Multiple sequence alignment - TraesCS2A01G198300

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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 TraesCS2A01G198300 chr2A 100.000 2362 0 0 1 2362 170068995 170071356 0.000000e+00 4362
1 TraesCS2A01G198300 chr2A 95.297 808 38 0 1555 2362 686608873 686609680 0.000000e+00 1282
2 TraesCS2A01G198300 chr2A 91.758 182 14 1 751 932 170069695 170069875 3.900000e-63 252
3 TraesCS2A01G198300 chr2A 91.758 182 14 1 701 881 170069745 170069926 3.900000e-63 252
4 TraesCS2A01G198300 chr2A 87.838 148 17 1 325 472 170069151 170069297 3.120000e-39 172
5 TraesCS2A01G198300 chr2A 87.838 148 17 1 157 303 170069319 170069466 3.120000e-39 172
6 TraesCS2A01G198300 chr2A 83.432 169 23 4 802 969 170069695 170069859 4.070000e-33 152
7 TraesCS2A01G198300 chr2A 83.432 169 23 4 701 865 170069796 170069963 4.070000e-33 152
8 TraesCS2A01G198300 chr6D 95.409 806 37 0 1557 2362 162801559 162802364 0.000000e+00 1284
9 TraesCS2A01G198300 chr4D 95.421 808 34 2 1555 2362 93840944 93840140 0.000000e+00 1284
10 TraesCS2A01G198300 chr2B 92.033 841 47 13 1 839 216341007 216341829 0.000000e+00 1164
11 TraesCS2A01G198300 chr2B 88.889 711 59 8 802 1506 216341691 216342387 0.000000e+00 857
12 TraesCS2A01G198300 chr5D 90.965 808 70 3 1555 2360 203057374 203056568 0.000000e+00 1085
13 TraesCS2A01G198300 chr6B 88.642 810 89 3 1555 2362 501070603 501071411 0.000000e+00 983
14 TraesCS2A01G198300 chr7A 84.119 806 125 3 1556 2360 174843539 174842736 0.000000e+00 776
15 TraesCS2A01G198300 chr6A 83.599 817 128 6 1544 2357 140138294 140139107 0.000000e+00 761
16 TraesCS2A01G198300 chr3D 83.960 798 123 5 1556 2351 380838011 380838805 0.000000e+00 760
17 TraesCS2A01G198300 chr7D 83.684 809 126 6 1555 2360 191502141 191501336 0.000000e+00 758


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 TraesCS2A01G198300 chr2A 170068995 170071356 2361 False 787.714286 4362 89.436571 1 2362 7 chr2A.!!$F2 2361
1 TraesCS2A01G198300 chr2A 686608873 686609680 807 False 1282.000000 1282 95.297000 1555 2362 1 chr2A.!!$F1 807
2 TraesCS2A01G198300 chr6D 162801559 162802364 805 False 1284.000000 1284 95.409000 1557 2362 1 chr6D.!!$F1 805
3 TraesCS2A01G198300 chr4D 93840140 93840944 804 True 1284.000000 1284 95.421000 1555 2362 1 chr4D.!!$R1 807
4 TraesCS2A01G198300 chr2B 216341007 216342387 1380 False 1010.500000 1164 90.461000 1 1506 2 chr2B.!!$F1 1505
5 TraesCS2A01G198300 chr5D 203056568 203057374 806 True 1085.000000 1085 90.965000 1555 2360 1 chr5D.!!$R1 805
6 TraesCS2A01G198300 chr6B 501070603 501071411 808 False 983.000000 983 88.642000 1555 2362 1 chr6B.!!$F1 807
7 TraesCS2A01G198300 chr7A 174842736 174843539 803 True 776.000000 776 84.119000 1556 2360 1 chr7A.!!$R1 804
8 TraesCS2A01G198300 chr6A 140138294 140139107 813 False 761.000000 761 83.599000 1544 2357 1 chr6A.!!$F1 813
9 TraesCS2A01G198300 chr3D 380838011 380838805 794 False 760.000000 760 83.960000 1556 2351 1 chr3D.!!$F1 795
10 TraesCS2A01G198300 chr7D 191501336 191502141 805 True 758.000000 758 83.684000 1555 2360 1 chr7D.!!$R1 805

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
281 283 0.038892 AAATGGCGACGTCGTACAGT 60.039 50.0 35.48 29.21 42.22 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1374 0.036875 CTAGAATTCATCCCCCGCCC 59.963 60.0 8.44 0.0 0.0 6.13 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
44 45 3.963476 AATATTGAAATCCGGGTCCCA 57.037 42.857 9.12 0.00 0.00 4.37
55 56 1.600107 GGGTCCCACATTCAGCGTA 59.400 57.895 1.78 0.00 0.00 4.42
58 59 1.134521 GGTCCCACATTCAGCGTATGA 60.135 52.381 3.30 0.00 35.62 2.15
79 80 6.558771 TGAGAAAAAGATTGATTCGCTTCA 57.441 33.333 0.00 0.00 0.00 3.02
119 121 3.136443 ACCTCGAGATCAAATTGGCCATA 59.864 43.478 15.71 0.00 0.00 2.74
120 122 4.202503 ACCTCGAGATCAAATTGGCCATAT 60.203 41.667 15.71 0.00 0.00 1.78
146 148 0.242825 TGTAACCTGAACTCCGCGAG 59.757 55.000 8.23 5.77 35.52 5.03
163 165 1.419381 GAGAATCCACCCTCCCTCTC 58.581 60.000 0.00 0.00 0.00 3.20
199 201 0.469917 ACTTCCACATATGCTCCGGG 59.530 55.000 0.00 0.00 0.00 5.73
205 207 4.664677 ATATGCTCCGGGCGTCGC 62.665 66.667 9.22 9.22 45.43 5.19
275 277 3.081133 CCAGAAATGGCGACGTCG 58.919 61.111 32.57 32.57 43.27 5.12
276 278 1.736645 CCAGAAATGGCGACGTCGT 60.737 57.895 35.48 18.40 42.22 4.34
277 279 0.457166 CCAGAAATGGCGACGTCGTA 60.457 55.000 35.48 25.79 42.22 3.43
278 280 0.638746 CAGAAATGGCGACGTCGTAC 59.361 55.000 35.48 28.20 42.22 3.67
279 281 0.241749 AGAAATGGCGACGTCGTACA 59.758 50.000 35.48 32.11 42.22 2.90
280 282 0.638746 GAAATGGCGACGTCGTACAG 59.361 55.000 35.48 11.31 42.22 2.74
281 283 0.038892 AAATGGCGACGTCGTACAGT 60.039 50.000 35.48 29.21 42.22 3.55
282 284 0.731514 AATGGCGACGTCGTACAGTG 60.732 55.000 35.48 9.81 42.22 3.66
283 285 2.503375 GGCGACGTCGTACAGTGG 60.503 66.667 35.48 9.06 42.22 4.00
284 286 3.170585 GCGACGTCGTACAGTGGC 61.171 66.667 35.48 15.25 42.22 5.01
285 287 2.559840 CGACGTCGTACAGTGGCT 59.440 61.111 29.08 0.00 34.11 4.75
286 288 1.511464 CGACGTCGTACAGTGGCTC 60.511 63.158 29.08 0.00 34.11 4.70
287 289 1.511464 GACGTCGTACAGTGGCTCG 60.511 63.158 0.00 0.00 0.00 5.03
288 290 2.202440 CGTCGTACAGTGGCTCGG 60.202 66.667 0.00 0.00 0.00 4.63
289 291 2.683859 CGTCGTACAGTGGCTCGGA 61.684 63.158 0.00 0.00 0.00 4.55
322 324 1.153939 CGCTTCTCCACTCCGACTG 60.154 63.158 0.00 0.00 0.00 3.51
323 325 1.587043 CGCTTCTCCACTCCGACTGA 61.587 60.000 0.00 0.00 0.00 3.41
371 374 1.183030 CCAGATATGCCCCGGACGTA 61.183 60.000 0.73 0.02 0.00 3.57
373 376 1.080025 GATATGCCCCGGACGTAGC 60.080 63.158 0.73 0.00 0.00 3.58
398 401 3.423154 CTCTGAACCGCCCGTTGC 61.423 66.667 0.00 0.00 33.74 4.17
399 402 3.883744 CTCTGAACCGCCCGTTGCT 62.884 63.158 0.00 0.00 38.05 3.91
451 454 1.859427 ATGGCGACGTCGTACTGTGT 61.859 55.000 35.48 14.48 42.22 3.72
460 463 2.577593 GTACTGTGTCTCCGGCCC 59.422 66.667 0.00 0.00 0.00 5.80
510 513 0.531532 CCTCTCCGGCTGTATGCAAG 60.532 60.000 0.00 0.00 45.15 4.01
590 593 0.101399 AAGTCGCTCGATACTGGCTG 59.899 55.000 0.00 0.00 0.00 4.85
651 654 2.046507 CTGGTCCTGGCTGTCTGC 60.047 66.667 0.00 0.00 41.94 4.26
801 804 2.695646 GTCCGCATCGACGAAAGC 59.304 61.111 13.71 13.71 34.06 3.51
804 807 4.559386 CGCATCGACGAAAGCGGC 62.559 66.667 29.06 15.76 45.83 6.53
893 896 4.873129 CGCAGTAGCCGTCCGCAT 62.873 66.667 0.00 0.00 41.38 4.73
894 897 2.962253 GCAGTAGCCGTCCGCATC 60.962 66.667 0.00 0.00 41.38 3.91
895 898 2.655364 CAGTAGCCGTCCGCATCG 60.655 66.667 0.00 0.00 41.38 3.84
942 945 2.022129 CGACACAGCGGTCTTCCAC 61.022 63.158 0.00 0.00 35.63 4.02
992 995 4.003788 CGGAGTCCAAGCCACCGT 62.004 66.667 10.49 0.00 38.97 4.83
1006 1009 0.524414 CACCGTCTGTCCGATGTGTA 59.476 55.000 0.00 0.00 0.00 2.90
1007 1010 0.524862 ACCGTCTGTCCGATGTGTAC 59.475 55.000 0.00 0.00 0.00 2.90
1030 1033 2.127118 CGTACGACAACGAGCCGT 60.127 61.111 10.44 0.00 45.68 5.68
1034 1037 3.767230 CGACAACGAGCCGTGCAG 61.767 66.667 0.94 0.00 39.99 4.41
1038 1041 4.988598 AACGAGCCGTGCAGGTGG 62.989 66.667 5.57 0.11 39.99 4.61
1062 1065 2.571548 AGAAAGGCTGAATTGCGGG 58.428 52.632 0.00 0.00 0.00 6.13
1068 1071 2.480555 CTGAATTGCGGGCACGTC 59.519 61.111 11.45 2.41 43.45 4.34
1078 1081 3.134127 GGCACGTCTTCCATGGGC 61.134 66.667 13.02 5.03 40.13 5.36
1088 1091 0.251698 TTCCATGGGCAGTGCATCAA 60.252 50.000 18.61 0.00 0.00 2.57
1091 1094 2.056223 ATGGGCAGTGCATCAAGCC 61.056 57.895 18.61 8.19 46.28 4.35
1097 1100 3.443045 GTGCATCAAGCCGTGGGG 61.443 66.667 0.00 0.00 44.83 4.96
1131 1134 1.077140 TTGCCCAGTCTGCAACACA 60.077 52.632 0.00 0.00 43.36 3.72
1141 1144 0.314935 CTGCAACACAACCCACATCC 59.685 55.000 0.00 0.00 0.00 3.51
1143 1146 0.314935 GCAACACAACCCACATCCAG 59.685 55.000 0.00 0.00 0.00 3.86
1147 1150 0.883833 CACAACCCACATCCAGCTTC 59.116 55.000 0.00 0.00 0.00 3.86
1172 1175 0.464916 AAGACGCCCGGTGAGTTTTT 60.465 50.000 4.58 0.00 0.00 1.94
1173 1176 1.164041 AGACGCCCGGTGAGTTTTTG 61.164 55.000 4.58 0.00 0.00 2.44
1174 1177 1.153127 ACGCCCGGTGAGTTTTTGA 60.153 52.632 4.58 0.00 0.00 2.69
1175 1178 0.536460 ACGCCCGGTGAGTTTTTGAT 60.536 50.000 4.58 0.00 0.00 2.57
1176 1179 0.596082 CGCCCGGTGAGTTTTTGATT 59.404 50.000 0.00 0.00 0.00 2.57
1177 1180 1.401018 CGCCCGGTGAGTTTTTGATTC 60.401 52.381 0.00 0.00 0.00 2.52
1178 1181 1.886542 GCCCGGTGAGTTTTTGATTCT 59.113 47.619 0.00 0.00 0.00 2.40
1179 1182 2.296190 GCCCGGTGAGTTTTTGATTCTT 59.704 45.455 0.00 0.00 0.00 2.52
1187 1190 7.381323 GGTGAGTTTTTGATTCTTGGATGAAT 58.619 34.615 0.00 0.00 39.14 2.57
1227 1230 7.936496 TTATGCCTTGTTAATTCTGACATCA 57.064 32.000 0.00 0.00 0.00 3.07
1236 1239 8.055279 TGTTAATTCTGACATCATTTTCCCTC 57.945 34.615 0.00 0.00 0.00 4.30
1237 1240 7.122650 TGTTAATTCTGACATCATTTTCCCTCC 59.877 37.037 0.00 0.00 0.00 4.30
1242 1245 5.419788 TCTGACATCATTTTCCCTCCAATTG 59.580 40.000 0.00 0.00 0.00 2.32
1250 1253 2.409870 CCCTCCAATTGCAGGCGAC 61.410 63.158 10.20 0.00 0.00 5.19
1277 1280 2.214216 AGCAAGGCACCGGTACTCA 61.214 57.895 6.87 0.00 0.00 3.41
1313 1316 1.983224 CTCGGTCACCACCAAGGAT 59.017 57.895 0.00 0.00 44.02 3.24
1320 1323 1.066215 TCACCACCAAGGATGACATCG 60.066 52.381 9.31 0.00 41.22 3.84
1371 1374 4.657952 GGGATTGAGTTTCCCGGG 57.342 61.111 16.85 16.85 43.38 5.73
1372 1375 1.076995 GGGATTGAGTTTCCCGGGG 60.077 63.158 23.50 6.77 43.38 5.73
1373 1376 1.076995 GGATTGAGTTTCCCGGGGG 60.077 63.158 23.50 0.00 0.00 5.40
1374 1377 1.753078 GATTGAGTTTCCCGGGGGC 60.753 63.158 23.50 11.31 34.68 5.80
1391 1394 1.056660 GGCGGGGGATGAATTCTAGA 58.943 55.000 7.05 0.00 0.00 2.43
1393 1396 2.040412 GGCGGGGGATGAATTCTAGAAT 59.960 50.000 12.37 12.37 0.00 2.40
1417 1426 5.405571 TGCTGTAGTGTTTTCTCTTTCGATC 59.594 40.000 0.00 0.00 0.00 3.69
1418 1427 5.443431 GCTGTAGTGTTTTCTCTTTCGATCG 60.443 44.000 9.36 9.36 0.00 3.69
1429 1438 6.438259 TCTCTTTCGATCGTAGAACTGAAT 57.562 37.500 15.94 0.00 43.58 2.57
1473 1482 2.152016 GTAGAGAAGTGGTGTTTGCCC 58.848 52.381 0.00 0.00 0.00 5.36
1482 1491 1.520600 GGTGTTTGCCCCGGTTGTAG 61.521 60.000 0.00 0.00 0.00 2.74
1483 1492 1.899534 TGTTTGCCCCGGTTGTAGC 60.900 57.895 0.00 0.00 0.00 3.58
1493 1502 2.406130 CCGGTTGTAGCGTAGTGAAAA 58.594 47.619 0.00 0.00 37.40 2.29
1506 1515 5.613795 GCGTAGTGAAAATTGACGATGTGAA 60.614 40.000 0.00 0.00 35.59 3.18
1507 1516 6.359545 CGTAGTGAAAATTGACGATGTGAAA 58.640 36.000 0.00 0.00 35.59 2.69
1508 1517 7.015289 CGTAGTGAAAATTGACGATGTGAAAT 58.985 34.615 0.00 0.00 35.59 2.17
1509 1518 7.533900 CGTAGTGAAAATTGACGATGTGAAATT 59.466 33.333 0.00 0.00 35.59 1.82
1510 1519 9.820229 GTAGTGAAAATTGACGATGTGAAATTA 57.180 29.630 0.00 0.00 0.00 1.40
1512 1521 9.180678 AGTGAAAATTGACGATGTGAAATTAAC 57.819 29.630 0.00 0.00 0.00 2.01
1513 1522 8.963130 GTGAAAATTGACGATGTGAAATTAACA 58.037 29.630 0.00 0.00 0.00 2.41
1514 1523 9.689976 TGAAAATTGACGATGTGAAATTAACAT 57.310 25.926 0.00 0.00 40.93 2.71
1515 1524 9.941991 GAAAATTGACGATGTGAAATTAACATG 57.058 29.630 0.00 0.00 38.37 3.21
1516 1525 9.689976 AAAATTGACGATGTGAAATTAACATGA 57.310 25.926 0.00 0.00 38.37 3.07
1517 1526 9.859427 AAATTGACGATGTGAAATTAACATGAT 57.141 25.926 0.00 0.00 38.37 2.45
1518 1527 8.845942 ATTGACGATGTGAAATTAACATGATG 57.154 30.769 0.00 0.00 38.37 3.07
1519 1528 7.376435 TGACGATGTGAAATTAACATGATGT 57.624 32.000 0.00 0.00 38.37 3.06
1520 1529 7.815641 TGACGATGTGAAATTAACATGATGTT 58.184 30.769 15.80 15.80 43.88 2.71
1521 1530 8.296000 TGACGATGTGAAATTAACATGATGTTT 58.704 29.630 16.75 0.00 41.45 2.83
1522 1531 8.451687 ACGATGTGAAATTAACATGATGTTTG 57.548 30.769 16.75 0.00 41.45 2.93
1523 1532 8.296000 ACGATGTGAAATTAACATGATGTTTGA 58.704 29.630 16.75 6.34 41.45 2.69
1524 1533 9.292846 CGATGTGAAATTAACATGATGTTTGAT 57.707 29.630 16.75 8.38 41.45 2.57
1526 1535 9.932207 ATGTGAAATTAACATGATGTTTGATGT 57.068 25.926 16.75 6.45 41.45 3.06
1527 1536 9.761504 TGTGAAATTAACATGATGTTTGATGTT 57.238 25.926 16.75 4.41 43.55 2.71
1534 1543 9.681692 TTAACATGATGTTTGATGTTTCTGAAG 57.318 29.630 16.75 0.00 41.79 3.02
1535 1544 7.281040 ACATGATGTTTGATGTTTCTGAAGT 57.719 32.000 0.00 0.00 27.94 3.01
1536 1545 7.143340 ACATGATGTTTGATGTTTCTGAAGTG 58.857 34.615 0.00 0.00 27.94 3.16
1537 1546 6.698008 TGATGTTTGATGTTTCTGAAGTGT 57.302 33.333 0.00 0.00 0.00 3.55
1538 1547 6.497437 TGATGTTTGATGTTTCTGAAGTGTG 58.503 36.000 0.00 0.00 0.00 3.82
1539 1548 4.671377 TGTTTGATGTTTCTGAAGTGTGC 58.329 39.130 0.00 0.00 0.00 4.57
1540 1549 3.988379 TTGATGTTTCTGAAGTGTGCC 57.012 42.857 0.00 0.00 0.00 5.01
1541 1550 3.213206 TGATGTTTCTGAAGTGTGCCT 57.787 42.857 0.00 0.00 0.00 4.75
1542 1551 3.554934 TGATGTTTCTGAAGTGTGCCTT 58.445 40.909 0.00 0.00 35.59 4.35
1543 1552 3.953612 TGATGTTTCTGAAGTGTGCCTTT 59.046 39.130 0.00 0.00 32.03 3.11
1544 1553 4.036734 TGATGTTTCTGAAGTGTGCCTTTC 59.963 41.667 0.00 0.00 32.03 2.62
1545 1554 3.620488 TGTTTCTGAAGTGTGCCTTTCT 58.380 40.909 0.00 0.00 32.03 2.52
1546 1555 4.016444 TGTTTCTGAAGTGTGCCTTTCTT 58.984 39.130 0.00 0.00 32.03 2.52
1547 1556 4.096382 TGTTTCTGAAGTGTGCCTTTCTTC 59.904 41.667 0.00 0.00 38.30 2.87
1548 1557 3.558931 TCTGAAGTGTGCCTTTCTTCA 57.441 42.857 0.00 0.00 43.09 3.02
1550 1559 1.949525 TGAAGTGTGCCTTTCTTCAGC 59.050 47.619 0.00 0.00 41.33 4.26
1551 1560 2.225467 GAAGTGTGCCTTTCTTCAGCT 58.775 47.619 0.00 0.00 37.89 4.24
1552 1561 3.181455 TGAAGTGTGCCTTTCTTCAGCTA 60.181 43.478 0.00 0.00 41.33 3.32
1553 1562 2.772287 AGTGTGCCTTTCTTCAGCTAC 58.228 47.619 0.00 0.00 0.00 3.58
1578 1587 4.895668 TTTTCGAGGGTACACCAATAGT 57.104 40.909 0.00 0.00 43.89 2.12
1664 1673 2.435069 TCACAAGTCGACCCTAACCAAA 59.565 45.455 13.01 0.00 0.00 3.28
1691 1700 2.043252 ACACCACTCCCTAGCTCTACTT 59.957 50.000 0.00 0.00 0.00 2.24
1818 1828 1.337354 TGCCAAATACTCTCGCGTTCA 60.337 47.619 5.77 0.00 0.00 3.18
1855 1865 3.307242 GTCCAACAGATTAGCATCACGAC 59.693 47.826 0.00 0.00 0.00 4.34
1930 1940 2.233271 CCACTGCACCAATCTTGAGTT 58.767 47.619 0.00 0.00 0.00 3.01
1941 1951 6.600822 CACCAATCTTGAGTTGTTAGATGGAT 59.399 38.462 0.00 0.00 0.00 3.41
1991 2001 2.186826 GCAGCGGAACCACACTTGT 61.187 57.895 0.00 0.00 0.00 3.16
2011 2021 1.761244 CGCGAGAACACACACTGCAA 61.761 55.000 0.00 0.00 0.00 4.08
2013 2023 1.006086 CGAGAACACACACTGCAACA 58.994 50.000 0.00 0.00 0.00 3.33
2094 2105 0.037326 CAAACCGTGCCTAGCTCTCA 60.037 55.000 0.00 0.00 0.00 3.27
2113 2124 3.295973 TCATATCCGATGTCCACAGTCA 58.704 45.455 0.00 0.00 0.00 3.41
2226 2237 3.398406 TCACACAACATCTTGTACGCAT 58.602 40.909 0.00 0.00 38.66 4.73
2245 2256 4.152402 CGCATAAGAAGCTGTGTAAACACT 59.848 41.667 13.95 0.00 46.55 3.55
2268 2279 2.342279 CGTTCCAAGCCCAGACGA 59.658 61.111 0.00 0.00 35.90 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.701731 ATGTGGGACCCGGATTTCAA 59.298 50.000 0.73 0.00 0.00 2.69
35 36 2.438434 GCTGAATGTGGGACCCGG 60.438 66.667 5.91 0.00 0.00 5.73
44 45 6.992063 ATCTTTTTCTCATACGCTGAATGT 57.008 33.333 0.00 0.00 32.14 2.71
55 56 7.025963 GTGAAGCGAATCAATCTTTTTCTCAT 58.974 34.615 0.00 0.00 0.00 2.90
58 59 6.566197 AGTGAAGCGAATCAATCTTTTTCT 57.434 33.333 0.00 0.00 0.00 2.52
119 121 1.705186 AGTTCAGGTTACACAGGGCAT 59.295 47.619 0.00 0.00 0.00 4.40
120 122 1.071699 GAGTTCAGGTTACACAGGGCA 59.928 52.381 0.00 0.00 0.00 5.36
146 148 1.057275 GGGAGAGGGAGGGTGGATTC 61.057 65.000 0.00 0.00 0.00 2.52
199 201 1.880340 CAGAGGAGGAATGCGACGC 60.880 63.158 14.19 14.19 0.00 5.19
205 207 0.807667 CGCGGTTCAGAGGAGGAATG 60.808 60.000 0.00 0.00 0.00 2.67
270 272 2.559840 CGAGCCACTGTACGACGT 59.440 61.111 5.52 5.52 0.00 4.34
273 275 2.338015 GGTCCGAGCCACTGTACGA 61.338 63.158 0.00 0.00 0.00 3.43
275 277 1.511768 GAGGTCCGAGCCACTGTAC 59.488 63.158 0.00 0.00 0.00 2.90
276 278 1.681327 GGAGGTCCGAGCCACTGTA 60.681 63.158 0.00 0.00 0.00 2.74
277 279 2.997897 GGAGGTCCGAGCCACTGT 60.998 66.667 0.00 0.00 0.00 3.55
301 303 0.456995 GTCGGAGTGGAGAAGCGAAG 60.457 60.000 0.00 0.00 0.00 3.79
302 304 0.894184 AGTCGGAGTGGAGAAGCGAA 60.894 55.000 0.00 0.00 0.00 4.70
304 306 1.153939 CAGTCGGAGTGGAGAAGCG 60.154 63.158 4.87 0.00 0.00 4.68
313 315 1.686741 GGAAGAGGGATCAGTCGGAGT 60.687 57.143 0.00 0.00 0.00 3.85
322 324 2.141448 GGGGACGGGAAGAGGGATC 61.141 68.421 0.00 0.00 0.00 3.36
323 325 2.040779 GGGGACGGGAAGAGGGAT 60.041 66.667 0.00 0.00 0.00 3.85
355 358 1.080025 GCTACGTCCGGGGCATATC 60.080 63.158 0.00 0.00 0.00 1.63
371 374 0.539051 CGGTTCAGAGGAGGAATGCT 59.461 55.000 0.00 0.00 0.00 3.79
373 376 0.462759 GGCGGTTCAGAGGAGGAATG 60.463 60.000 0.00 0.00 0.00 2.67
398 401 1.600636 TTTGGCCAAGACGGAGCAG 60.601 57.895 19.48 0.00 36.56 4.24
399 402 1.896660 GTTTGGCCAAGACGGAGCA 60.897 57.895 19.48 0.00 36.56 4.26
433 436 2.253154 CACAGTACGACGTCGCCA 59.747 61.111 35.92 22.22 44.43 5.69
460 463 1.132199 CGTTATATAGCGCGGCGGAG 61.132 60.000 25.03 0.00 0.00 4.63
470 473 6.153680 AGAGGAGGATCAAAGCCGTTATATAG 59.846 42.308 0.00 0.00 36.25 1.31
481 484 0.105778 GCCGGAGAGGAGGATCAAAG 59.894 60.000 5.05 0.00 45.00 2.77
510 513 2.923121 TGTAAGCTGCTGGAATCCATC 58.077 47.619 0.87 0.00 30.82 3.51
582 585 2.477104 TGAGGATGATCCAGCCAGTA 57.523 50.000 14.90 0.00 43.12 2.74
590 593 2.869636 GCCAAGACGATGAGGATGATCC 60.870 54.545 2.46 2.46 36.58 3.36
784 787 2.695646 GCTTTCGTCGATGCGGAC 59.304 61.111 0.00 0.00 0.00 4.79
785 788 2.878991 CGCTTTCGTCGATGCGGA 60.879 61.111 25.40 0.00 43.97 5.54
787 790 4.559386 GCCGCTTTCGTCGATGCG 62.559 66.667 25.85 25.85 46.74 4.73
788 791 4.559386 CGCCGCTTTCGTCGATGC 62.559 66.667 0.00 3.17 39.65 3.91
789 792 4.559386 GCGCCGCTTTCGTCGATG 62.559 66.667 0.00 0.00 39.65 3.84
872 875 4.849329 GGACGGCTACTGCGTCGG 62.849 72.222 0.00 0.00 40.70 4.79
876 879 4.873129 ATGCGGACGGCTACTGCG 62.873 66.667 6.55 0.00 44.05 5.18
877 880 2.962253 GATGCGGACGGCTACTGC 60.962 66.667 6.55 4.98 44.05 4.40
878 881 2.655364 CGATGCGGACGGCTACTG 60.655 66.667 6.55 0.00 44.05 2.74
928 931 2.029073 CGTGTGGAAGACCGCTGT 59.971 61.111 0.00 0.00 45.89 4.40
937 940 2.975799 GCTTTCGCCCGTGTGGAA 60.976 61.111 0.00 0.00 37.49 3.53
992 995 1.940883 GCGGGTACACATCGGACAGA 61.941 60.000 0.00 0.00 0.00 3.41
1006 1009 4.362476 GTTGTCGTACGGGCGGGT 62.362 66.667 16.52 0.00 0.00 5.28
1038 1041 1.067354 CAATTCAGCCTTTCTGGTGCC 60.067 52.381 0.00 0.00 43.06 5.01
1044 1047 1.598701 GCCCGCAATTCAGCCTTTCT 61.599 55.000 0.00 0.00 0.00 2.52
1062 1065 2.359850 TGCCCATGGAAGACGTGC 60.360 61.111 15.22 6.63 34.66 5.34
1068 1071 0.681887 TGATGCACTGCCCATGGAAG 60.682 55.000 15.22 13.05 0.00 3.46
1078 1081 2.693762 CCCACGGCTTGATGCACTG 61.694 63.158 0.00 0.00 45.15 3.66
1101 1104 3.365265 GGGCAAGCCAGGTTGACG 61.365 66.667 13.87 0.00 36.16 4.35
1122 1125 0.314935 GGATGTGGGTTGTGTTGCAG 59.685 55.000 0.00 0.00 0.00 4.41
1131 1134 1.548582 CCAAGAAGCTGGATGTGGGTT 60.549 52.381 0.00 0.00 38.96 4.11
1147 1150 4.016706 ACCGGGCGTCTTCCCAAG 62.017 66.667 6.32 0.00 46.92 3.61
1172 1175 7.835682 AGGTGTTCATTATTCATCCAAGAATCA 59.164 33.333 0.00 0.00 38.97 2.57
1173 1176 8.230472 AGGTGTTCATTATTCATCCAAGAATC 57.770 34.615 0.00 0.00 38.97 2.52
1174 1177 8.057623 AGAGGTGTTCATTATTCATCCAAGAAT 58.942 33.333 0.00 0.00 40.99 2.40
1175 1178 7.337689 CAGAGGTGTTCATTATTCATCCAAGAA 59.662 37.037 0.00 0.00 0.00 2.52
1176 1179 6.825213 CAGAGGTGTTCATTATTCATCCAAGA 59.175 38.462 0.00 0.00 0.00 3.02
1177 1180 6.825213 TCAGAGGTGTTCATTATTCATCCAAG 59.175 38.462 0.00 0.00 0.00 3.61
1178 1181 6.720309 TCAGAGGTGTTCATTATTCATCCAA 58.280 36.000 0.00 0.00 0.00 3.53
1179 1182 6.312141 TCAGAGGTGTTCATTATTCATCCA 57.688 37.500 0.00 0.00 0.00 3.41
1187 1190 6.252599 AGGCATAATCAGAGGTGTTCATTA 57.747 37.500 0.00 0.00 0.00 1.90
1236 1239 4.481112 GGCGTCGCCTGCAATTGG 62.481 66.667 28.98 0.00 46.69 3.16
1261 1264 1.338674 TGAATGAGTACCGGTGCCTTG 60.339 52.381 19.93 0.00 0.00 3.61
1271 1274 3.316588 TCTCGAGATGGCTGAATGAGTAC 59.683 47.826 12.08 0.00 0.00 2.73
1277 1280 1.340889 GAGCTCTCGAGATGGCTGAAT 59.659 52.381 28.03 9.37 35.01 2.57
1299 1302 2.359900 GATGTCATCCTTGGTGGTGAC 58.640 52.381 0.90 12.15 42.18 3.67
1331 1334 3.181967 CGTTGCCGGAAGCTCGAG 61.182 66.667 5.05 8.45 44.23 4.04
1357 1360 2.359011 GCCCCCGGGAAACTCAAT 59.641 61.111 26.32 0.00 37.50 2.57
1370 1373 1.423794 TAGAATTCATCCCCCGCCCC 61.424 60.000 8.44 0.00 0.00 5.80
1371 1374 0.036875 CTAGAATTCATCCCCCGCCC 59.963 60.000 8.44 0.00 0.00 6.13
1372 1375 1.056660 TCTAGAATTCATCCCCCGCC 58.943 55.000 8.44 0.00 0.00 6.13
1373 1376 2.930826 TTCTAGAATTCATCCCCCGC 57.069 50.000 8.44 0.00 0.00 6.13
1374 1377 3.077359 GCATTCTAGAATTCATCCCCCG 58.923 50.000 15.49 2.60 0.00 5.73
1391 1394 5.758296 TCGAAAGAGAAAACACTACAGCATT 59.242 36.000 0.00 0.00 34.84 3.56
1393 1396 4.689071 TCGAAAGAGAAAACACTACAGCA 58.311 39.130 0.00 0.00 34.84 4.41
1417 1426 7.330946 TCAATAGACCAACAATTCAGTTCTACG 59.669 37.037 0.00 0.00 0.00 3.51
1418 1427 8.547967 TCAATAGACCAACAATTCAGTTCTAC 57.452 34.615 0.00 0.00 0.00 2.59
1429 1438 7.112122 ACTGATGCTAATCAATAGACCAACAA 58.888 34.615 0.00 0.00 42.28 2.83
1473 1482 2.068837 TTTCACTACGCTACAACCGG 57.931 50.000 0.00 0.00 0.00 5.28
1482 1491 4.081761 CACATCGTCAATTTTCACTACGC 58.918 43.478 0.00 0.00 33.75 4.42
1483 1492 5.509605 TCACATCGTCAATTTTCACTACG 57.490 39.130 0.00 0.00 34.99 3.51
1493 1502 8.461222 ACATCATGTTAATTTCACATCGTCAAT 58.539 29.630 0.00 0.00 32.25 2.57
1508 1517 9.681692 CTTCAGAAACATCAAACATCATGTTAA 57.318 29.630 2.67 0.00 41.42 2.01
1509 1518 8.849168 ACTTCAGAAACATCAAACATCATGTTA 58.151 29.630 2.67 0.00 41.42 2.41
1510 1519 7.650504 CACTTCAGAAACATCAAACATCATGTT 59.349 33.333 0.00 0.00 43.61 2.71
1511 1520 7.143340 CACTTCAGAAACATCAAACATCATGT 58.857 34.615 0.00 0.00 34.58 3.21
1512 1521 7.114388 CACACTTCAGAAACATCAAACATCATG 59.886 37.037 0.00 0.00 0.00 3.07
1513 1522 7.143340 CACACTTCAGAAACATCAAACATCAT 58.857 34.615 0.00 0.00 0.00 2.45
1514 1523 6.497437 CACACTTCAGAAACATCAAACATCA 58.503 36.000 0.00 0.00 0.00 3.07
1515 1524 5.400485 GCACACTTCAGAAACATCAAACATC 59.600 40.000 0.00 0.00 0.00 3.06
1516 1525 5.284079 GCACACTTCAGAAACATCAAACAT 58.716 37.500 0.00 0.00 0.00 2.71
1517 1526 4.439974 GGCACACTTCAGAAACATCAAACA 60.440 41.667 0.00 0.00 0.00 2.83
1518 1527 4.044426 GGCACACTTCAGAAACATCAAAC 58.956 43.478 0.00 0.00 0.00 2.93
1519 1528 3.953612 AGGCACACTTCAGAAACATCAAA 59.046 39.130 0.00 0.00 0.00 2.69
1520 1529 3.554934 AGGCACACTTCAGAAACATCAA 58.445 40.909 0.00 0.00 0.00 2.57
1521 1530 3.213206 AGGCACACTTCAGAAACATCA 57.787 42.857 0.00 0.00 0.00 3.07
1522 1531 4.276926 AGAAAGGCACACTTCAGAAACATC 59.723 41.667 0.00 0.00 38.85 3.06
1523 1532 4.210331 AGAAAGGCACACTTCAGAAACAT 58.790 39.130 0.00 0.00 38.85 2.71
1524 1533 3.620488 AGAAAGGCACACTTCAGAAACA 58.380 40.909 0.00 0.00 38.85 2.83
1525 1534 4.096382 TGAAGAAAGGCACACTTCAGAAAC 59.904 41.667 13.29 0.00 42.91 2.78
1526 1535 4.269183 TGAAGAAAGGCACACTTCAGAAA 58.731 39.130 13.29 0.00 42.91 2.52
1527 1536 3.884895 TGAAGAAAGGCACACTTCAGAA 58.115 40.909 13.29 0.00 42.91 3.02
1528 1537 3.558931 TGAAGAAAGGCACACTTCAGA 57.441 42.857 13.29 0.00 42.91 3.27
1530 1539 1.949525 GCTGAAGAAAGGCACACTTCA 59.050 47.619 15.36 15.36 44.66 3.02
1531 1540 2.225467 AGCTGAAGAAAGGCACACTTC 58.775 47.619 0.00 0.00 38.85 3.01
1532 1541 2.355010 AGCTGAAGAAAGGCACACTT 57.645 45.000 0.00 0.00 42.52 3.16
1533 1542 2.370189 AGTAGCTGAAGAAAGGCACACT 59.630 45.455 0.00 0.00 0.00 3.55
1534 1543 2.772287 AGTAGCTGAAGAAAGGCACAC 58.228 47.619 0.00 0.00 0.00 3.82
1535 1544 3.492102 AAGTAGCTGAAGAAAGGCACA 57.508 42.857 0.00 0.00 0.00 4.57
1536 1545 4.837896 AAAAGTAGCTGAAGAAAGGCAC 57.162 40.909 0.00 0.00 0.00 5.01
1630 1639 3.305131 CGACTTGTGACACCTAACTAGCA 60.305 47.826 2.45 0.00 0.00 3.49
1664 1673 0.252284 CTAGGGAGTGGTGTGGAGGT 60.252 60.000 0.00 0.00 0.00 3.85
1691 1700 9.742144 GGAGGTCATCTATTATTAGAGTAGTCA 57.258 37.037 0.00 0.00 37.86 3.41
1855 1865 1.532868 CTCGGAAAGGCTTTGACACTG 59.467 52.381 18.79 8.01 0.00 3.66
1930 1940 3.767673 GGCGGACCTATATCCATCTAACA 59.232 47.826 0.00 0.00 38.87 2.41
1941 1951 0.963962 GGATTGACGGCGGACCTATA 59.036 55.000 13.24 0.00 0.00 1.31
1991 2001 1.949133 GCAGTGTGTGTTCTCGCGA 60.949 57.895 9.26 9.26 0.00 5.87
2011 2021 3.078837 GACACGGTGGACCATATTTTGT 58.921 45.455 13.48 0.00 35.14 2.83
2013 2023 2.307686 AGGACACGGTGGACCATATTTT 59.692 45.455 21.90 4.48 35.14 1.82
2094 2105 3.300388 ACTGACTGTGGACATCGGATAT 58.700 45.455 0.00 0.00 0.00 1.63
2113 2124 0.962356 GTGGCTGGCTGTGCAATACT 60.962 55.000 2.00 0.00 0.00 2.12
2161 2172 0.105039 CGGGGCCATCTAGAAGTGTC 59.895 60.000 4.39 0.00 0.00 3.67
2169 2180 1.048724 CACTCCTTCGGGGCCATCTA 61.049 60.000 4.39 0.00 35.37 1.98


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

AutoCloner maintained by Alex Coulton.