Multiple sequence alignment - TraesCS7A01G226300

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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 TraesCS7A01G226300 chr7A 100.000 2911 0 0 1 2911 195566918 195569828 0.000000e+00 5376.0
1 TraesCS7A01G226300 chr7A 85.890 1630 156 34 1296 2911 195734615 195736184 0.000000e+00 1668.0
2 TraesCS7A01G226300 chr7A 93.856 472 13 7 835 1305 195733695 195734151 0.000000e+00 697.0
3 TraesCS7A01G226300 chr7A 82.800 500 72 6 1 493 195732938 195733430 4.460000e-118 435.0
4 TraesCS7A01G226300 chr7A 80.259 309 40 11 1460 1762 195550554 195550847 2.270000e-51 213.0
5 TraesCS7A01G226300 chr7A 87.013 77 10 0 3 79 76186204 76186280 1.440000e-13 87.9
6 TraesCS7A01G226300 chr7A 83.333 72 12 0 1529 1600 194009806 194009735 1.870000e-07 67.6
7 TraesCS7A01G226300 chr7B 89.081 1731 132 30 1206 2911 332242765 332241067 0.000000e+00 2097.0
8 TraesCS7A01G226300 chr7B 91.518 1285 81 10 837 2098 332172975 332171696 0.000000e+00 1744.0
9 TraesCS7A01G226300 chr7B 87.853 815 82 5 2100 2911 332171482 332170682 0.000000e+00 941.0
10 TraesCS7A01G226300 chr7B 92.757 497 25 3 712 1206 332243374 332242887 0.000000e+00 708.0
11 TraesCS7A01G226300 chr7B 78.357 767 116 25 1 731 332174010 332173258 4.420000e-123 451.0
12 TraesCS7A01G226300 chr7B 82.609 460 49 12 769 1202 332256363 332255909 7.610000e-101 377.0
13 TraesCS7A01G226300 chr7B 85.455 330 36 3 1 325 332248511 332248189 1.670000e-87 333.0
14 TraesCS7A01G226300 chr7B 81.887 265 24 8 1529 1790 332255454 332255211 4.920000e-48 202.0
15 TraesCS7A01G226300 chr7D 88.462 1430 121 16 976 2379 188319259 188317848 0.000000e+00 1687.0
16 TraesCS7A01G226300 chr7D 85.817 698 59 19 314 993 188319957 188319282 0.000000e+00 704.0
17 TraesCS7A01G226300 chr7D 84.278 547 74 10 2371 2911 188309112 188308572 9.240000e-145 523.0
18 TraesCS7A01G226300 chr7D 88.153 287 26 3 5 291 188344103 188343825 4.650000e-88 335.0
19 TraesCS7A01G226300 chr7D 83.402 241 19 10 1529 1763 188360553 188360328 1.370000e-48 204.0
20 TraesCS7A01G226300 chr7D 95.122 41 2 0 1529 1569 185927240 185927200 6.730000e-07 65.8
21 TraesCS7A01G226300 chr1D 83.478 115 16 2 124 237 479917592 479917480 1.430000e-18 104.0
22 TraesCS7A01G226300 chr2D 76.316 190 32 8 1 183 603631091 603631274 4.000000e-14 89.8


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 TraesCS7A01G226300 chr7A 195566918 195569828 2910 False 5376.000000 5376 100.000000 1 2911 1 chr7A.!!$F3 2910
1 TraesCS7A01G226300 chr7A 195732938 195736184 3246 False 933.333333 1668 87.515333 1 2911 3 chr7A.!!$F4 2910
2 TraesCS7A01G226300 chr7B 332241067 332243374 2307 True 1402.500000 2097 90.919000 712 2911 2 chr7B.!!$R3 2199
3 TraesCS7A01G226300 chr7B 332170682 332174010 3328 True 1045.333333 1744 85.909333 1 2911 3 chr7B.!!$R2 2910
4 TraesCS7A01G226300 chr7B 332255211 332256363 1152 True 289.500000 377 82.248000 769 1790 2 chr7B.!!$R4 1021
5 TraesCS7A01G226300 chr7D 188317848 188319957 2109 True 1195.500000 1687 87.139500 314 2379 2 chr7D.!!$R5 2065
6 TraesCS7A01G226300 chr7D 188308572 188309112 540 True 523.000000 523 84.278000 2371 2911 1 chr7D.!!$R2 540

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
627 657 0.102663 GCTACGTCCAGACTTAGGCC 59.897 60.0 11.84 0.0 34.76 5.19 F
749 846 0.664166 CACGGATGCACAAAAGTGGC 60.664 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 2442 0.107361 CCATACCCTCCACCGTTTCC 60.107 60.0 0.00 0.00 0.0 3.13 R
2345 3633 0.182775 ACCAAAGCTTTCGTGAGGGT 59.817 50.0 9.23 9.74 0.0 4.34 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 2.282462 CCGGCCAACTCCTGCTTT 60.282 61.111 2.24 0.00 0.00 3.51
77 78 2.941333 GCGATCATGGCGGATGTG 59.059 61.111 10.16 0.00 33.29 3.21
78 79 2.610694 GCGATCATGGCGGATGTGG 61.611 63.158 10.16 0.00 33.29 4.17
79 80 1.069596 CGATCATGGCGGATGTGGA 59.930 57.895 0.00 0.00 33.29 4.02
80 81 0.321034 CGATCATGGCGGATGTGGAT 60.321 55.000 0.00 0.00 33.29 3.41
90 91 1.610363 CGGATGTGGATGTGTTGTGGA 60.610 52.381 0.00 0.00 0.00 4.02
97 101 1.523758 GATGTGTTGTGGAGTGGGTC 58.476 55.000 0.00 0.00 0.00 4.46
126 130 3.451894 GGAGGCGGCATTTGGGTG 61.452 66.667 13.08 0.00 0.00 4.61
188 192 4.011517 TGGGTTTCTCGGTCGCCC 62.012 66.667 0.00 0.00 39.73 6.13
190 194 3.703127 GGTTTCTCGGTCGCCCCT 61.703 66.667 0.00 0.00 0.00 4.79
192 196 2.283676 TTTCTCGGTCGCCCCTCT 60.284 61.111 0.00 0.00 0.00 3.69
202 206 1.132453 GTCGCCCCTCTTGTTTAATGC 59.868 52.381 0.00 0.00 0.00 3.56
206 210 0.455815 CCCTCTTGTTTAATGCCGGC 59.544 55.000 22.73 22.73 0.00 6.13
207 211 1.173043 CCTCTTGTTTAATGCCGGCA 58.827 50.000 34.80 34.80 0.00 5.69
248 252 0.888619 TTGAATGCTCCGTCGAGAGT 59.111 50.000 10.95 0.00 38.52 3.24
255 259 0.177141 CTCCGTCGAGAGTCTCTCCT 59.823 60.000 21.72 0.00 40.34 3.69
260 264 3.199677 CGTCGAGAGTCTCTCCTACATT 58.800 50.000 21.72 0.00 40.34 2.71
282 286 0.830023 TCCAGTCATGTCCGGTCACA 60.830 55.000 2.72 0.00 0.00 3.58
300 309 3.014623 CACACATCTCTGGAACATGCAT 58.985 45.455 0.00 0.00 38.20 3.96
309 318 0.107703 GGAACATGCATGGAGACCGA 60.108 55.000 29.41 0.00 0.00 4.69
311 320 0.615331 AACATGCATGGAGACCGAGT 59.385 50.000 29.41 3.16 0.00 4.18
325 334 2.583441 CGAGTGTCCCTCTTGCCCA 61.583 63.158 0.00 0.00 38.11 5.36
345 354 0.109179 GCATGCCGCTTCAATGTTGA 60.109 50.000 6.36 0.00 37.77 3.18
368 377 1.604023 AGTGAGAGGTCGCTTCCGT 60.604 57.895 0.00 0.00 40.90 4.69
377 386 2.048222 CGCTTCCGTTCTGAGCCA 60.048 61.111 0.00 0.00 32.90 4.75
388 397 3.871006 CGTTCTGAGCCAGCATTAATGTA 59.129 43.478 16.61 0.00 0.00 2.29
395 404 7.176515 TCTGAGCCAGCATTAATGTAAAGAAAA 59.823 33.333 16.61 0.00 0.00 2.29
515 525 1.511464 CGCGTACGTGACAGAGGTC 60.511 63.158 23.95 0.00 44.57 3.85
532 542 1.407437 GGTCTGGATGTCCGCAAAGAT 60.407 52.381 0.00 0.00 39.43 2.40
542 552 1.032114 CCGCAAAGATCCCCTGGTTC 61.032 60.000 0.00 0.00 0.00 3.62
548 558 3.735037 GATCCCCTGGTTCGCGTCC 62.735 68.421 5.77 11.09 0.00 4.79
563 573 5.427036 TCGCGTCCAGTTTTTAGAATTTT 57.573 34.783 5.77 0.00 0.00 1.82
572 582 8.682710 TCCAGTTTTTAGAATTTTGGATATCCG 58.317 33.333 17.04 0.00 39.43 4.18
574 584 9.503427 CAGTTTTTAGAATTTTGGATATCCGAC 57.497 33.333 17.04 3.42 39.43 4.79
575 585 9.462606 AGTTTTTAGAATTTTGGATATCCGACT 57.537 29.630 17.04 10.55 39.43 4.18
576 586 9.503427 GTTTTTAGAATTTTGGATATCCGACTG 57.497 33.333 17.04 0.00 39.43 3.51
577 587 9.456147 TTTTTAGAATTTTGGATATCCGACTGA 57.544 29.630 17.04 4.53 39.43 3.41
578 588 9.627123 TTTTAGAATTTTGGATATCCGACTGAT 57.373 29.630 17.04 6.58 39.43 2.90
579 589 8.833231 TTAGAATTTTGGATATCCGACTGATC 57.167 34.615 17.04 10.43 39.43 2.92
580 590 6.830912 AGAATTTTGGATATCCGACTGATCA 58.169 36.000 17.04 0.00 39.43 2.92
598 628 2.781923 TCATGTTGGATGACACACTGG 58.218 47.619 0.00 0.00 31.30 4.00
603 633 1.079127 GGATGACACACTGGGTCCG 60.079 63.158 9.01 0.00 34.36 4.79
609 639 3.626924 ACACTGGGTCCGGACAGC 61.627 66.667 34.40 18.84 38.25 4.40
612 642 1.982938 ACTGGGTCCGGACAGCTAC 60.983 63.158 34.40 17.35 38.25 3.58
624 654 3.408288 GACAGCTACGTCCAGACTTAG 57.592 52.381 6.89 6.89 36.56 2.18
627 657 0.102663 GCTACGTCCAGACTTAGGCC 59.897 60.000 11.84 0.00 34.76 5.19
646 676 1.877443 CCAGTGTTTTAAGGGTCCGTG 59.123 52.381 0.00 0.00 0.00 4.94
647 677 2.567985 CAGTGTTTTAAGGGTCCGTGT 58.432 47.619 0.00 0.00 0.00 4.49
650 680 2.944349 GTGTTTTAAGGGTCCGTGTTGA 59.056 45.455 0.00 0.00 0.00 3.18
652 682 4.015084 TGTTTTAAGGGTCCGTGTTGAAA 58.985 39.130 0.00 0.00 0.00 2.69
656 686 2.358322 AGGGTCCGTGTTGAAAATGT 57.642 45.000 0.00 0.00 0.00 2.71
662 692 5.048294 GGGTCCGTGTTGAAAATGTCTTTAT 60.048 40.000 0.00 0.00 0.00 1.40
677 707 8.991243 AATGTCTTTATACTGTACGTTAGCAA 57.009 30.769 0.00 0.00 0.00 3.91
679 709 7.596494 TGTCTTTATACTGTACGTTAGCAAGT 58.404 34.615 0.00 0.00 0.00 3.16
700 736 7.065563 GCAAGTGAATCAATAGCCAGGATATAG 59.934 40.741 0.00 0.00 0.00 1.31
715 751 7.632462 GCCAGGATATAGTCGATCAATGAATCT 60.632 40.741 0.00 0.00 0.00 2.40
749 846 0.664166 CACGGATGCACAAAAGTGGC 60.664 55.000 0.00 0.00 0.00 5.01
762 859 4.762251 ACAAAAGTGGCCAATCTCTACTTC 59.238 41.667 7.24 0.00 31.71 3.01
860 1137 5.417580 GGGGTAGCTAATCAAATGTGACAAA 59.582 40.000 0.00 0.00 36.31 2.83
950 1227 5.699458 TGGAGTTATCGAAGGTTGAAACTTC 59.301 40.000 12.82 12.82 40.64 3.01
1037 1369 4.693538 TCTAGCAGCGATATCATCTCAC 57.306 45.455 3.12 0.00 0.00 3.51
1056 1388 5.717178 TCTCACCCCAAGCTAGCTATTATAG 59.283 44.000 19.70 9.97 0.00 1.31
1308 2281 3.838317 TGTTCACTACTTGCCTACCTCAT 59.162 43.478 0.00 0.00 0.00 2.90
1342 2315 5.769662 ACTAAGGAATTGTGTTCATGCAGAA 59.230 36.000 0.00 0.00 0.00 3.02
1349 2322 3.753815 TGTGTTCATGCAGAATCCAAGA 58.246 40.909 0.00 0.00 38.76 3.02
1433 2424 4.508551 AACAAGCATGATGGAGGATACA 57.491 40.909 0.00 0.00 41.41 2.29
1443 2434 1.283905 TGGAGGATACAGAGACGGTGA 59.716 52.381 0.00 0.00 41.41 4.02
1451 2442 1.825474 ACAGAGACGGTGAAGGGTATG 59.175 52.381 0.00 0.00 0.00 2.39
1452 2443 1.137086 CAGAGACGGTGAAGGGTATGG 59.863 57.143 0.00 0.00 0.00 2.74
1453 2444 1.006758 AGAGACGGTGAAGGGTATGGA 59.993 52.381 0.00 0.00 0.00 3.41
1454 2445 1.829222 GAGACGGTGAAGGGTATGGAA 59.171 52.381 0.00 0.00 0.00 3.53
1455 2446 2.235402 GAGACGGTGAAGGGTATGGAAA 59.765 50.000 0.00 0.00 0.00 3.13
1456 2447 2.027469 AGACGGTGAAGGGTATGGAAAC 60.027 50.000 0.00 0.00 0.00 2.78
1457 2448 1.338389 ACGGTGAAGGGTATGGAAACG 60.338 52.381 0.00 0.00 0.00 3.60
1458 2449 1.746470 GGTGAAGGGTATGGAAACGG 58.254 55.000 0.00 0.00 0.00 4.44
1459 2450 1.003928 GGTGAAGGGTATGGAAACGGT 59.996 52.381 0.00 0.00 0.00 4.83
1460 2451 2.081462 GTGAAGGGTATGGAAACGGTG 58.919 52.381 0.00 0.00 0.00 4.94
1461 2452 1.003812 TGAAGGGTATGGAAACGGTGG 59.996 52.381 0.00 0.00 0.00 4.61
1462 2453 1.279846 GAAGGGTATGGAAACGGTGGA 59.720 52.381 0.00 0.00 0.00 4.02
1463 2454 0.909623 AGGGTATGGAAACGGTGGAG 59.090 55.000 0.00 0.00 0.00 3.86
1464 2455 0.107361 GGGTATGGAAACGGTGGAGG 60.107 60.000 0.00 0.00 0.00 4.30
1465 2456 0.107361 GGTATGGAAACGGTGGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
1466 2457 0.616891 GTATGGAAACGGTGGAGGGT 59.383 55.000 0.00 0.00 0.00 4.34
1467 2458 1.832998 GTATGGAAACGGTGGAGGGTA 59.167 52.381 0.00 0.00 0.00 3.69
1468 2459 1.591768 ATGGAAACGGTGGAGGGTAT 58.408 50.000 0.00 0.00 0.00 2.73
1473 2467 4.910585 CGGTGGAGGGTATGGCGC 62.911 72.222 0.00 0.00 0.00 6.53
1489 2483 0.249741 GCGCTGGTGGATACGGTAAT 60.250 55.000 0.00 0.00 42.51 1.89
1508 2502 0.548989 TGGTGGGGGATATGGAAACG 59.451 55.000 0.00 0.00 0.00 3.60
1513 2543 0.822121 GGGGATATGGAAACGGTGGC 60.822 60.000 0.00 0.00 0.00 5.01
1659 2716 2.203139 CGGGTATGGCAATGGCGA 60.203 61.111 1.51 0.00 42.47 5.54
1766 2823 1.414919 GCGGATATGGTGGAGGTTACA 59.585 52.381 0.00 0.00 0.00 2.41
1767 2824 2.158871 GCGGATATGGTGGAGGTTACAA 60.159 50.000 0.00 0.00 0.00 2.41
1768 2825 3.463944 CGGATATGGTGGAGGTTACAAC 58.536 50.000 0.00 0.00 0.00 3.32
1823 2880 3.117776 TGGATATGTGCAAGAGCCAAGAT 60.118 43.478 0.00 0.00 41.13 2.40
1935 3000 7.775053 ATAAAAGTTGTTCCTTATGCTTCCA 57.225 32.000 0.00 0.00 0.00 3.53
1936 3001 6.670695 AAAAGTTGTTCCTTATGCTTCCAT 57.329 33.333 0.00 0.00 35.44 3.41
1980 3045 0.392706 TGAGAAGTCAGGCGAGCAAA 59.607 50.000 0.00 0.00 0.00 3.68
2091 3165 5.126222 ACACGAGGAGATATATGTGCCTATG 59.874 44.000 0.00 4.86 0.00 2.23
2221 3507 5.479124 AAGTATTGTTTCCTACTGTCCGT 57.521 39.130 0.00 0.00 0.00 4.69
2299 3587 2.892425 GAAGACATGCCGGCTCCG 60.892 66.667 29.70 17.99 39.44 4.63
2315 3603 0.874390 TCCGCTCAAGTCAAATGCAC 59.126 50.000 0.00 0.00 0.00 4.57
2317 3605 0.877071 CGCTCAAGTCAAATGCACCT 59.123 50.000 0.00 0.00 0.00 4.00
2345 3633 0.250124 AAATCACCGCCGAGTTGACA 60.250 50.000 0.00 0.00 0.00 3.58
2350 3638 2.432628 CGCCGAGTTGACACCCTC 60.433 66.667 0.00 0.00 0.00 4.30
2351 3639 2.741092 GCCGAGTTGACACCCTCA 59.259 61.111 3.05 0.00 0.00 3.86
2354 3642 1.658114 CGAGTTGACACCCTCACGA 59.342 57.895 0.00 0.00 0.00 4.35
2364 3652 0.182775 ACCCTCACGAAAGCTTTGGT 59.817 50.000 19.76 19.76 0.00 3.67
2404 3692 4.310740 AGAGGTCCACCATTGAAGGATAT 58.689 43.478 0.00 0.00 38.89 1.63
2425 3713 2.038387 ATCATTCACCGTTAGGGCAC 57.962 50.000 0.00 0.00 43.47 5.01
2428 3716 0.390735 ATTCACCGTTAGGGCACGAC 60.391 55.000 0.00 0.00 43.15 4.34
2471 3759 3.009723 CCAGCGAAGTACACCATTTGAT 58.990 45.455 0.00 0.00 0.00 2.57
2516 3806 2.478539 GCCATCTTCGATCAAAAGCACC 60.479 50.000 0.00 0.00 0.00 5.01
2517 3807 3.012518 CCATCTTCGATCAAAAGCACCT 58.987 45.455 0.00 0.00 0.00 4.00
2521 3811 2.839486 TCGATCAAAAGCACCTCACT 57.161 45.000 0.00 0.00 0.00 3.41
2563 3870 2.028130 ACCGAGCCATTGTTTCAAACA 58.972 42.857 0.00 0.00 40.21 2.83
2644 3952 7.725251 TCAGCATATCTACATATGACAACACA 58.275 34.615 10.38 0.00 43.37 3.72
2692 4000 6.691508 AGGTTGACATAAAGAAAAGGAATGC 58.308 36.000 0.00 0.00 0.00 3.56
2698 4006 7.178983 TGACATAAAGAAAAGGAATGCCAAGAT 59.821 33.333 0.00 0.00 36.29 2.40
2699 4007 8.593945 ACATAAAGAAAAGGAATGCCAAGATA 57.406 30.769 0.00 0.00 36.29 1.98
2732 4040 2.083774 ACATGACATGGTAGTTTGGCG 58.916 47.619 19.39 0.00 33.60 5.69
2735 4043 1.001393 ACATGGTAGTTTGGCGGGG 60.001 57.895 0.00 0.00 0.00 5.73
2795 4103 4.346730 TCGACCTAAACTGTAATCTCCCA 58.653 43.478 0.00 0.00 0.00 4.37
2813 4121 5.602145 TCTCCCAATCAAACTCAACCAAAAT 59.398 36.000 0.00 0.00 0.00 1.82
2819 4127 7.095523 CCAATCAAACTCAACCAAAATCATCAC 60.096 37.037 0.00 0.00 0.00 3.06
2851 4159 4.658063 TGTTTAATACCAAGGACCACTGG 58.342 43.478 10.40 10.40 0.00 4.00
2874 4182 1.338105 CCACATCAAGAGTCCTTCGCA 60.338 52.381 0.00 0.00 0.00 5.10
2881 4189 0.671781 AGAGTCCTTCGCACATGCAC 60.672 55.000 4.49 0.00 42.21 4.57
2882 4190 1.639298 GAGTCCTTCGCACATGCACC 61.639 60.000 4.49 0.00 42.21 5.01
2891 4199 1.601419 GCACATGCACCCTCATGCTT 61.601 55.000 0.00 0.00 45.75 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.982127 GTCTCTAGACGAAGCAAAAGC 57.018 47.619 0.00 0.00 35.12 3.51
30 31 1.213182 AGCGATGTGGGAGAGTCTCTA 59.787 52.381 19.45 6.81 0.00 2.43
35 36 1.213182 TCTAGAGCGATGTGGGAGAGT 59.787 52.381 0.00 0.00 0.00 3.24
60 61 2.610694 CCACATCCGCCATGATCGC 61.611 63.158 0.00 0.00 36.21 4.58
74 75 1.476652 CCACTCCACAACACATCCACA 60.477 52.381 0.00 0.00 0.00 4.17
75 76 1.238439 CCACTCCACAACACATCCAC 58.762 55.000 0.00 0.00 0.00 4.02
76 77 0.110295 CCCACTCCACAACACATCCA 59.890 55.000 0.00 0.00 0.00 3.41
77 78 0.110486 ACCCACTCCACAACACATCC 59.890 55.000 0.00 0.00 0.00 3.51
78 79 1.523758 GACCCACTCCACAACACATC 58.476 55.000 0.00 0.00 0.00 3.06
79 80 0.250295 CGACCCACTCCACAACACAT 60.250 55.000 0.00 0.00 0.00 3.21
80 81 1.145156 CGACCCACTCCACAACACA 59.855 57.895 0.00 0.00 0.00 3.72
105 109 1.678635 CCAAATGCCGCCTCCTTGA 60.679 57.895 0.00 0.00 0.00 3.02
107 111 2.362889 CCCAAATGCCGCCTCCTT 60.363 61.111 0.00 0.00 0.00 3.36
148 152 2.477176 GGCGCCCGCATTGATACAA 61.477 57.895 18.11 0.00 44.11 2.41
150 154 2.896801 CTGGCGCCCGCATTGATAC 61.897 63.158 26.77 0.00 44.11 2.24
188 192 1.133025 CTGCCGGCATTAAACAAGAGG 59.867 52.381 32.87 9.83 0.00 3.69
190 194 1.173043 CCTGCCGGCATTAAACAAGA 58.827 50.000 32.87 1.81 0.00 3.02
206 210 4.135153 CTCCAGTCCGTCCGCCTG 62.135 72.222 0.00 0.00 0.00 4.85
217 221 1.244019 GCATTCAAACCGGCTCCAGT 61.244 55.000 0.00 0.00 0.00 4.00
218 222 0.962356 AGCATTCAAACCGGCTCCAG 60.962 55.000 0.00 0.00 28.71 3.86
219 223 0.960364 GAGCATTCAAACCGGCTCCA 60.960 55.000 0.00 0.00 45.31 3.86
248 252 3.027412 GACTGGAGCAATGTAGGAGAGA 58.973 50.000 0.00 0.00 0.00 3.10
255 259 2.418609 CGGACATGACTGGAGCAATGTA 60.419 50.000 0.00 0.00 0.00 2.29
260 264 1.888436 GACCGGACATGACTGGAGCA 61.888 60.000 26.79 0.00 39.41 4.26
282 286 2.240414 TCCATGCATGTTCCAGAGATGT 59.760 45.455 24.58 0.00 0.00 3.06
309 318 2.900106 GCTGGGCAAGAGGGACACT 61.900 63.158 0.00 0.00 0.00 3.55
311 320 2.233566 ATGCTGGGCAAGAGGGACA 61.234 57.895 0.00 0.00 43.62 4.02
342 351 1.248486 CGACCTCTCACTGGAGTCAA 58.752 55.000 0.00 0.00 42.05 3.18
345 354 0.540830 AAGCGACCTCTCACTGGAGT 60.541 55.000 0.00 0.00 42.05 3.85
368 377 6.179756 TCTTTACATTAATGCTGGCTCAGAA 58.820 36.000 15.48 0.00 32.44 3.02
377 386 7.145932 AGAGCGTTTTCTTTACATTAATGCT 57.854 32.000 15.48 1.90 42.10 3.79
511 521 0.036010 CTTTGCGGACATCCAGACCT 60.036 55.000 0.00 0.00 35.14 3.85
513 523 1.936547 GATCTTTGCGGACATCCAGAC 59.063 52.381 0.00 0.00 35.14 3.51
515 525 1.303309 GGATCTTTGCGGACATCCAG 58.697 55.000 0.00 0.00 35.72 3.86
520 530 1.299648 CAGGGGATCTTTGCGGACA 59.700 57.895 0.00 0.00 0.00 4.02
542 552 4.381566 CCAAAATTCTAAAAACTGGACGCG 59.618 41.667 3.53 3.53 0.00 6.01
548 558 9.503427 GTCGGATATCCAAAATTCTAAAAACTG 57.497 33.333 21.70 0.00 35.14 3.16
563 573 4.262592 CCAACATGATCAGTCGGATATCCA 60.263 45.833 21.70 6.20 36.00 3.41
572 582 4.093998 GTGTGTCATCCAACATGATCAGTC 59.906 45.833 0.00 0.00 0.00 3.51
574 584 4.094442 CAGTGTGTCATCCAACATGATCAG 59.906 45.833 0.00 0.00 0.00 2.90
575 585 4.004982 CAGTGTGTCATCCAACATGATCA 58.995 43.478 0.00 0.00 0.00 2.92
576 586 3.376234 CCAGTGTGTCATCCAACATGATC 59.624 47.826 0.00 0.00 0.00 2.92
577 587 3.349927 CCAGTGTGTCATCCAACATGAT 58.650 45.455 0.00 0.00 0.00 2.45
578 588 2.552809 CCCAGTGTGTCATCCAACATGA 60.553 50.000 0.00 0.00 0.00 3.07
579 589 1.814394 CCCAGTGTGTCATCCAACATG 59.186 52.381 0.00 0.00 0.00 3.21
580 590 1.425066 ACCCAGTGTGTCATCCAACAT 59.575 47.619 0.00 0.00 0.00 2.71
598 628 2.488820 GACGTAGCTGTCCGGACC 59.511 66.667 31.19 17.09 32.61 4.46
609 639 1.405821 CTGGCCTAAGTCTGGACGTAG 59.594 57.143 3.32 13.88 41.15 3.51
612 642 0.108615 CACTGGCCTAAGTCTGGACG 60.109 60.000 3.32 0.00 34.69 4.79
617 647 4.506802 CCCTTAAAACACTGGCCTAAGTCT 60.507 45.833 3.32 0.00 0.00 3.24
621 651 3.499021 GGACCCTTAAAACACTGGCCTAA 60.499 47.826 3.32 0.00 0.00 2.69
624 654 1.254026 GGACCCTTAAAACACTGGCC 58.746 55.000 0.00 0.00 0.00 5.36
627 657 2.567985 ACACGGACCCTTAAAACACTG 58.432 47.619 0.00 0.00 0.00 3.66
650 680 9.426837 TGCTAACGTACAGTATAAAGACATTTT 57.573 29.630 0.00 0.00 0.00 1.82
652 682 8.991243 TTGCTAACGTACAGTATAAAGACATT 57.009 30.769 0.00 0.00 0.00 2.71
656 686 7.819644 TCACTTGCTAACGTACAGTATAAAGA 58.180 34.615 0.00 0.00 0.00 2.52
662 692 6.016213 TGATTCACTTGCTAACGTACAGTA 57.984 37.500 0.00 0.00 0.00 2.74
677 707 7.363355 CGACTATATCCTGGCTATTGATTCACT 60.363 40.741 6.10 0.00 0.00 3.41
679 709 6.663523 TCGACTATATCCTGGCTATTGATTCA 59.336 38.462 6.10 0.00 0.00 2.57
715 751 9.495572 TGTGCATCCGTGTATTAAATATTATCA 57.504 29.630 0.00 0.00 0.00 2.15
749 846 5.289675 CACTTGCTAACGAAGTAGAGATTGG 59.710 44.000 0.00 0.00 45.00 3.16
762 859 3.650139 AGTGTAGAACCACTTGCTAACG 58.350 45.455 0.00 0.00 42.99 3.18
830 1101 1.052124 TGATTAGCTACCCCCACCCG 61.052 60.000 0.00 0.00 0.00 5.28
860 1137 3.257127 GGACCGAGCTTTGCTATATCTCT 59.743 47.826 0.00 0.00 39.88 3.10
869 1146 4.699522 ACCGGGACCGAGCTTTGC 62.700 66.667 13.13 0.00 42.83 3.68
950 1227 5.352569 CGCCTATGCCTATCTCCAATTTTAG 59.647 44.000 0.00 0.00 0.00 1.85
1086 1418 6.268847 ACACCAAGAAGAACTAGAGACTTGAT 59.731 38.462 0.00 0.00 37.49 2.57
1308 2281 5.301551 ACACAATTCCTTAGTGAACATTGCA 59.698 36.000 0.00 0.00 37.05 4.08
1342 2315 6.208204 CAGGTTTCACATTCTTCTTCTTGGAT 59.792 38.462 0.00 0.00 0.00 3.41
1349 2322 3.571401 CCTGCAGGTTTCACATTCTTCTT 59.429 43.478 25.53 0.00 0.00 2.52
1433 2424 1.006758 TCCATACCCTTCACCGTCTCT 59.993 52.381 0.00 0.00 0.00 3.10
1443 2434 1.280998 CTCCACCGTTTCCATACCCTT 59.719 52.381 0.00 0.00 0.00 3.95
1451 2442 0.107361 CCATACCCTCCACCGTTTCC 60.107 60.000 0.00 0.00 0.00 3.13
1452 2443 0.746923 GCCATACCCTCCACCGTTTC 60.747 60.000 0.00 0.00 0.00 2.78
1453 2444 1.301954 GCCATACCCTCCACCGTTT 59.698 57.895 0.00 0.00 0.00 3.60
1454 2445 2.995547 GCCATACCCTCCACCGTT 59.004 61.111 0.00 0.00 0.00 4.44
1455 2446 3.467226 CGCCATACCCTCCACCGT 61.467 66.667 0.00 0.00 0.00 4.83
1456 2447 4.910585 GCGCCATACCCTCCACCG 62.911 72.222 0.00 0.00 0.00 4.94
1457 2448 3.480133 AGCGCCATACCCTCCACC 61.480 66.667 2.29 0.00 0.00 4.61
1458 2449 2.203070 CAGCGCCATACCCTCCAC 60.203 66.667 2.29 0.00 0.00 4.02
1459 2450 3.479203 CCAGCGCCATACCCTCCA 61.479 66.667 2.29 0.00 0.00 3.86
1460 2451 3.480133 ACCAGCGCCATACCCTCC 61.480 66.667 2.29 0.00 0.00 4.30
1461 2452 2.203070 CACCAGCGCCATACCCTC 60.203 66.667 2.29 0.00 0.00 4.30
1462 2453 3.797353 CCACCAGCGCCATACCCT 61.797 66.667 2.29 0.00 0.00 4.34
1463 2454 1.764571 TATCCACCAGCGCCATACCC 61.765 60.000 2.29 0.00 0.00 3.69
1464 2455 0.602905 GTATCCACCAGCGCCATACC 60.603 60.000 2.29 0.00 0.00 2.73
1465 2456 0.944311 CGTATCCACCAGCGCCATAC 60.944 60.000 2.29 0.64 0.00 2.39
1466 2457 1.365999 CGTATCCACCAGCGCCATA 59.634 57.895 2.29 0.00 0.00 2.74
1467 2458 2.108976 CGTATCCACCAGCGCCAT 59.891 61.111 2.29 0.00 0.00 4.40
1468 2459 4.155733 CCGTATCCACCAGCGCCA 62.156 66.667 2.29 0.00 0.00 5.69
1473 2467 2.484770 CCACCATTACCGTATCCACCAG 60.485 54.545 0.00 0.00 0.00 4.00
1489 2483 0.548989 CGTTTCCATATCCCCCACCA 59.451 55.000 0.00 0.00 0.00 4.17
1508 2502 1.692173 TAGCCATAACCTCCGCCACC 61.692 60.000 0.00 0.00 0.00 4.61
1513 2543 1.276421 CCTCCATAGCCATAACCTCCG 59.724 57.143 0.00 0.00 0.00 4.63
1659 2716 2.502538 CTGCCAAATCCACCATTTCCAT 59.497 45.455 0.00 0.00 31.79 3.41
1766 2823 2.990479 GCCACCAGATCCTCCGTT 59.010 61.111 0.00 0.00 0.00 4.44
1767 2824 3.461773 CGCCACCAGATCCTCCGT 61.462 66.667 0.00 0.00 0.00 4.69
1768 2825 4.227134 CCGCCACCAGATCCTCCG 62.227 72.222 0.00 0.00 0.00 4.63
1823 2880 7.825331 TTTCATAGTTCCAACCATTGTAACA 57.175 32.000 0.74 0.00 32.58 2.41
1917 2981 8.352942 CCTATTAATGGAAGCATAAGGAACAAC 58.647 37.037 0.00 0.00 0.00 3.32
1918 2983 8.278639 TCCTATTAATGGAAGCATAAGGAACAA 58.721 33.333 0.00 0.00 0.00 2.83
1932 2997 4.721776 ACAGACCTTGCTCCTATTAATGGA 59.278 41.667 0.00 3.76 0.00 3.41
1933 2998 5.041191 ACAGACCTTGCTCCTATTAATGG 57.959 43.478 0.00 0.00 0.00 3.16
1935 3000 6.387220 ACCTTACAGACCTTGCTCCTATTAAT 59.613 38.462 0.00 0.00 0.00 1.40
1936 3001 5.724854 ACCTTACAGACCTTGCTCCTATTAA 59.275 40.000 0.00 0.00 0.00 1.40
2061 3135 7.316640 GCACATATATCTCCTCGTGTTCTAAT 58.683 38.462 0.00 0.00 0.00 1.73
2107 3393 6.838612 GGGGCTACTCATCTAGATCATAGATT 59.161 42.308 1.03 0.00 32.37 2.40
2160 3446 0.544697 AGTCCCTTGTTGTTGACCGT 59.455 50.000 0.00 0.00 0.00 4.83
2166 3452 5.578157 AGTACCATAAGTCCCTTGTTGTT 57.422 39.130 0.00 0.00 0.00 2.83
2201 3487 4.624452 GTGACGGACAGTAGGAAACAATAC 59.376 45.833 0.00 0.00 0.00 1.89
2221 3507 6.809869 AGTAATTGATCATCGTCATGAGTGA 58.190 36.000 0.00 1.46 42.53 3.41
2299 3587 3.671702 GCTAAGGTGCATTTGACTTGAGC 60.672 47.826 0.00 0.00 0.00 4.26
2317 3605 1.459450 GGCGGTGATTTCCTTGCTAA 58.541 50.000 0.00 0.00 0.00 3.09
2334 3622 1.668151 GTGAGGGTGTCAACTCGGC 60.668 63.158 0.00 0.00 36.74 5.54
2345 3633 0.182775 ACCAAAGCTTTCGTGAGGGT 59.817 50.000 9.23 9.74 0.00 4.34
2350 3638 1.068333 CATCCCACCAAAGCTTTCGTG 60.068 52.381 24.82 24.82 0.00 4.35
2351 3639 1.247567 CATCCCACCAAAGCTTTCGT 58.752 50.000 9.23 6.11 0.00 3.85
2354 3642 2.629017 ATCCATCCCACCAAAGCTTT 57.371 45.000 5.69 5.69 0.00 3.51
2364 3652 2.173356 CTCTTGGCAACTATCCATCCCA 59.827 50.000 0.00 0.00 32.92 4.37
2404 3692 3.537580 GTGCCCTAACGGTGAATGATTA 58.462 45.455 0.00 0.00 0.00 1.75
2471 3759 8.736244 GGCTATGATTTCCACTGTTTTTACTTA 58.264 33.333 0.00 0.00 0.00 2.24
2496 3786 3.012518 AGGTGCTTTTGATCGAAGATGG 58.987 45.455 11.59 0.00 45.12 3.51
2668 3976 6.295292 GGCATTCCTTTTCTTTATGTCAACCT 60.295 38.462 0.00 0.00 0.00 3.50
2692 4000 5.733226 TGTATTCATGTTGCGTATCTTGG 57.267 39.130 0.00 0.00 0.00 3.61
2720 4028 0.185416 TTTTCCCCGCCAAACTACCA 59.815 50.000 0.00 0.00 0.00 3.25
2795 4103 7.499292 TGTGATGATTTTGGTTGAGTTTGATT 58.501 30.769 0.00 0.00 0.00 2.57
2819 4127 9.573133 GTCCTTGGTATTAAACAGAAATCATTG 57.427 33.333 0.00 0.00 0.00 2.82
2830 4138 3.442625 GCCAGTGGTCCTTGGTATTAAAC 59.557 47.826 11.74 0.00 36.81 2.01
2851 4159 0.674895 AAGGACTCTTGATGTGGCGC 60.675 55.000 0.00 0.00 0.00 6.53
2881 4189 2.969238 CGCGGCTAAGCATGAGGG 60.969 66.667 0.00 0.00 36.85 4.30
2882 4190 2.969238 CCGCGGCTAAGCATGAGG 60.969 66.667 14.67 0.00 36.85 3.86
2891 4199 2.574929 CTTGTACACCCGCGGCTA 59.425 61.111 22.85 5.38 0.00 3.93


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

AutoCloner maintained by Alex Coulton.