Multiple sequence alignment - TraesCS2A01G019700

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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 TraesCS2A01G019700 chr2A 100.000 2690 0 0 1 2690 9112116 9109427 0.000000e+00 4968
1 TraesCS2A01G019700 chr2A 81.894 1806 273 31 879 2648 9847483 9849270 0.000000e+00 1474
2 TraesCS2A01G019700 chr2A 81.585 1640 277 19 845 2470 8630806 8632434 0.000000e+00 1332
3 TraesCS2A01G019700 chr2A 80.916 1682 294 20 817 2489 9982770 9984433 0.000000e+00 1303
4 TraesCS2A01G019700 chr2A 80.726 1681 304 14 817 2489 9094665 9092997 0.000000e+00 1291
5 TraesCS2A01G019700 chr2A 80.580 1483 265 17 999 2470 9944092 9945562 0.000000e+00 1122
6 TraesCS2A01G019700 chr2B 92.729 1224 55 12 1470 2690 13085880 13084688 0.000000e+00 1736
7 TraesCS2A01G019700 chr2B 93.191 1028 57 6 461 1487 13087724 13086709 0.000000e+00 1498
8 TraesCS2A01G019700 chr2B 82.254 1606 258 18 897 2492 13131628 13130040 0.000000e+00 1362
9 TraesCS2A01G019700 chr2B 80.071 1686 313 16 817 2492 13068686 13067014 0.000000e+00 1230
10 TraesCS2A01G019700 chr2B 80.545 1357 241 14 845 2193 11725415 11724074 0.000000e+00 1022
11 TraesCS2A01G019700 chr2B 85.442 419 53 6 2 418 13088249 13087837 1.910000e-116 429
12 TraesCS2A01G019700 chr2D 81.713 1553 256 20 923 2458 9380368 9381909 0.000000e+00 1269
13 TraesCS2A01G019700 chr2D 80.804 1542 282 11 924 2456 9588218 9589754 0.000000e+00 1195
14 TraesCS2A01G019700 chr2D 88.702 416 40 7 817 1229 9758678 9758267 4.000000e-138 501
15 TraesCS2A01G019700 chr5D 86.166 253 33 2 1 252 255600030 255599779 3.410000e-69 272
16 TraesCS2A01G019700 chr5B 77.593 241 50 4 12 250 351149621 351149383 2.790000e-30 143


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 TraesCS2A01G019700 chr2A 9109427 9112116 2689 True 4968 4968 100.000 1 2690 1 chr2A.!!$R2 2689
1 TraesCS2A01G019700 chr2A 9847483 9849270 1787 False 1474 1474 81.894 879 2648 1 chr2A.!!$F2 1769
2 TraesCS2A01G019700 chr2A 8630806 8632434 1628 False 1332 1332 81.585 845 2470 1 chr2A.!!$F1 1625
3 TraesCS2A01G019700 chr2A 9982770 9984433 1663 False 1303 1303 80.916 817 2489 1 chr2A.!!$F4 1672
4 TraesCS2A01G019700 chr2A 9092997 9094665 1668 True 1291 1291 80.726 817 2489 1 chr2A.!!$R1 1672
5 TraesCS2A01G019700 chr2A 9944092 9945562 1470 False 1122 1122 80.580 999 2470 1 chr2A.!!$F3 1471
6 TraesCS2A01G019700 chr2B 13130040 13131628 1588 True 1362 1362 82.254 897 2492 1 chr2B.!!$R3 1595
7 TraesCS2A01G019700 chr2B 13067014 13068686 1672 True 1230 1230 80.071 817 2492 1 chr2B.!!$R2 1675
8 TraesCS2A01G019700 chr2B 13084688 13088249 3561 True 1221 1736 90.454 2 2690 3 chr2B.!!$R4 2688
9 TraesCS2A01G019700 chr2B 11724074 11725415 1341 True 1022 1022 80.545 845 2193 1 chr2B.!!$R1 1348
10 TraesCS2A01G019700 chr2D 9380368 9381909 1541 False 1269 1269 81.713 923 2458 1 chr2D.!!$F1 1535
11 TraesCS2A01G019700 chr2D 9588218 9589754 1536 False 1195 1195 80.804 924 2456 1 chr2D.!!$F2 1532

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
305 306 0.109342 CCCCTACACATCTGGATGCC 59.891 60.0 10.13 0.0 42.39 4.4 F
1111 1194 0.467804 GGAGGAGAAGGTGATGGAGC 59.532 60.0 0.00 0.0 0.00 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1447 0.249489 GAGGCGCGTGACCTTATCAT 60.249 55.0 7.63 0.00 40.28 2.45 R
2542 3516 1.433053 TTCCGTTGCCACGTCAACAG 61.433 55.0 17.26 8.48 45.62 3.16 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
20 21 1.149361 TAATAACTGCCGGCGCTTCG 61.149 55.000 23.90 9.89 35.36 3.79
48 49 4.796231 CGGCTTCTCGACGGTGGG 62.796 72.222 0.00 0.00 41.63 4.61
106 107 0.667792 GGGATTGGCTCGCGAGATAC 60.668 60.000 38.74 26.01 40.84 2.24
120 121 1.001268 GAGATACTGCCGATTCGAGCA 60.001 52.381 17.28 17.28 37.46 4.26
123 124 0.875908 TACTGCCGATTCGAGCATGC 60.876 55.000 10.51 10.51 38.56 4.06
125 126 2.590007 GCCGATTCGAGCATGCCT 60.590 61.111 15.66 1.01 0.00 4.75
127 128 1.227350 CCGATTCGAGCATGCCTCA 60.227 57.895 15.66 0.00 40.78 3.86
128 129 1.493950 CCGATTCGAGCATGCCTCAC 61.494 60.000 15.66 2.86 40.78 3.51
129 130 1.815212 CGATTCGAGCATGCCTCACG 61.815 60.000 15.66 15.07 40.78 4.35
130 131 0.528466 GATTCGAGCATGCCTCACGA 60.528 55.000 15.66 17.10 40.78 4.35
131 132 0.529337 ATTCGAGCATGCCTCACGAG 60.529 55.000 15.66 0.00 40.78 4.18
132 133 1.595093 TTCGAGCATGCCTCACGAGA 61.595 55.000 15.66 8.89 40.78 4.04
133 134 1.875813 CGAGCATGCCTCACGAGAC 60.876 63.158 15.66 0.00 40.78 3.36
140 141 2.997315 CCTCACGAGACAGGCCCA 60.997 66.667 0.00 0.00 0.00 5.36
147 148 1.915769 GAGACAGGCCCAGAGGTGT 60.916 63.158 0.00 0.00 34.57 4.16
157 158 3.005472 GGCCCAGAGGTGTTTTAAACTTC 59.995 47.826 9.33 4.80 34.57 3.01
161 162 4.334481 CCAGAGGTGTTTTAAACTTCGTGT 59.666 41.667 9.33 0.97 0.00 4.49
163 164 5.064198 CAGAGGTGTTTTAAACTTCGTGTGA 59.936 40.000 9.33 0.00 0.00 3.58
165 166 6.987992 AGAGGTGTTTTAAACTTCGTGTGATA 59.012 34.615 9.33 0.00 0.00 2.15
166 167 7.170998 AGAGGTGTTTTAAACTTCGTGTGATAG 59.829 37.037 9.33 0.00 0.00 2.08
170 171 8.002665 GTGTTTTAAACTTCGTGTGATAGAGAC 58.997 37.037 9.33 0.00 0.00 3.36
174 175 3.162666 ACTTCGTGTGATAGAGACCCAA 58.837 45.455 0.00 0.00 0.00 4.12
191 192 1.396996 CCAATAGTGTACGCTGGCAAC 59.603 52.381 19.20 0.00 0.00 4.17
212 213 2.162408 CCAATCAGCTCGTTTTCTTCCC 59.838 50.000 0.00 0.00 0.00 3.97
216 217 2.474712 CTCGTTTTCTTCCCGCGC 59.525 61.111 0.00 0.00 0.00 6.86
258 259 0.170339 GGCAACCAAACGCATCCTAC 59.830 55.000 0.00 0.00 0.00 3.18
268 269 5.273170 CAAACGCATCCTACACCATTTATG 58.727 41.667 0.00 0.00 0.00 1.90
305 306 0.109342 CCCCTACACATCTGGATGCC 59.891 60.000 10.13 0.00 42.39 4.40
316 317 3.219198 GGATGCCCCAACCGATGC 61.219 66.667 0.00 0.00 34.14 3.91
328 329 3.247442 CAACCGATGCGACTAGTGTAAA 58.753 45.455 0.00 0.00 0.00 2.01
340 341 8.332464 TGCGACTAGTGTAAACATATTTAATGC 58.668 33.333 0.00 0.00 32.04 3.56
361 363 2.224281 CCAATAGGACATGCGCTAGGAA 60.224 50.000 9.73 0.00 36.89 3.36
363 365 4.067896 CAATAGGACATGCGCTAGGAAAT 58.932 43.478 9.73 0.00 0.00 2.17
414 436 1.268352 GCCACTCGCAAACACCAAATA 59.732 47.619 0.00 0.00 37.47 1.40
514 588 3.437049 GGTCAAACATTGCCAGAGTAGAC 59.563 47.826 0.00 0.00 0.00 2.59
517 591 2.393271 ACATTGCCAGAGTAGACTGC 57.607 50.000 0.00 0.00 36.67 4.40
522 596 0.539051 GCCAGAGTAGACTGCCATGT 59.461 55.000 0.00 0.00 36.67 3.21
538 612 4.220382 TGCCATGTAAAATGTTGGAAGGAG 59.780 41.667 0.00 0.00 0.00 3.69
650 724 4.872691 CCTTGTGTCACCTATCATCTTGTC 59.127 45.833 0.00 0.00 0.00 3.18
670 744 5.060506 TGTCGCCATCAACTTCTTAGAAAA 58.939 37.500 0.00 0.00 0.00 2.29
694 768 3.568538 CTGGAGACTTTTCCATTTTGCG 58.431 45.455 0.00 0.00 45.80 4.85
697 771 4.215399 TGGAGACTTTTCCATTTTGCGTAG 59.785 41.667 0.00 0.00 42.24 3.51
724 798 0.737715 GCGAGACTTGTTCGGCAGAT 60.738 55.000 0.00 0.00 38.45 2.90
729 803 1.734465 GACTTGTTCGGCAGATGGAAG 59.266 52.381 0.00 0.00 0.00 3.46
735 809 2.552315 GTTCGGCAGATGGAAGAAAACA 59.448 45.455 0.00 0.00 0.00 2.83
742 816 5.234972 GGCAGATGGAAGAAAACAAAGTTTG 59.765 40.000 14.13 14.13 0.00 2.93
763 837 0.608130 CGACCCTCCAAGTCACATCA 59.392 55.000 0.00 0.00 33.70 3.07
771 845 5.005740 CCTCCAAGTCACATCAGATGAAAA 58.994 41.667 17.81 0.00 0.00 2.29
780 854 7.064371 AGTCACATCAGATGAAAATTCTTCTCG 59.936 37.037 17.81 5.77 39.00 4.04
857 931 8.712228 AAAGGAGAAAATGACAAGTATCCTTT 57.288 30.769 14.55 14.55 46.11 3.11
1084 1164 1.891150 ACAAGTACCATTCGAGTCGGT 59.109 47.619 13.54 5.02 36.79 4.69
1111 1194 0.467804 GGAGGAGAAGGTGATGGAGC 59.532 60.000 0.00 0.00 0.00 4.70
1158 1241 1.598701 GCACCATTGTTGAGGAGGCC 61.599 60.000 0.00 0.00 0.00 5.19
1163 1246 1.827399 ATTGTTGAGGAGGCCGACGT 61.827 55.000 0.00 0.00 0.00 4.34
1226 1309 2.700371 CACTATCAGAGGCCATGTACCA 59.300 50.000 5.01 0.00 0.00 3.25
1346 1441 1.710013 TTAGCCAAGCGTTCTCGAAG 58.290 50.000 0.00 0.00 39.71 3.79
1347 1442 0.601558 TAGCCAAGCGTTCTCGAAGT 59.398 50.000 0.00 0.00 39.71 3.01
1348 1443 0.601558 AGCCAAGCGTTCTCGAAGTA 59.398 50.000 0.00 0.00 39.71 2.24
1352 1447 2.798283 CCAAGCGTTCTCGAAGTACAAA 59.202 45.455 0.00 0.00 39.71 2.83
1517 2471 0.321210 TTCATGTTCGGCCGACACAT 60.321 50.000 32.15 32.15 0.00 3.21
1535 2489 4.227538 CACATTGAGAAGCAAAAGCTCTG 58.772 43.478 0.00 0.00 40.48 3.35
1615 2569 3.643199 TCATAGGTGGTGCAGCAATTA 57.357 42.857 22.04 15.77 33.95 1.40
1616 2570 3.961849 TCATAGGTGGTGCAGCAATTAA 58.038 40.909 22.04 7.05 33.95 1.40
1726 2681 3.184628 TGAGAAGACCTGACCATGGAAT 58.815 45.455 21.47 0.00 0.00 3.01
1749 2704 4.478317 TGACCATGGAAGGAAGGATATTGT 59.522 41.667 21.47 0.00 0.00 2.71
1785 2740 7.615365 AGTTTTCTTGTGATATTGGCCAAGATA 59.385 33.333 25.06 13.30 41.91 1.98
2017 2972 5.927689 CAGATGAAAATTTGGCAAGCTGTTA 59.072 36.000 0.00 0.00 0.00 2.41
2031 2986 1.879380 GCTGTTACACAATGTGCCAGA 59.121 47.619 23.44 7.13 36.98 3.86
2038 2996 4.551702 ACACAATGTGCCAGATACACTA 57.448 40.909 14.01 0.00 38.86 2.74
2323 3293 2.478894 CAGTGTTACGCCGAAACAAGAT 59.521 45.455 0.00 0.00 38.50 2.40
2403 3373 2.110967 CAAGTCATGCTCAGGGCGG 61.111 63.158 0.00 0.00 45.43 6.13
2460 3430 6.868339 CGAAGAGGAGTGCCAATTTAATTTTT 59.132 34.615 0.00 0.00 36.29 1.94
2461 3431 7.148755 CGAAGAGGAGTGCCAATTTAATTTTTG 60.149 37.037 0.00 0.00 36.29 2.44
2470 3440 8.519459 GTGCCAATTTAATTTTTGTTCAAAACG 58.481 29.630 9.76 0.00 37.18 3.60
2481 3451 6.698359 TTTGTTCAAAACGCCTATAAATGC 57.302 33.333 0.00 0.00 0.00 3.56
2482 3452 5.378292 TGTTCAAAACGCCTATAAATGCA 57.622 34.783 0.00 0.00 0.00 3.96
2484 3454 5.631512 TGTTCAAAACGCCTATAAATGCAAC 59.368 36.000 0.00 0.00 0.00 4.17
2485 3455 5.637006 TCAAAACGCCTATAAATGCAACT 57.363 34.783 0.00 0.00 0.00 3.16
2486 3456 5.636837 TCAAAACGCCTATAAATGCAACTC 58.363 37.500 0.00 0.00 0.00 3.01
2487 3457 5.414454 TCAAAACGCCTATAAATGCAACTCT 59.586 36.000 0.00 0.00 0.00 3.24
2488 3458 5.897377 AAACGCCTATAAATGCAACTCTT 57.103 34.783 0.00 0.00 0.00 2.85
2489 3459 5.485662 AACGCCTATAAATGCAACTCTTC 57.514 39.130 0.00 0.00 0.00 2.87
2490 3460 4.770795 ACGCCTATAAATGCAACTCTTCT 58.229 39.130 0.00 0.00 0.00 2.85
2491 3461 5.186198 ACGCCTATAAATGCAACTCTTCTT 58.814 37.500 0.00 0.00 0.00 2.52
2492 3462 5.294552 ACGCCTATAAATGCAACTCTTCTTC 59.705 40.000 0.00 0.00 0.00 2.87
2493 3463 5.525378 CGCCTATAAATGCAACTCTTCTTCT 59.475 40.000 0.00 0.00 0.00 2.85
2501 3471 6.799926 ATGCAACTCTTCTTCTTCTTCTTC 57.200 37.500 0.00 0.00 0.00 2.87
2504 3474 6.481644 TGCAACTCTTCTTCTTCTTCTTCTTC 59.518 38.462 0.00 0.00 0.00 2.87
2542 3516 6.259638 TGTTTTTGTAGATGTGAAACGGTTC 58.740 36.000 6.16 6.16 42.39 3.62
2557 3531 0.028902 GGTTCTGTTGACGTGGCAAC 59.971 55.000 11.65 11.65 46.33 4.17
2573 3547 4.266739 GTGGCAACGGAAAAACTGTTTTAG 59.733 41.667 17.97 14.31 44.61 1.85
2584 3558 5.453567 AAACTGTTTTAGGGAGTGATTGC 57.546 39.130 0.00 0.00 0.00 3.56
2651 3630 4.933330 TGTTCTATCAGATCCAACTACGC 58.067 43.478 6.13 0.00 0.00 4.42
2653 3632 5.216648 GTTCTATCAGATCCAACTACGCTC 58.783 45.833 0.00 0.00 0.00 5.03
2654 3633 2.783828 ATCAGATCCAACTACGCTCG 57.216 50.000 0.00 0.00 0.00 5.03
2670 3649 3.555956 ACGCTCGGCACTTATTTGATAAG 59.444 43.478 6.23 6.23 45.97 1.73
2671 3650 3.604772 CGCTCGGCACTTATTTGATAAGC 60.605 47.826 7.43 0.00 44.73 3.09
2672 3651 3.312421 GCTCGGCACTTATTTGATAAGCA 59.688 43.478 7.43 0.00 44.73 3.91
2674 3653 5.229921 TCGGCACTTATTTGATAAGCAAC 57.770 39.130 7.43 0.00 44.73 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.002011 AGAAGCCGCCTTTCTTCCC 60.002 57.895 0.00 0.00 39.48 3.97
23 24 0.670854 GTCGAGAAGCCGCCTTTCTT 60.671 55.000 0.00 0.00 0.00 2.52
26 27 2.432628 CGTCGAGAAGCCGCCTTT 60.433 61.111 0.00 0.00 0.00 3.11
88 89 0.315568 AGTATCTCGCGAGCCAATCC 59.684 55.000 30.97 10.82 0.00 3.01
90 91 0.598680 GCAGTATCTCGCGAGCCAAT 60.599 55.000 30.97 20.99 0.00 3.16
91 92 1.226974 GCAGTATCTCGCGAGCCAA 60.227 57.895 30.97 15.08 0.00 4.52
92 93 2.413351 GCAGTATCTCGCGAGCCA 59.587 61.111 30.97 17.66 0.00 4.75
106 107 2.630317 GCATGCTCGAATCGGCAG 59.370 61.111 19.65 13.99 41.88 4.85
123 124 2.997315 TGGGCCTGTCTCGTGAGG 60.997 66.667 4.53 0.00 0.00 3.86
125 126 1.979155 CTCTGGGCCTGTCTCGTGA 60.979 63.158 4.53 0.00 0.00 4.35
127 128 2.681778 CCTCTGGGCCTGTCTCGT 60.682 66.667 4.53 0.00 0.00 4.18
128 129 2.681778 ACCTCTGGGCCTGTCTCG 60.682 66.667 4.53 0.00 35.63 4.04
129 130 1.484444 AACACCTCTGGGCCTGTCTC 61.484 60.000 4.53 0.00 35.63 3.36
130 131 1.062488 AAACACCTCTGGGCCTGTCT 61.062 55.000 4.53 0.00 35.63 3.41
131 132 0.178990 AAAACACCTCTGGGCCTGTC 60.179 55.000 4.53 0.00 35.63 3.51
132 133 1.145571 TAAAACACCTCTGGGCCTGT 58.854 50.000 4.53 0.00 35.63 4.00
133 134 2.286365 TTAAAACACCTCTGGGCCTG 57.714 50.000 4.53 4.06 35.63 4.85
140 141 5.180271 TCACACGAAGTTTAAAACACCTCT 58.820 37.500 0.00 0.00 41.61 3.69
147 148 6.647895 GGGTCTCTATCACACGAAGTTTAAAA 59.352 38.462 0.00 0.00 41.61 1.52
157 158 4.098044 ACACTATTGGGTCTCTATCACACG 59.902 45.833 0.00 0.00 0.00 4.49
161 162 4.277672 GCGTACACTATTGGGTCTCTATCA 59.722 45.833 0.00 0.00 0.00 2.15
163 164 4.278669 CAGCGTACACTATTGGGTCTCTAT 59.721 45.833 0.00 0.00 0.00 1.98
165 166 2.427453 CAGCGTACACTATTGGGTCTCT 59.573 50.000 0.00 0.00 0.00 3.10
166 167 2.481449 CCAGCGTACACTATTGGGTCTC 60.481 54.545 0.00 0.00 0.00 3.36
170 171 0.107897 TGCCAGCGTACACTATTGGG 60.108 55.000 0.00 0.00 0.00 4.12
174 175 0.611200 TGGTTGCCAGCGTACACTAT 59.389 50.000 0.00 0.00 0.00 2.12
191 192 2.162408 GGGAAGAAAACGAGCTGATTGG 59.838 50.000 0.00 0.00 0.00 3.16
216 217 0.958876 GTAAGGTCCAACAAGGCCCG 60.959 60.000 0.00 0.00 41.56 6.13
220 221 1.296056 CCGCGTAAGGTCCAACAAGG 61.296 60.000 4.92 0.00 36.73 3.61
223 224 2.344500 CCCGCGTAAGGTCCAACA 59.656 61.111 4.92 0.00 38.28 3.33
227 228 3.122971 GTTGCCCGCGTAAGGTCC 61.123 66.667 4.92 0.00 38.28 4.46
289 290 0.839277 TGGGGCATCCAGATGTGTAG 59.161 55.000 9.29 0.00 41.46 2.74
298 299 2.275089 CATCGGTTGGGGCATCCA 59.725 61.111 0.00 0.00 45.43 3.41
300 301 3.585990 CGCATCGGTTGGGGCATC 61.586 66.667 0.00 0.00 34.74 3.91
305 306 0.806102 CACTAGTCGCATCGGTTGGG 60.806 60.000 0.00 0.00 39.56 4.12
316 317 8.822855 TGGCATTAAATATGTTTACACTAGTCG 58.177 33.333 0.00 0.00 29.82 4.18
328 329 7.575532 CGCATGTCCTATTGGCATTAAATATGT 60.576 37.037 0.00 0.00 31.15 2.29
340 341 1.344438 TCCTAGCGCATGTCCTATTGG 59.656 52.381 11.47 0.00 0.00 3.16
344 345 4.948341 TTATTTCCTAGCGCATGTCCTA 57.052 40.909 11.47 0.00 0.00 2.94
345 346 3.838244 TTATTTCCTAGCGCATGTCCT 57.162 42.857 11.47 0.00 0.00 3.85
452 474 3.496884 TGCGCTTTTCGAGATAAAACTGT 59.503 39.130 9.73 0.00 41.67 3.55
456 478 5.103290 AGTTTGCGCTTTTCGAGATAAAA 57.897 34.783 9.73 0.00 41.67 1.52
458 480 4.927425 ACTAGTTTGCGCTTTTCGAGATAA 59.073 37.500 9.73 0.00 41.67 1.75
459 481 4.491676 ACTAGTTTGCGCTTTTCGAGATA 58.508 39.130 9.73 0.00 41.67 1.98
464 537 3.369756 TGGATACTAGTTTGCGCTTTTCG 59.630 43.478 9.73 0.00 38.45 3.46
514 588 4.220382 TCCTTCCAACATTTTACATGGCAG 59.780 41.667 0.00 0.00 32.87 4.85
517 591 5.105756 GGACTCCTTCCAACATTTTACATGG 60.106 44.000 0.00 0.00 45.10 3.66
538 612 0.385974 GCATGTGTCTTGCGTTGGAC 60.386 55.000 0.00 0.00 0.00 4.02
630 704 3.676049 GCGACAAGATGATAGGTGACACA 60.676 47.826 8.08 0.00 0.00 3.72
631 705 2.860735 GCGACAAGATGATAGGTGACAC 59.139 50.000 0.00 0.00 0.00 3.67
632 706 2.159099 GGCGACAAGATGATAGGTGACA 60.159 50.000 0.00 0.00 0.00 3.58
633 707 2.159099 TGGCGACAAGATGATAGGTGAC 60.159 50.000 0.00 0.00 37.44 3.67
634 708 2.107366 TGGCGACAAGATGATAGGTGA 58.893 47.619 0.00 0.00 37.44 4.02
635 709 2.602257 TGGCGACAAGATGATAGGTG 57.398 50.000 0.00 0.00 37.44 4.00
650 724 5.355350 AGGATTTTCTAAGAAGTTGATGGCG 59.645 40.000 0.00 0.00 0.00 5.69
724 798 5.395642 GTCGACAAACTTTGTTTTCTTCCA 58.604 37.500 11.55 0.00 45.52 3.53
729 803 4.348656 GAGGGTCGACAAACTTTGTTTTC 58.651 43.478 18.91 2.91 45.52 2.29
735 809 2.092592 ACTTGGAGGGTCGACAAACTTT 60.093 45.455 18.91 0.00 0.00 2.66
742 816 0.608640 ATGTGACTTGGAGGGTCGAC 59.391 55.000 7.13 7.13 36.58 4.20
743 817 0.895530 GATGTGACTTGGAGGGTCGA 59.104 55.000 0.00 0.00 36.58 4.20
763 837 8.970859 ATGGTAATCGAGAAGAATTTTCATCT 57.029 30.769 0.00 0.00 37.89 2.90
771 845 6.551601 ACTCCACTATGGTAATCGAGAAGAAT 59.448 38.462 0.00 0.00 39.03 2.40
780 854 7.047891 TGATGTTGAACTCCACTATGGTAATC 58.952 38.462 0.00 0.00 39.03 1.75
790 864 2.771089 TGAGCTGATGTTGAACTCCAC 58.229 47.619 0.00 0.00 0.00 4.02
857 931 2.035237 GACGAGTGGGTGGGTGACAA 62.035 60.000 0.00 0.00 0.00 3.18
1084 1164 0.112606 ACCTTCTCCTCCGAGTGTGA 59.887 55.000 0.00 0.00 37.40 3.58
1111 1194 3.270027 TCATTAGGAGATGTTGCAACCG 58.730 45.455 26.14 0.00 0.00 4.44
1158 1241 1.830086 TGGTTATGTATCGCACGTCG 58.170 50.000 0.00 0.00 40.15 5.12
1163 1246 2.482316 CCGGAGTTGGTTATGTATCGCA 60.482 50.000 0.00 0.00 0.00 5.10
1226 1309 4.885426 CCAGCGCATGGTATCCTT 57.115 55.556 11.47 0.00 44.91 3.36
1346 1441 3.543460 GCGCGTGACCTTATCATTTGTAC 60.543 47.826 8.43 0.00 40.28 2.90
1347 1442 2.605818 GCGCGTGACCTTATCATTTGTA 59.394 45.455 8.43 0.00 40.28 2.41
1348 1443 1.396996 GCGCGTGACCTTATCATTTGT 59.603 47.619 8.43 0.00 40.28 2.83
1352 1447 0.249489 GAGGCGCGTGACCTTATCAT 60.249 55.000 7.63 0.00 40.28 2.45
1615 2569 5.659440 TGAGCAACCAAAGTTTTCTTCTT 57.341 34.783 0.00 0.00 39.48 2.52
1616 2570 5.594926 CATGAGCAACCAAAGTTTTCTTCT 58.405 37.500 0.00 0.00 39.48 2.85
1726 2681 4.478317 ACAATATCCTTCCTTCCATGGTCA 59.522 41.667 12.58 0.00 0.00 4.02
1785 2740 7.659799 GGCAAATAAGTAAAACCTGTTCCAATT 59.340 33.333 0.00 0.00 0.00 2.32
2017 2972 3.423539 AGTGTATCTGGCACATTGTGT 57.576 42.857 17.64 0.68 38.20 3.72
2038 2996 7.331934 ACATCTGCGAGTATATTTATTGCGATT 59.668 33.333 0.00 0.00 0.00 3.34
2323 3293 9.767228 CTTGATTCCCATGCAATTATAATGAAA 57.233 29.630 0.00 0.00 0.00 2.69
2403 3373 2.162408 GGCAAGGCACTAACTTCATGTC 59.838 50.000 0.00 0.00 38.49 3.06
2460 3430 5.378292 TGCATTTATAGGCGTTTTGAACA 57.622 34.783 0.00 0.00 32.67 3.18
2461 3431 5.861787 AGTTGCATTTATAGGCGTTTTGAAC 59.138 36.000 0.00 0.00 32.67 3.18
2470 3440 6.934048 AGAAGAAGAGTTGCATTTATAGGC 57.066 37.500 0.00 0.00 0.00 3.93
2478 3448 6.532826 AGAAGAAGAAGAAGAAGAGTTGCAT 58.467 36.000 0.00 0.00 0.00 3.96
2479 3449 5.923204 AGAAGAAGAAGAAGAAGAGTTGCA 58.077 37.500 0.00 0.00 0.00 4.08
2480 3450 6.705825 AGAAGAAGAAGAAGAAGAAGAGTTGC 59.294 38.462 0.00 0.00 0.00 4.17
2481 3451 8.550376 CAAGAAGAAGAAGAAGAAGAAGAGTTG 58.450 37.037 0.00 0.00 0.00 3.16
2482 3452 8.264347 ACAAGAAGAAGAAGAAGAAGAAGAGTT 58.736 33.333 0.00 0.00 0.00 3.01
2484 3454 8.661352 AACAAGAAGAAGAAGAAGAAGAAGAG 57.339 34.615 0.00 0.00 0.00 2.85
2485 3455 9.454859 AAAACAAGAAGAAGAAGAAGAAGAAGA 57.545 29.630 0.00 0.00 0.00 2.87
2487 3457 9.846248 CAAAAACAAGAAGAAGAAGAAGAAGAA 57.154 29.630 0.00 0.00 0.00 2.52
2488 3458 9.014297 ACAAAAACAAGAAGAAGAAGAAGAAGA 57.986 29.630 0.00 0.00 0.00 2.87
2542 3516 1.433053 TTCCGTTGCCACGTCAACAG 61.433 55.000 17.26 8.48 45.62 3.16
2557 3531 4.577283 TCACTCCCTAAAACAGTTTTTCCG 59.423 41.667 16.44 6.11 36.32 4.30
2573 3547 3.554934 TGAATGGTATGCAATCACTCCC 58.445 45.455 0.00 0.00 0.00 4.30
2584 3558 9.734620 CACCAGTACATTTATTTGAATGGTATG 57.265 33.333 0.00 0.00 40.50 2.39
2651 3630 5.163764 TGTTGCTTATCAAATAAGTGCCGAG 60.164 40.000 8.15 0.00 43.22 4.63
2653 3632 4.980590 TGTTGCTTATCAAATAAGTGCCG 58.019 39.130 8.15 0.00 43.22 5.69
2654 3633 9.185192 GATATTGTTGCTTATCAAATAAGTGCC 57.815 33.333 8.15 0.00 43.22 5.01


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

AutoCloner maintained by Alex Coulton.