0.00 0.00 2.24
1744 2601 1.953686 TGAGGTTTTGGTTAGTGCAGC 59.046 47.619 0.00 0.00 0.00 5.25
1745 2602 1.953686 GAGGTTTTGGTTAGTGCAGCA 59.046 47.619 0.00 0.00 0.00 4.41
1919 2776 7.004691 ACTGCAAAAATCTTAAGGTTCCTACT 58.995 34.615 0.38 0.00 0.00 2.57
2274 3133 3.255395 GGTTCTCGCTTATACCCCTACTC 59.745 52.174 0.00 0.00 0.00 2.59
2338 3199 5.689383 TCACTGAAAGGCATGTTAGTTTC 57.311 39.130 0.00 0.00 39.30 2.78
2458 3320 5.437060 TGTTCTTTACAGTCCTCTTTTGCT 58.563 37.500 0.00 0.00 31.68 3.91
2704 3694 9.995003 TTTTGCATTCTTAATGGTCTTGTTTAT 57.005 25.926 0.00 0.00 39.31 1.40
2839 3837 6.566141 TCTGCCATTTCATTACATGATGTTG 58.434 36.000 2.29 0.00 39.39 3.33
2941 3939 1.002379 CTGCTGCAGAGGAAGCCTT 60.002 57.895 24.88 0.00 45.98 4.35
2946 3944 1.538950 CTGCAGAGGAAGCCTTGTTTC 59.461 52.381 8.42 0.00 31.76 2.78
2959 3957 4.083110 AGCCTTGTTTCATCACTGAATTCG 60.083 41.667 0.04 0.00 40.95 3.34
3083 4082 6.037098 CCGTTTTGGTGTTTTGAAGTGATAA 58.963 36.000 0.00 0.00 0.00 1.75
3188 4187 2.035066 CAGGCTTTCAAACCTGTCCTTG 59.965 50.000 9.46 0.00 46.95 3.61
3287 4286 8.565896 TTCACATGCTAATTAATGGGCTATAG 57.434 34.615 12.18 0.00 0.00 1.31
3340 4340 1.670811 CTTATGTAAGCCTGGGTTGCG 59.329 52.381 20.77 3.43 0.00 4.85
3365 4365 7.115520 CGTGTTTGTGATATTTGCAATTTACCA 59.884 33.333 0.00 0.00 0.00 3.25
3366 4366 8.220434 GTGTTTGTGATATTTGCAATTTACCAC 58.780 33.333 0.00 3.75 0.00 4.16
3514 4514 0.036010 AGCAGTAGTGGCGCAAGAAT 60.036 50.000 10.83 0.00 43.02 2.40
3571 4580 1.937191 TTTCCCTTGGATCCCTTTGC 58.063 50.000 9.90 0.00 0.00 3.68
3841 4850 3.119245 TCAGTTACGTACCTGATTCAGCC 60.119 47.826 17.80 0.00 0.00 4.85
3963 4991 2.031012 CGCTCTGGTGGTTCAGCA 59.969 61.111 0.00 0.00 39.63 4.41
3979 5007 1.259770 CAGCAACGACGATGATCATGG 59.740 52.381 14.30 14.93 0.00 3.66
4052 5080 1.156736 GCCACACACAGCGACTAAAT 58.843 50.000 0.00 0.00 0.00 1.40
4055 5083 3.374058 GCCACACACAGCGACTAAATATT 59.626 43.478 0.00 0.00 0.00 1.28
4081 5109 6.533819 ACGTTCGACAAACATATTTCTTGA 57.466 33.333 0.00 0.00 37.77 3.02
4141 5169 5.766150 ACATTCAGAAAATCGTTTGGTGA 57.234 34.783 0.00 0.00 0.00 4.02
4144 5172 7.530010 ACATTCAGAAAATCGTTTGGTGATAG 58.470 34.615 0.00 0.00 0.00 2.08
4145 5173 5.545658 TCAGAAAATCGTTTGGTGATAGC 57.454 39.130 0.00 0.00 0.00 2.97
4146 5174 4.394920 TCAGAAAATCGTTTGGTGATAGCC 59.605 41.667 0.00 0.00 0.00 3.93
4203 5232 0.972883 TATGGTTGCCCCTTTGTTGC 59.027 50.000 0.00 0.00 0.00 4.17
4220 5249 4.337145 TGTTGCACGTTATTATTTCCCCT 58.663 39.130 0.00 0.00 0.00 4.79
4294 5325 5.617751 GCCTACTATTTTGTCACTGCAACAG 60.618 44.000 0.00 0.00 37.52 3.16
4299 5330 5.779529 ATTTTGTCACTGCAACAGAGATT 57.220 34.783 0.78 0.00 34.09 2.40
4432 5466 4.396166 AGTGGAATTGGCGATTAACTTCAG 59.604 41.667 0.00 0.00 0.00 3.02
4578 5614 1.352156 GCGTTGTAGTCGAGGCCAAG 61.352 60.000 5.01 0.00 34.04 3.61
4592 5628 3.600388 AGGCCAAGAAATTGTAGACTCG 58.400 45.455 5.01 0.00 0.00 4.18
4659 5697 9.962759 GACAAATACACTACAAAGGTTTATACG 57.037 33.333 0.00 0.00 0.00 3.06
4718 5756 2.304180 CTCCAGTGTTCAGAGTTCCCAT 59.696 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.654085 ACGCGGCGATGTCATACG 60.654 61.111 30.94 4.09 0.00 3.06
40 41 1.883084 CCTCGGCTGGACGTAATGC 60.883 63.158 0.00 0.00 34.94 3.56
51 52 2.351244 TTCATCTCGTGCCTCGGCT 61.351 57.895 9.65 0.00 42.51 5.52
85 86 5.071788 ACTCCAAGTCTACTTCAACATCCAA 59.928 40.000 0.00 0.00 33.11 3.53
87 88 5.153950 ACTCCAAGTCTACTTCAACATCC 57.846 43.478 0.00 0.00 33.11 3.51
91 92 7.451501 ACTACTACTCCAAGTCTACTTCAAC 57.548 40.000 0.00 0.00 33.11 3.18
144 145 9.862371 TTTGAAGCAAACATAGTTCTTAAAACA 57.138 25.926 0.00 0.00 0.00 2.83
150 151 9.768662 AATTCATTTGAAGCAAACATAGTTCTT 57.231 25.926 0.00 0.00 36.13 2.52
151 152 9.768662 AAATTCATTTGAAGCAAACATAGTTCT 57.231 25.926 0.00 0.00 36.13 3.01
232 233 8.494433 TCCAAAAACTAGTGCTCCAATAGATAT 58.506 33.333 0.00 0.00 35.86 1.63
233 234 7.857456 TCCAAAAACTAGTGCTCCAATAGATA 58.143 34.615 0.00 0.00 35.86 1.98
234 235 6.721318 TCCAAAAACTAGTGCTCCAATAGAT 58.279 36.000 0.00 0.00 35.86 1.98
302 426 6.092748 AGCATTAATCCAACGAACATGAAAC 58.907 36.000 0.00 0.00 0.00 2.78
311 436 2.309528 AGCGAGCATTAATCCAACGA 57.690 45.000 0.00 0.00 0.00 3.85
322 454 2.294233 ACAATGAAACACAAGCGAGCAT 59.706 40.909 0.00 0.00 0.00 3.79
395 1187 2.930950 TGCTGTAAAGACTTGTTGGCT 58.069 42.857 0.00 0.00 33.68 4.75
417 1209 0.482887 GAGGTATTGGGGAATGGGGG 59.517 60.000 0.00 0.00 0.00 5.40
431 1223 4.362470 TTCGAAGGATAGATCGGAGGTA 57.638 45.455 0.00 0.00 39.45 3.08
444 1236 5.579511 GGTTATCGTCAAATCTTTCGAAGGA 59.420 40.000 12.75 12.75 35.99 3.36
445 1237 5.220605 GGGTTATCGTCAAATCTTTCGAAGG 60.221 44.000 0.00 0.00 35.99 3.46
446 1238 5.220605 GGGGTTATCGTCAAATCTTTCGAAG 60.221 44.000 0.00 0.00 35.99 3.79
447 1239 4.632688 GGGGTTATCGTCAAATCTTTCGAA 59.367 41.667 0.00 0.00 35.99 3.71
448 1240 4.186159 GGGGTTATCGTCAAATCTTTCGA 58.814 43.478 0.00 0.00 36.77 3.71
449 1241 3.311596 GGGGGTTATCGTCAAATCTTTCG 59.688 47.826 0.00 0.00 0.00 3.46
450 1242 4.895224 GGGGGTTATCGTCAAATCTTTC 57.105 45.455 0.00 0.00 0.00 2.62
469 1261 0.695803 AGAGGCAGACCAATAGGGGG 60.696 60.000 0.00 0.00 42.91 5.40
470 1262 0.761802 GAGAGGCAGACCAATAGGGG 59.238 60.000 0.00 0.00 42.91 4.79
471 1263 0.390860 CGAGAGGCAGACCAATAGGG 59.609 60.000 0.00 0.00 44.81 3.53
472 1264 1.403814 TCGAGAGGCAGACCAATAGG 58.596 55.000 0.00 0.00 39.06 2.57
473 1265 2.625314 TGATCGAGAGGCAGACCAATAG 59.375 50.000 0.00 0.00 39.06 1.73
474 1266 2.666317 TGATCGAGAGGCAGACCAATA 58.334 47.619 0.00 0.00 39.06 1.90
475 1267 1.489481 TGATCGAGAGGCAGACCAAT 58.511 50.000 0.00 0.00 39.06 3.16
476 1268 1.489481 ATGATCGAGAGGCAGACCAA 58.511 50.000 0.00 0.00 39.06 3.67
477 1269 2.364972 TATGATCGAGAGGCAGACCA 57.635 50.000 0.00 0.00 39.06 4.02
478 1270 2.609244 GCTTATGATCGAGAGGCAGACC 60.609 54.545 0.00 0.00 0.00 3.85
479 1271 2.609244 GGCTTATGATCGAGAGGCAGAC 60.609 54.545 9.67 0.00 35.07 3.51
480 1272 1.615883 GGCTTATGATCGAGAGGCAGA 59.384 52.381 9.67 0.00 35.07 4.26
481 1273 1.337635 GGGCTTATGATCGAGAGGCAG 60.338 57.143 14.49 0.00 36.51 4.85
482 1274 0.681733 GGGCTTATGATCGAGAGGCA 59.318 55.000 14.49 0.00 36.51 4.75
483 1275 0.036858 GGGGCTTATGATCGAGAGGC 60.037 60.000 6.94 6.94 0.00 4.70
484 1276 1.638529 AGGGGCTTATGATCGAGAGG 58.361 55.000 0.00 0.00 0.00 3.69
485 1277 3.057174 GTGTAGGGGCTTATGATCGAGAG 60.057 52.174 0.00 0.00 0.00 3.20
486 1278 2.891580 GTGTAGGGGCTTATGATCGAGA 59.108 50.000 0.00 0.00 0.00 4.04
487 1279 2.628178 TGTGTAGGGGCTTATGATCGAG 59.372 50.000 0.00 0.00 0.00 4.04
488 1280 2.364324 GTGTGTAGGGGCTTATGATCGA 59.636 50.000 0.00 0.00 0.00 3.59
489 1281 2.365617 AGTGTGTAGGGGCTTATGATCG 59.634 50.000 0.00 0.00 0.00 3.69
490 1282 3.134804 ACAGTGTGTAGGGGCTTATGATC 59.865 47.826 0.00 0.00 0.00 2.92
491 1283 3.115390 ACAGTGTGTAGGGGCTTATGAT 58.885 45.455 0.00 0.00 0.00 2.45
492 1284 2.236146 CACAGTGTGTAGGGGCTTATGA 59.764 50.000 15.43 0.00 0.00 2.15
493 1285 2.632377 CACAGTGTGTAGGGGCTTATG 58.368 52.381 15.43 0.00 0.00 1.90
494 1286 1.065418 GCACAGTGTGTAGGGGCTTAT 60.065 52.381 23.73 0.00 35.75 1.73
495 1287 0.323629 GCACAGTGTGTAGGGGCTTA 59.676 55.000 23.73 0.00 35.75 3.09
496 1288 1.073199 GCACAGTGTGTAGGGGCTT 59.927 57.895 23.73 0.00 35.75 4.35
497 1289 1.843376 AGCACAGTGTGTAGGGGCT 60.843 57.895 23.73 11.15 35.75 5.19
498 1290 1.672356 CAGCACAGTGTGTAGGGGC 60.672 63.158 23.73 8.93 35.75 5.80
499 1291 1.672356 GCAGCACAGTGTGTAGGGG 60.672 63.158 23.73 10.45 35.75 4.79
500 1292 1.071299 TGCAGCACAGTGTGTAGGG 59.929 57.895 23.73 12.06 35.75 3.53
501 1293 0.250038 AGTGCAGCACAGTGTGTAGG 60.250 55.000 27.35 14.34 36.74 3.18
502 1294 0.863799 CAGTGCAGCACAGTGTGTAG 59.136 55.000 27.35 16.94 43.60 2.74
503 1295 2.990642 CAGTGCAGCACAGTGTGTA 58.009 52.632 27.35 6.37 43.60 2.90
504 1296 3.817787 CAGTGCAGCACAGTGTGT 58.182 55.556 27.35 8.65 43.60 3.72
508 1300 1.439353 CCGAAACAGTGCAGCACAGT 61.439 55.000 27.35 22.39 35.69 3.55
509 1301 1.280746 CCGAAACAGTGCAGCACAG 59.719 57.895 27.35 21.67 36.74 3.66
510 1302 2.833533 GCCGAAACAGTGCAGCACA 61.834 57.895 27.35 0.00 36.74 4.57
511 1303 2.050985 GCCGAAACAGTGCAGCAC 60.051 61.111 18.55 18.55 34.10 4.40
512 1304 3.286751 GGCCGAAACAGTGCAGCA 61.287 61.111 0.00 0.00 0.00 4.41
513 1305 4.043200 GGGCCGAAACAGTGCAGC 62.043 66.667 0.00 0.00 0.00 5.25
514 1306 2.281761 AGGGCCGAAACAGTGCAG 60.282 61.111 0.00 0.00 0.00 4.41
515 1307 2.281484 GAGGGCCGAAACAGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
516 1308 2.032681 AGAGGGCCGAAACAGTGC 59.967 61.111 0.00 0.00 0.00 4.40
517 1309 0.951040 GTGAGAGGGCCGAAACAGTG 60.951 60.000 0.00 0.00 0.00 3.66
518 1310 1.371558 GTGAGAGGGCCGAAACAGT 59.628 57.895 0.00 0.00 0.00 3.55
519 1311 0.250295 TTGTGAGAGGGCCGAAACAG 60.250 55.000 0.00 0.00 0.00 3.16
520 1312 0.181587 TTTGTGAGAGGGCCGAAACA 59.818 50.000 0.00 0.00 0.00 2.83
521 1313 1.266989 CTTTTGTGAGAGGGCCGAAAC 59.733 52.381 0.00 0.00 0.00 2.78
522 1314 1.604604 CTTTTGTGAGAGGGCCGAAA 58.395 50.000 0.00 0.00 0.00 3.46
523 1315 0.250727 CCTTTTGTGAGAGGGCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
524 1316 1.374947 CCTTTTGTGAGAGGGCCGA 59.625 57.895 0.00 0.00 0.00 5.54
525 1317 1.675641 CCCTTTTGTGAGAGGGCCG 60.676 63.158 0.00 0.00 45.72 6.13
526 1318 4.423231 CCCTTTTGTGAGAGGGCC 57.577 61.111 0.00 0.00 45.72 5.80
529 1321 2.879103 TAAGCCCCTTTTGTGAGAGG 57.121 50.000 0.00 0.00 0.00 3.69
530 1322 4.021102 TCTTAAGCCCCTTTTGTGAGAG 57.979 45.455 0.00 0.00 0.00 3.20
531 1323 4.042809 TGATCTTAAGCCCCTTTTGTGAGA 59.957 41.667 0.00 0.00 0.00 3.27
532 1324 4.335416 TGATCTTAAGCCCCTTTTGTGAG 58.665 43.478 0.00 0.00 0.00 3.51
533 1325 4.380843 TGATCTTAAGCCCCTTTTGTGA 57.619 40.909 0.00 0.00 0.00 3.58
534 1326 5.467035 TTTGATCTTAAGCCCCTTTTGTG 57.533 39.130 0.00 0.00 0.00 3.33
535 1327 4.528206 CCTTTGATCTTAAGCCCCTTTTGT 59.472 41.667 0.00 0.00 0.00 2.83
536 1328 4.621510 GCCTTTGATCTTAAGCCCCTTTTG 60.622 45.833 0.00 0.00 0.00 2.44
537 1329 3.515502 GCCTTTGATCTTAAGCCCCTTTT 59.484 43.478 0.00 0.00 0.00 2.27
538 1330 3.099905 GCCTTTGATCTTAAGCCCCTTT 58.900 45.455 0.00 0.00 0.00 3.11
539 1331 2.042979 TGCCTTTGATCTTAAGCCCCTT 59.957 45.455 0.00 0.00 0.00 3.95
540 1332 1.640670 TGCCTTTGATCTTAAGCCCCT 59.359 47.619 0.00 0.00 0.00 4.79
541 1333 2.027385 CTGCCTTTGATCTTAAGCCCC 58.973 52.381 0.00 0.00 0.00 5.80
542 1334 2.685388 GTCTGCCTTTGATCTTAAGCCC 59.315 50.000 0.00 0.00 0.00 5.19
543 1335 2.685388 GGTCTGCCTTTGATCTTAAGCC 59.315 50.000 0.00 0.00 0.00 4.35
544 1336 3.347216 TGGTCTGCCTTTGATCTTAAGC 58.653 45.455 0.00 0.00 35.27 3.09
545 1337 4.761739 TGTTGGTCTGCCTTTGATCTTAAG 59.238 41.667 0.00 0.00 35.27 1.85
546 1338 4.724399 TGTTGGTCTGCCTTTGATCTTAA 58.276 39.130 0.00 0.00 35.27 1.85
547 1339 4.365514 TGTTGGTCTGCCTTTGATCTTA 57.634 40.909 0.00 0.00 35.27 2.10
548 1340 3.228188 TGTTGGTCTGCCTTTGATCTT 57.772 42.857 0.00 0.00 35.27 2.40
549 1341 2.957402 TGTTGGTCTGCCTTTGATCT 57.043 45.000 0.00 0.00 35.27 2.75
978 1770 1.143889 GAAGCTTTGAGGGATAGGGGG 59.856 57.143 0.00 0.00 0.00 5.40
979 1771 1.143889 GGAAGCTTTGAGGGATAGGGG 59.856 57.143 0.00 0.00 0.00 4.79
980 1772 1.846439 TGGAAGCTTTGAGGGATAGGG 59.154 52.381 0.00 0.00 0.00 3.53
981 1773 3.484407 CATGGAAGCTTTGAGGGATAGG 58.516 50.000 0.00 0.00 0.00 2.57
1010 1802 2.571757 GATCGCCCGTGTCTGACA 59.428 61.111 6.36 6.36 0.00 3.58
1012 1804 3.458163 GGGATCGCCCGTGTCTGA 61.458 66.667 0.00 0.00 46.48 3.27
1122 1974 1.293498 CTTGGTGAGGAGGACACGG 59.707 63.158 0.00 0.00 38.90 4.94
1311 2163 4.809426 CAGACACCTATGGACCGTAAAATC 59.191 45.833 0.00 0.00 0.00 2.17
1427 2282 2.017782 TGCTAAACACCAACGCTTTCA 58.982 42.857 0.00 0.00 0.00 2.69
1497 2352 9.203668 CAACAGTCGTTATACGTAGTTTACTAG 57.796 37.037 0.08 0.00 43.14 2.57
1574 2429 9.305555 AGTATACCTACTCGCAAGGAATATTTA 57.694 33.333 0.00 0.00 37.57 1.40
1598 2455 5.562298 AAGTAACTGAACACCATGGTAGT 57.438 39.130 19.28 14.82 0.00 2.73
1618 2475 7.765307 AGACAAAACATCATGGTAGCATAAAG 58.235 34.615 7.18 2.86 0.00 1.85
1712 2569 0.773644 AAACCTCAGGACCAGCATGT 59.226 50.000 0.00 0.00 0.00 3.21
1736 2593 1.275010 TCTCCAAATCGTGCTGCACTA 59.725 47.619 28.04 19.53 31.34 2.74
1739 2596 1.603456 TTTCTCCAAATCGTGCTGCA 58.397 45.000 0.00 0.00 0.00 4.41
1744 2601 3.129287 CCAAGGGATTTCTCCAAATCGTG 59.871 47.826 2.23 1.38 46.33 4.35
1745 2602 3.245264 ACCAAGGGATTTCTCCAAATCGT 60.245 43.478 2.23 0.00 46.33 3.73
2016 2875 3.260632 GGGTTGGCATCCATTTGTTAACT 59.739 43.478 16.10 0.00 31.53 2.24
2375 3237 9.678260 AATAAGCATATCCTAAATCTTAGCTGG 57.322 33.333 0.00 0.00 0.00 4.85
2458 3320 9.753674 AAGGACAAAAAGATAACATTCTATCCA 57.246 29.630 0.00 0.00 0.00 3.41
2564 3427 7.537596 TGGTCCATTTCAAATTACAGTCAAT 57.462 32.000 0.00 0.00 0.00 2.57
2704 3694 6.209192 ACACAATCCTTAGTGCAATCAAATCA 59.791 34.615 0.00 0.00 39.30 2.57
2941 3939 5.749596 ACAACGAATTCAGTGATGAAACA 57.250 34.783 6.22 0.00 0.00 2.83
2946 3944 9.265938 CATTTTACTACAACGAATTCAGTGATG 57.734 33.333 6.22 3.95 0.00 3.07
2959 3957 8.827677 CCTATGTCTTAGCCATTTTACTACAAC 58.172 37.037 0.00 0.00 0.00 3.32
3083 4082 9.681062 TGGAAAATATTAATCTCGAAGGAAGTT 57.319 29.630 0.00 0.00 0.00 2.66
3105 4104 3.167485 AGATGCTGCCAAAGAAATGGAA 58.833 40.909 0.00 0.00 43.54 3.53
3188 4187 2.271800 GTCGTCCACCTCATCAACATC 58.728 52.381 0.00 0.00 0.00 3.06
3340 4340 8.220434 GTGGTAAATTGCAAATATCACAAACAC 58.780 33.333 23.65 11.71 32.25 3.32
3486 4486 1.630148 CCACTACTGCTGCGTAAGAC 58.370 55.000 0.00 0.00 43.02 3.01
3539 4548 1.318576 AGGGAAAACGGCTTTCAGTG 58.681 50.000 12.56 0.00 44.61 3.66
3571 4580 1.756408 ATCTCCTGCGCTCATCCTGG 61.756 60.000 9.73 0.00 0.00 4.45
3841 4850 6.510879 TGTGGTGTATGTAGTCTTCTGTAG 57.489 41.667 0.00 0.00 0.00 2.74
3878 4890 6.705381 CAGCACATGATTTGGAAACCTTTTAA 59.295 34.615 0.00 0.00 0.00 1.52
3925 4953 2.758356 GCGCTTCACATAAATCGCG 58.242 52.632 0.00 0.00 43.03 5.87
3949 4977 0.531974 GTCGTTGCTGAACCACCAGA 60.532 55.000 0.00 0.00 36.29 3.86
3963 4991 1.539065 GCCTCCATGATCATCGTCGTT 60.539 52.381 4.86 0.00 0.00 3.85
4052 5080 8.714179 AGAAATATGTTTGTCGAACGTTCAATA 58.286 29.630 26.71 12.59 41.29 1.90
4055 5083 6.533819 AGAAATATGTTTGTCGAACGTTCA 57.466 33.333 26.71 12.05 41.29 3.18
4119 5147 5.766150 TCACCAAACGATTTTCTGAATGT 57.234 34.783 0.00 0.00 0.00 2.71
4132 5160 2.386661 ACTCAGGCTATCACCAAACG 57.613 50.000 0.00 0.00 0.00 3.60
4133 5161 3.933332 GTGTACTCAGGCTATCACCAAAC 59.067 47.826 0.00 0.00 0.00 2.93
4141 5169 4.290093 TGATTGGAGTGTACTCAGGCTAT 58.710 43.478 13.51 0.15 44.60 2.97
4144 5172 3.550437 ATGATTGGAGTGTACTCAGGC 57.450 47.619 13.51 0.00 44.60 4.85
4145 5173 3.624861 GCAATGATTGGAGTGTACTCAGG 59.375 47.826 13.51 0.00 44.60 3.86
4146 5174 4.511527 AGCAATGATTGGAGTGTACTCAG 58.488 43.478 13.51 0.00 44.60 3.35
4203 5232 6.753107 AAAGACAGGGGAAATAATAACGTG 57.247 37.500 0.00 0.00 0.00 4.49
4220 5249 3.819368 TCAGATTGGTGAGCAAAAGACA 58.181 40.909 0.00 0.00 0.00 3.41
4412 5446 4.965119 ACTGAAGTTAATCGCCAATTCC 57.035 40.909 0.00 0.00 0.00 3.01
4432 5466 2.359531 TGACACCCGGAAATGTTTGAAC 59.640 45.455 0.73 0.00 0.00 3.18
4578 5614 2.093658 TGGAGGCCGAGTCTACAATTTC 60.094 50.000 0.00 0.00 0.00 2.17
4592 5628 4.799564 TTGTAATTTGACAATGGAGGCC 57.200 40.909 0.00 0.00 34.40 5.19
4644 5682 7.064134 CAGATTGCAGTCGTATAAACCTTTGTA 59.936 37.037 3.29 0.00 0.00 2.41
4659 5697 3.497640 GCTGGATCATACAGATTGCAGTC 59.502 47.826 0.00 0.00 37.00 3.51
4699 5737 2.038952 TGATGGGAACTCTGAACACTGG 59.961 50.000 0.00 0.00 0.00 4.00
4718 5756 3.515502 CCCCGAGGATATTTGATAGCTGA 59.484 47.826 0.00 0.00 33.47 4.26


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

AutoCloner maintained by Alex Coulton.