Multiple sequence alignment - TraesCS2A01G578300

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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 TraesCS2A01G578300 chr2A 100.000 2974 0 0 1 2974 771707160 771710133 0.000000e+00 5493.0
1 TraesCS2A01G578300 chr2A 99.499 999 2 2 1 997 55883069 55884066 0.000000e+00 1814.0
2 TraesCS2A01G578300 chr2A 91.250 80 7 0 2895 2974 510195250 510195171 3.130000e-20 110.0
3 TraesCS2A01G578300 chr2A 75.720 243 39 13 2664 2891 771709228 771709465 1.460000e-18 104.0
4 TraesCS2A01G578300 chr2A 75.720 243 39 13 2069 2306 771709823 771710050 1.460000e-18 104.0
5 TraesCS2A01G578300 chr2D 89.415 1521 106 26 1475 2949 645942910 645944421 0.000000e+00 1866.0
6 TraesCS2A01G578300 chr2D 94.634 410 18 2 997 1406 645942503 645942908 1.500000e-177 632.0
7 TraesCS2A01G578300 chr6D 99.502 1004 2 2 1 1002 432916707 432917709 0.000000e+00 1823.0
8 TraesCS2A01G578300 chr7B 99.500 1000 3 1 1 998 99220133 99221132 0.000000e+00 1818.0
9 TraesCS2A01G578300 chr5B 99.402 1004 2 3 1 1002 362954801 362955802 0.000000e+00 1818.0
10 TraesCS2A01G578300 chr3D 99.599 998 1 2 1 996 3363854 3362858 0.000000e+00 1818.0
11 TraesCS2A01G578300 chrUn 99.500 1000 2 2 1 998 2003117 2002119 0.000000e+00 1816.0
12 TraesCS2A01G578300 chr6B 99.500 1000 2 2 1 998 717854873 717855871 0.000000e+00 1816.0
13 TraesCS2A01G578300 chr2B 99.500 1000 2 2 1 998 199166239 199167237 0.000000e+00 1816.0
14 TraesCS2A01G578300 chr2B 99.499 999 2 2 1 997 528831263 528830266 0.000000e+00 1814.0
15 TraesCS2A01G578300 chr2B 87.845 1522 112 31 1475 2951 789606032 789604539 0.000000e+00 1718.0
16 TraesCS2A01G578300 chr2B 92.683 410 29 1 997 1406 789606442 789606034 9.180000e-165 590.0
17 TraesCS2A01G578300 chr2B 77.895 190 29 7 2121 2306 789604777 789604597 4.050000e-19 106.0
18 TraesCS2A01G578300 chr7A 91.026 78 7 0 2897 2974 32864180 32864257 4.050000e-19 106.0
19 TraesCS2A01G578300 chr7A 90.909 77 7 0 2898 2974 717936972 717937048 1.460000e-18 104.0
20 TraesCS2A01G578300 chr7A 91.549 71 6 0 2904 2974 536956070 536956000 6.780000e-17 99.0
21 TraesCS2A01G578300 chr7A 95.082 61 3 0 2896 2956 539609643 539609703 2.440000e-16 97.1
22 TraesCS2A01G578300 chr3A 89.744 78 8 0 2897 2974 698277422 698277499 1.890000e-17 100.0
23 TraesCS2A01G578300 chr1A 89.744 78 8 0 2897 2974 508163296 508163219 1.890000e-17 100.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G578300 chr2A 771707160 771710133 2973 False 1900.333333 5493 83.813333 1 2974 3 chr2A.!!$F2 2973
1 TraesCS2A01G578300 chr2A 55883069 55884066 997 False 1814.000000 1814 99.499000 1 997 1 chr2A.!!$F1 996
2 TraesCS2A01G578300 chr2D 645942503 645944421 1918 False 1249.000000 1866 92.024500 997 2949 2 chr2D.!!$F1 1952
3 TraesCS2A01G578300 chr6D 432916707 432917709 1002 False 1823.000000 1823 99.502000 1 1002 1 chr6D.!!$F1 1001
4 TraesCS2A01G578300 chr7B 99220133 99221132 999 False 1818.000000 1818 99.500000 1 998 1 chr7B.!!$F1 997
5 TraesCS2A01G578300 chr5B 362954801 362955802 1001 False 1818.000000 1818 99.402000 1 1002 1 chr5B.!!$F1 1001
6 TraesCS2A01G578300 chr3D 3362858 3363854 996 True 1818.000000 1818 99.599000 1 996 1 chr3D.!!$R1 995
7 TraesCS2A01G578300 chrUn 2002119 2003117 998 True 1816.000000 1816 99.500000 1 998 1 chrUn.!!$R1 997
8 TraesCS2A01G578300 chr6B 717854873 717855871 998 False 1816.000000 1816 99.500000 1 998 1 chr6B.!!$F1 997
9 TraesCS2A01G578300 chr2B 199166239 199167237 998 False 1816.000000 1816 99.500000 1 998 1 chr2B.!!$F1 997
10 TraesCS2A01G578300 chr2B 528830266 528831263 997 True 1814.000000 1814 99.499000 1 997 1 chr2B.!!$R1 996
11 TraesCS2A01G578300 chr2B 789604539 789606442 1903 True 804.666667 1718 86.141000 997 2951 3 chr2B.!!$R2 1954

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
727 728 0.877213 GTTCAAGGCGGTGTGTACGT 60.877 55.0 0.0 0.0 0.0 3.57 F
1201 1204 0.529555 GCCTGTCTGCGAATCTCTCC 60.530 60.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1687 0.250901 GTCTTTCTTGGCCTGCTCCA 60.251 55.0 3.32 0.00 0.0 3.86 R
2954 3003 0.323816 TGTTTAATGATGGGGCGCCA 60.324 50.0 30.85 26.32 0.0 5.69 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
727 728 0.877213 GTTCAAGGCGGTGTGTACGT 60.877 55.000 0.00 0.00 0.00 3.57
991 994 4.813296 AATAAAAGCGCCCTTTATCGAG 57.187 40.909 19.70 0.00 40.30 4.04
1017 1020 1.304381 AATGGCCGATGTGGTGCTT 60.304 52.632 0.00 0.00 41.21 3.91
1201 1204 0.529555 GCCTGTCTGCGAATCTCTCC 60.530 60.000 0.00 0.00 0.00 3.71
1227 1230 0.678684 TCACCTACATCGACGAGGCA 60.679 55.000 9.79 0.00 33.28 4.75
1322 1325 9.524106 CTACATCGACAACAAGGTATATACAAA 57.476 33.333 14.70 0.00 0.00 2.83
1370 1373 5.183713 CAGAGAATAGAACAAAACCATGCCA 59.816 40.000 0.00 0.00 0.00 4.92
1383 1386 6.610075 AAACCATGCCACTTCATTTATCTT 57.390 33.333 0.00 0.00 0.00 2.40
1428 1431 3.634568 TTTTCGCGACATTTCATTGGT 57.365 38.095 9.15 0.00 0.00 3.67
1429 1432 4.750952 TTTTCGCGACATTTCATTGGTA 57.249 36.364 9.15 0.00 0.00 3.25
1430 1433 4.335082 TTTCGCGACATTTCATTGGTAG 57.665 40.909 9.15 0.00 0.00 3.18
1431 1434 3.239587 TCGCGACATTTCATTGGTAGA 57.760 42.857 3.71 0.00 0.00 2.59
1432 1435 3.186909 TCGCGACATTTCATTGGTAGAG 58.813 45.455 3.71 0.00 0.00 2.43
1433 1436 2.285220 CGCGACATTTCATTGGTAGAGG 59.715 50.000 0.00 0.00 0.00 3.69
1434 1437 3.531538 GCGACATTTCATTGGTAGAGGA 58.468 45.455 0.00 0.00 0.00 3.71
1435 1438 3.938963 GCGACATTTCATTGGTAGAGGAA 59.061 43.478 0.00 0.00 0.00 3.36
1436 1439 4.034510 GCGACATTTCATTGGTAGAGGAAG 59.965 45.833 0.00 0.00 0.00 3.46
1437 1440 5.178797 CGACATTTCATTGGTAGAGGAAGT 58.821 41.667 0.00 0.00 0.00 3.01
1438 1441 5.643777 CGACATTTCATTGGTAGAGGAAGTT 59.356 40.000 0.00 0.00 0.00 2.66
1439 1442 6.816640 CGACATTTCATTGGTAGAGGAAGTTA 59.183 38.462 0.00 0.00 0.00 2.24
1440 1443 7.333423 CGACATTTCATTGGTAGAGGAAGTTAA 59.667 37.037 0.00 0.00 0.00 2.01
1441 1444 8.567285 ACATTTCATTGGTAGAGGAAGTTAAG 57.433 34.615 0.00 0.00 0.00 1.85
1442 1445 8.383175 ACATTTCATTGGTAGAGGAAGTTAAGA 58.617 33.333 0.00 0.00 0.00 2.10
1443 1446 8.887717 CATTTCATTGGTAGAGGAAGTTAAGAG 58.112 37.037 0.00 0.00 0.00 2.85
1444 1447 7.554959 TTCATTGGTAGAGGAAGTTAAGAGT 57.445 36.000 0.00 0.00 0.00 3.24
1445 1448 6.936279 TCATTGGTAGAGGAAGTTAAGAGTG 58.064 40.000 0.00 0.00 0.00 3.51
1446 1449 6.724441 TCATTGGTAGAGGAAGTTAAGAGTGA 59.276 38.462 0.00 0.00 0.00 3.41
1447 1450 6.989155 TTGGTAGAGGAAGTTAAGAGTGAA 57.011 37.500 0.00 0.00 0.00 3.18
1448 1451 6.989155 TGGTAGAGGAAGTTAAGAGTGAAA 57.011 37.500 0.00 0.00 0.00 2.69
1449 1452 7.369551 TGGTAGAGGAAGTTAAGAGTGAAAA 57.630 36.000 0.00 0.00 0.00 2.29
1450 1453 7.215085 TGGTAGAGGAAGTTAAGAGTGAAAAC 58.785 38.462 0.00 0.00 0.00 2.43
1451 1454 7.147620 TGGTAGAGGAAGTTAAGAGTGAAAACA 60.148 37.037 0.00 0.00 0.00 2.83
1452 1455 7.385478 GGTAGAGGAAGTTAAGAGTGAAAACAG 59.615 40.741 0.00 0.00 0.00 3.16
1453 1456 6.292150 AGAGGAAGTTAAGAGTGAAAACAGG 58.708 40.000 0.00 0.00 0.00 4.00
1454 1457 6.002653 AGGAAGTTAAGAGTGAAAACAGGT 57.997 37.500 0.00 0.00 0.00 4.00
1455 1458 5.823045 AGGAAGTTAAGAGTGAAAACAGGTG 59.177 40.000 0.00 0.00 0.00 4.00
1456 1459 5.820947 GGAAGTTAAGAGTGAAAACAGGTGA 59.179 40.000 0.00 0.00 0.00 4.02
1457 1460 6.317893 GGAAGTTAAGAGTGAAAACAGGTGAA 59.682 38.462 0.00 0.00 0.00 3.18
1458 1461 6.679327 AGTTAAGAGTGAAAACAGGTGAAC 57.321 37.500 0.00 0.00 0.00 3.18
1459 1462 6.177610 AGTTAAGAGTGAAAACAGGTGAACA 58.822 36.000 0.00 0.00 0.00 3.18
1460 1463 6.657541 AGTTAAGAGTGAAAACAGGTGAACAA 59.342 34.615 0.00 0.00 0.00 2.83
1461 1464 4.965119 AGAGTGAAAACAGGTGAACAAC 57.035 40.909 0.00 0.00 0.00 3.32
1462 1465 4.331968 AGAGTGAAAACAGGTGAACAACA 58.668 39.130 0.00 0.00 0.00 3.33
1478 1481 5.176774 TGAACAACACATGACACGAATCTAC 59.823 40.000 0.00 0.00 0.00 2.59
1598 1601 5.394115 GGGTGCATGAACTATTTTTCCGATT 60.394 40.000 3.21 0.00 0.00 3.34
1635 1638 7.148590 GGACTAACATTCCAAATGTGAAATTGC 60.149 37.037 6.11 0.00 32.82 3.56
1641 1644 5.725325 TCCAAATGTGAAATTGCAGATCA 57.275 34.783 0.00 0.00 0.00 2.92
1673 1676 1.952133 CCGCCTGTTGACGACGAAA 60.952 57.895 0.00 0.00 0.00 3.46
1684 1687 3.009714 GACGAAAGGGGAGGCCCT 61.010 66.667 0.00 0.00 44.66 5.19
1720 1723 0.683973 GACATGATCGGGGCTCTCAT 59.316 55.000 0.00 0.00 0.00 2.90
1787 1790 1.289109 CGTTCGGCTTCGTGGACATT 61.289 55.000 0.00 0.00 35.06 2.71
1975 1978 4.385310 GGAGGAGTATGGTGCCAACTAAAT 60.385 45.833 0.00 0.00 0.00 1.40
2098 2102 8.919145 TGGTCAAACTTTATGAAATGTACCTTT 58.081 29.630 0.00 0.00 0.00 3.11
2099 2103 9.406828 GGTCAAACTTTATGAAATGTACCTTTC 57.593 33.333 14.60 14.60 36.00 2.62
2101 2105 8.842280 TCAAACTTTATGAAATGTACCTTTCGT 58.158 29.630 18.48 18.48 37.84 3.85
2143 2147 5.995897 ACTATATTGAACGAAAGGGGTATGC 59.004 40.000 0.00 0.00 0.00 3.14
2300 2305 1.586154 TACGGTTCTTCGACCCCGAC 61.586 60.000 15.56 0.00 45.50 4.79
2306 2311 3.528532 GTTCTTCGACCCCGACATATTT 58.471 45.455 0.00 0.00 45.50 1.40
2307 2312 3.447918 TCTTCGACCCCGACATATTTC 57.552 47.619 0.00 0.00 45.50 2.17
2308 2313 2.124903 CTTCGACCCCGACATATTTCG 58.875 52.381 4.25 4.25 45.50 3.46
2309 2314 1.105457 TCGACCCCGACATATTTCGT 58.895 50.000 10.18 0.00 40.30 3.85
2325 2338 1.929230 TCGTCGACACATGTGTTGTT 58.071 45.000 34.70 15.16 45.05 2.83
2358 2371 7.698163 AGGTTCCCATTGTCTCTCTTATATT 57.302 36.000 0.00 0.00 0.00 1.28
2460 2473 9.657419 AAAGACATGACAAAAGAAAGTCAAATT 57.343 25.926 0.00 0.00 46.62 1.82
2900 2949 3.907474 ACCCCGACATATTGGATGTATCA 59.093 43.478 0.00 0.00 31.52 2.15
2902 2951 5.014123 ACCCCGACATATTGGATGTATCATT 59.986 40.000 0.00 0.00 31.52 2.57
2944 2993 5.409826 CCTCCACTAACATGTTTCTCTCAAC 59.590 44.000 17.78 0.00 0.00 3.18
2945 2994 5.924356 TCCACTAACATGTTTCTCTCAACA 58.076 37.500 17.78 0.00 40.92 3.33
2946 2995 6.533730 TCCACTAACATGTTTCTCTCAACAT 58.466 36.000 17.78 0.00 46.34 2.71
2952 3001 3.631145 TGTTTCTCTCAACATGCAAGC 57.369 42.857 0.00 0.00 31.48 4.01
2953 3002 2.950975 TGTTTCTCTCAACATGCAAGCA 59.049 40.909 0.00 0.00 31.48 3.91
2954 3003 3.570975 TGTTTCTCTCAACATGCAAGCAT 59.429 39.130 0.86 0.86 37.08 3.79
2972 3021 2.499214 TGGCGCCCCATCATTAAAC 58.501 52.632 26.77 0.00 35.79 2.01
2973 3022 0.323816 TGGCGCCCCATCATTAAACA 60.324 50.000 26.77 0.00 35.79 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1017 1020 2.650116 GCTCGCCCAGAAGTCCAGA 61.650 63.158 0.00 0.00 0.00 3.86
1077 1080 3.786635 CTCACTGTACTCATAGGCAACC 58.213 50.000 0.00 0.00 37.17 3.77
1201 1204 2.031595 CGTCGATGTAGGTGAGGATGAG 60.032 54.545 0.00 0.00 0.00 2.90
1322 1325 5.416271 TGTCTTAATAAAGCGAGGTTCCT 57.584 39.130 0.00 0.00 32.36 3.36
1370 1373 7.177392 CCCAACTTTGAGGAAGATAAATGAAGT 59.823 37.037 0.00 0.00 38.77 3.01
1383 1386 6.816616 AAAATTTAACCCCAACTTTGAGGA 57.183 33.333 0.00 0.00 29.62 3.71
1407 1410 3.971150 ACCAATGAAATGTCGCGAAAAA 58.029 36.364 12.06 0.00 0.00 1.94
1408 1411 3.634568 ACCAATGAAATGTCGCGAAAA 57.365 38.095 12.06 1.84 0.00 2.29
1409 1412 3.997681 TCTACCAATGAAATGTCGCGAAA 59.002 39.130 12.06 5.59 0.00 3.46
1410 1413 3.591023 TCTACCAATGAAATGTCGCGAA 58.409 40.909 12.06 1.13 0.00 4.70
1411 1414 3.186909 CTCTACCAATGAAATGTCGCGA 58.813 45.455 3.71 3.71 0.00 5.87
1412 1415 2.285220 CCTCTACCAATGAAATGTCGCG 59.715 50.000 0.00 0.00 0.00 5.87
1413 1416 3.531538 TCCTCTACCAATGAAATGTCGC 58.468 45.455 0.00 0.00 0.00 5.19
1414 1417 5.178797 ACTTCCTCTACCAATGAAATGTCG 58.821 41.667 0.00 0.00 0.00 4.35
1415 1418 8.561738 TTAACTTCCTCTACCAATGAAATGTC 57.438 34.615 0.00 0.00 0.00 3.06
1416 1419 8.383175 TCTTAACTTCCTCTACCAATGAAATGT 58.617 33.333 0.00 0.00 0.00 2.71
1417 1420 8.792830 TCTTAACTTCCTCTACCAATGAAATG 57.207 34.615 0.00 0.00 0.00 2.32
1418 1421 8.606830 ACTCTTAACTTCCTCTACCAATGAAAT 58.393 33.333 0.00 0.00 0.00 2.17
1419 1422 7.878127 CACTCTTAACTTCCTCTACCAATGAAA 59.122 37.037 0.00 0.00 0.00 2.69
1420 1423 7.234782 TCACTCTTAACTTCCTCTACCAATGAA 59.765 37.037 0.00 0.00 0.00 2.57
1421 1424 6.724441 TCACTCTTAACTTCCTCTACCAATGA 59.276 38.462 0.00 0.00 0.00 2.57
1422 1425 6.936279 TCACTCTTAACTTCCTCTACCAATG 58.064 40.000 0.00 0.00 0.00 2.82
1423 1426 7.554959 TTCACTCTTAACTTCCTCTACCAAT 57.445 36.000 0.00 0.00 0.00 3.16
1424 1427 6.989155 TTCACTCTTAACTTCCTCTACCAA 57.011 37.500 0.00 0.00 0.00 3.67
1425 1428 6.989155 TTTCACTCTTAACTTCCTCTACCA 57.011 37.500 0.00 0.00 0.00 3.25
1426 1429 7.215085 TGTTTTCACTCTTAACTTCCTCTACC 58.785 38.462 0.00 0.00 0.00 3.18
1427 1430 7.385478 CCTGTTTTCACTCTTAACTTCCTCTAC 59.615 40.741 0.00 0.00 0.00 2.59
1428 1431 7.070821 ACCTGTTTTCACTCTTAACTTCCTCTA 59.929 37.037 0.00 0.00 0.00 2.43
1429 1432 6.126739 ACCTGTTTTCACTCTTAACTTCCTCT 60.127 38.462 0.00 0.00 0.00 3.69
1430 1433 6.017852 CACCTGTTTTCACTCTTAACTTCCTC 60.018 42.308 0.00 0.00 0.00 3.71
1431 1434 5.823045 CACCTGTTTTCACTCTTAACTTCCT 59.177 40.000 0.00 0.00 0.00 3.36
1432 1435 5.820947 TCACCTGTTTTCACTCTTAACTTCC 59.179 40.000 0.00 0.00 0.00 3.46
1433 1436 6.920569 TCACCTGTTTTCACTCTTAACTTC 57.079 37.500 0.00 0.00 0.00 3.01
1434 1437 6.657541 TGTTCACCTGTTTTCACTCTTAACTT 59.342 34.615 0.00 0.00 0.00 2.66
1435 1438 6.177610 TGTTCACCTGTTTTCACTCTTAACT 58.822 36.000 0.00 0.00 0.00 2.24
1436 1439 6.431198 TGTTCACCTGTTTTCACTCTTAAC 57.569 37.500 0.00 0.00 0.00 2.01
1437 1440 6.431543 TGTTGTTCACCTGTTTTCACTCTTAA 59.568 34.615 0.00 0.00 0.00 1.85
1438 1441 5.941058 TGTTGTTCACCTGTTTTCACTCTTA 59.059 36.000 0.00 0.00 0.00 2.10
1439 1442 4.764823 TGTTGTTCACCTGTTTTCACTCTT 59.235 37.500 0.00 0.00 0.00 2.85
1440 1443 4.156008 GTGTTGTTCACCTGTTTTCACTCT 59.844 41.667 0.00 0.00 40.84 3.24
1441 1444 4.083003 TGTGTTGTTCACCTGTTTTCACTC 60.083 41.667 0.00 0.00 45.61 3.51
1442 1445 3.823873 TGTGTTGTTCACCTGTTTTCACT 59.176 39.130 0.00 0.00 45.61 3.41
1443 1446 4.167554 TGTGTTGTTCACCTGTTTTCAC 57.832 40.909 0.00 0.00 45.61 3.18
1444 1447 4.460731 TCATGTGTTGTTCACCTGTTTTCA 59.539 37.500 0.00 0.00 45.61 2.69
1445 1448 4.798387 GTCATGTGTTGTTCACCTGTTTTC 59.202 41.667 0.00 0.00 45.61 2.29
1446 1449 4.219507 TGTCATGTGTTGTTCACCTGTTTT 59.780 37.500 0.00 0.00 45.61 2.43
1447 1450 3.761218 TGTCATGTGTTGTTCACCTGTTT 59.239 39.130 0.00 0.00 45.61 2.83
1448 1451 3.128589 GTGTCATGTGTTGTTCACCTGTT 59.871 43.478 0.00 0.00 45.61 3.16
1449 1452 2.682856 GTGTCATGTGTTGTTCACCTGT 59.317 45.455 0.00 0.00 45.61 4.00
1450 1453 2.286359 CGTGTCATGTGTTGTTCACCTG 60.286 50.000 0.00 0.00 45.61 4.00
1451 1454 1.939934 CGTGTCATGTGTTGTTCACCT 59.060 47.619 0.00 0.00 45.61 4.00
1452 1455 1.937223 TCGTGTCATGTGTTGTTCACC 59.063 47.619 0.00 0.00 45.61 4.02
1453 1456 3.666883 TTCGTGTCATGTGTTGTTCAC 57.333 42.857 0.00 0.00 46.31 3.18
1454 1457 4.126437 AGATTCGTGTCATGTGTTGTTCA 58.874 39.130 0.00 0.00 0.00 3.18
1455 1458 4.732285 AGATTCGTGTCATGTGTTGTTC 57.268 40.909 0.00 0.00 0.00 3.18
1456 1459 5.050363 GTGTAGATTCGTGTCATGTGTTGTT 60.050 40.000 0.00 0.00 0.00 2.83
1457 1460 4.447724 GTGTAGATTCGTGTCATGTGTTGT 59.552 41.667 0.00 0.00 0.00 3.32
1458 1461 4.447389 TGTGTAGATTCGTGTCATGTGTTG 59.553 41.667 0.00 0.00 0.00 3.33
1459 1462 4.447724 GTGTGTAGATTCGTGTCATGTGTT 59.552 41.667 0.00 0.00 0.00 3.32
1460 1463 3.987868 GTGTGTAGATTCGTGTCATGTGT 59.012 43.478 0.00 0.00 0.00 3.72
1461 1464 3.367932 GGTGTGTAGATTCGTGTCATGTG 59.632 47.826 0.00 0.00 0.00 3.21
1462 1465 3.258372 AGGTGTGTAGATTCGTGTCATGT 59.742 43.478 0.00 0.00 0.00 3.21
1463 1466 3.849911 AGGTGTGTAGATTCGTGTCATG 58.150 45.455 0.00 0.00 0.00 3.07
1464 1467 4.705507 ACTAGGTGTGTAGATTCGTGTCAT 59.294 41.667 0.00 0.00 0.00 3.06
1465 1468 4.077108 ACTAGGTGTGTAGATTCGTGTCA 58.923 43.478 0.00 0.00 0.00 3.58
1466 1469 4.698583 ACTAGGTGTGTAGATTCGTGTC 57.301 45.455 0.00 0.00 0.00 3.67
1467 1470 5.474532 TGTTACTAGGTGTGTAGATTCGTGT 59.525 40.000 0.00 0.00 0.00 4.49
1468 1471 5.946298 TGTTACTAGGTGTGTAGATTCGTG 58.054 41.667 0.00 0.00 0.00 4.35
1469 1472 6.579666 TTGTTACTAGGTGTGTAGATTCGT 57.420 37.500 0.00 0.00 0.00 3.85
1470 1473 5.515626 GCTTGTTACTAGGTGTGTAGATTCG 59.484 44.000 0.00 0.00 0.00 3.34
1471 1474 6.395629 TGCTTGTTACTAGGTGTGTAGATTC 58.604 40.000 0.00 0.00 0.00 2.52
1472 1475 6.354794 TGCTTGTTACTAGGTGTGTAGATT 57.645 37.500 0.00 0.00 0.00 2.40
1473 1476 5.995565 TGCTTGTTACTAGGTGTGTAGAT 57.004 39.130 0.00 0.00 0.00 1.98
1478 1481 6.398918 ACTAGAATGCTTGTTACTAGGTGTG 58.601 40.000 0.00 0.00 36.06 3.82
1538 1541 4.666512 AGTTTACTTGCTGGATTCATGGT 58.333 39.130 0.00 0.00 0.00 3.55
1584 1587 7.201821 CCTGCATCCTTTAATCGGAAAAATAGT 60.202 37.037 0.00 0.00 33.55 2.12
1598 1601 5.045213 TGGAATGTTAGTCCTGCATCCTTTA 60.045 40.000 0.00 0.00 36.03 1.85
1635 1638 3.529533 GGGTCTGACAGTCAATGATCTG 58.470 50.000 10.38 9.98 37.65 2.90
1641 1644 1.194781 AGGCGGGTCTGACAGTCAAT 61.195 55.000 10.38 0.00 0.00 2.57
1684 1687 0.250901 GTCTTTCTTGGCCTGCTCCA 60.251 55.000 3.32 0.00 0.00 3.86
1720 1723 0.613292 GAGCTCTGAGTCCAGGGTCA 60.613 60.000 6.43 0.00 42.91 4.02
1787 1790 1.593209 GGTCAAGGTCACGAACGCA 60.593 57.895 0.00 0.00 0.00 5.24
1886 1889 2.125753 CTCTCACGCTCCCTGCAC 60.126 66.667 0.00 0.00 43.06 4.57
1975 1978 9.109246 TGCCTACATAGATAACCTAGTACTCTA 57.891 37.037 0.00 0.00 0.00 2.43
2300 2305 4.840401 ACACATGTGTCGACGAAATATG 57.160 40.909 25.76 19.71 40.24 1.78
2306 2311 1.855978 GAACAACACATGTGTCGACGA 59.144 47.619 30.64 0.00 44.13 4.20
2307 2312 1.590698 TGAACAACACATGTGTCGACG 59.409 47.619 30.64 20.54 44.13 5.12
2460 2473 4.890158 TTTGTCAGGCACTCATTCTCTA 57.110 40.909 0.00 0.00 34.60 2.43
2658 2706 7.575414 TCATAAAGCTTGACCAAGTTTACAA 57.425 32.000 11.28 3.03 40.24 2.41
2660 2708 7.918562 TGTTTCATAAAGCTTGACCAAGTTTAC 59.081 33.333 11.28 6.53 40.24 2.01
2753 2802 6.256104 TGATTTTGACAATGACAACTTGCTTG 59.744 34.615 0.00 0.00 35.77 4.01
2816 2865 3.117663 TCCCTGGCTTCTTTTAAGTGTGT 60.118 43.478 0.00 0.00 0.00 3.72
2817 2866 3.486383 TCCCTGGCTTCTTTTAAGTGTG 58.514 45.455 0.00 0.00 0.00 3.82
2823 2872 1.354368 CCCACTCCCTGGCTTCTTTTA 59.646 52.381 0.00 0.00 39.01 1.52
2827 2876 1.083706 ATCCCACTCCCTGGCTTCT 59.916 57.895 0.00 0.00 39.01 2.85
2828 2877 1.225704 CATCCCACTCCCTGGCTTC 59.774 63.158 0.00 0.00 39.01 3.86
2922 2971 5.924356 TGTTGAGAGAAACATGTTAGTGGA 58.076 37.500 12.39 0.00 35.16 4.02
2944 2993 4.884257 GGGCGCCATGCTTGCATG 62.884 66.667 30.85 23.99 45.43 4.06
2948 2997 3.908081 GATGGGGCGCCATGCTTG 61.908 66.667 37.29 0.00 45.43 4.01
2949 2998 3.744003 ATGATGGGGCGCCATGCTT 62.744 57.895 37.29 22.21 45.43 3.91
2950 2999 2.356173 TAATGATGGGGCGCCATGCT 62.356 55.000 37.29 22.68 45.43 3.79
2951 3000 1.462731 TTAATGATGGGGCGCCATGC 61.463 55.000 37.29 26.55 45.38 4.06
2952 3001 1.039068 TTTAATGATGGGGCGCCATG 58.961 50.000 37.29 0.00 0.00 3.66
2953 3002 1.039856 GTTTAATGATGGGGCGCCAT 58.960 50.000 33.43 33.43 0.00 4.40
2954 3003 0.323816 TGTTTAATGATGGGGCGCCA 60.324 50.000 30.85 26.32 0.00 5.69
2955 3004 2.499214 TGTTTAATGATGGGGCGCC 58.501 52.632 21.18 21.18 0.00 6.53


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

AutoCloner maintained by Alex Coulton.