Multiple sequence alignment - TraesCS7A01G063500

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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 TraesCS7A01G063500 chr7A 100.000 2366 0 0 1 2366 31686531 31688896 0.000000e+00 4370.0
1 TraesCS7A01G063500 chr7A 88.041 878 93 9 863 1737 31582243 31581375 0.000000e+00 1029.0
2 TraesCS7A01G063500 chr7A 81.941 814 99 28 1 773 31583164 31582358 0.000000e+00 645.0
3 TraesCS7A01G063500 chr7A 79.646 452 61 18 151 574 31693444 31693892 1.780000e-76 296.0
4 TraesCS7A01G063500 chr7D 88.128 876 99 4 863 1737 31114297 31115168 0.000000e+00 1037.0
5 TraesCS7A01G063500 chr7D 87.748 555 59 5 133 683 31113324 31113873 7.130000e-180 640.0
6 TraesCS7A01G063500 chr7D 79.288 309 56 7 139 440 31281440 31281747 2.380000e-50 209.0
7 TraesCS7A01G063500 chr7D 100.000 33 0 0 506 538 31281840 31281872 7.060000e-06 62.1
8 TraesCS7A01G063500 chr3A 94.582 646 15 6 1738 2366 696335502 696336144 0.000000e+00 981.0
9 TraesCS7A01G063500 chr3A 89.881 672 19 10 1738 2366 724713974 724713309 0.000000e+00 819.0
10 TraesCS7A01G063500 chr6A 94.453 649 14 5 1738 2366 148888458 148889104 0.000000e+00 979.0
11 TraesCS7A01G063500 chr6A 94.145 649 15 4 1738 2366 606661357 606660712 0.000000e+00 966.0
12 TraesCS7A01G063500 chr6A 91.190 647 30 6 1738 2366 28272861 28273498 0.000000e+00 854.0
13 TraesCS7A01G063500 chr6A 88.235 289 26 7 1738 2019 48054343 48054056 2.910000e-89 339.0
14 TraesCS7A01G063500 chr6A 87.500 72 9 0 974 1045 596485916 596485987 1.510000e-12 84.2
15 TraesCS7A01G063500 chr5A 94.272 646 17 5 1738 2366 694636119 694635477 0.000000e+00 970.0
16 TraesCS7A01G063500 chr5A 92.178 652 29 5 1736 2366 17562535 17561885 0.000000e+00 902.0
17 TraesCS7A01G063500 chr1A 90.951 652 27 12 1738 2366 590203868 590203226 0.000000e+00 848.0
18 TraesCS7A01G063500 chr4A 90.644 652 36 8 1738 2366 600954269 600954918 0.000000e+00 843.0
19 TraesCS7A01G063500 chr4A 90.337 652 27 13 1737 2366 634168537 634169174 0.000000e+00 822.0
20 TraesCS7A01G063500 chr4A 76.364 495 75 24 871 1361 34680014 34680470 6.580000e-56 228.0
21 TraesCS7A01G063500 chr4A 79.233 313 46 13 131 425 34677916 34678227 1.430000e-47 200.0
22 TraesCS7A01G063500 chr4A 91.026 78 7 0 369 446 696576847 696576924 3.220000e-19 106.0
23 TraesCS7A01G063500 chr1B 91.765 255 16 4 1738 1990 291988654 291988905 1.350000e-92 350.0
24 TraesCS7A01G063500 chr2A 87.857 280 26 5 1738 2012 40332050 40331774 2.930000e-84 322.0
25 TraesCS7A01G063500 chr5D 81.081 407 65 10 173 573 34063951 34064351 4.910000e-82 315.0
26 TraesCS7A01G063500 chr5D 77.826 230 29 11 366 574 24915438 24915666 3.190000e-24 122.0
27 TraesCS7A01G063500 chr4D 77.568 477 63 22 130 574 433365476 433365940 5.050000e-62 248.0
28 TraesCS7A01G063500 chr4D 76.113 494 77 25 871 1361 433366406 433366861 1.100000e-53 220.0
29 TraesCS7A01G063500 chrUn 74.735 471 83 25 903 1361 287417714 287418160 6.720000e-41 178.0
30 TraesCS7A01G063500 chrUn 74.735 471 83 25 903 1361 295022186 295021740 6.720000e-41 178.0
31 TraesCS7A01G063500 chrUn 95.714 70 3 0 505 574 287417372 287417441 1.920000e-21 113.0
32 TraesCS7A01G063500 chrUn 95.714 70 3 0 505 574 295022528 295022459 1.920000e-21 113.0
33 TraesCS7A01G063500 chr6B 80.723 83 14 2 932 1013 693300277 693300196 1.960000e-06 63.9
34 TraesCS7A01G063500 chr6D 94.595 37 2 0 977 1013 455906304 455906268 9.130000e-05 58.4


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 TraesCS7A01G063500 chr7A 31686531 31688896 2365 False 4370.0 4370 100.0000 1 2366 1 chr7A.!!$F1 2365
1 TraesCS7A01G063500 chr7A 31581375 31583164 1789 True 837.0 1029 84.9910 1 1737 2 chr7A.!!$R1 1736
2 TraesCS7A01G063500 chr7D 31113324 31115168 1844 False 838.5 1037 87.9380 133 1737 2 chr7D.!!$F1 1604
3 TraesCS7A01G063500 chr3A 696335502 696336144 642 False 981.0 981 94.5820 1738 2366 1 chr3A.!!$F1 628
4 TraesCS7A01G063500 chr3A 724713309 724713974 665 True 819.0 819 89.8810 1738 2366 1 chr3A.!!$R1 628
5 TraesCS7A01G063500 chr6A 148888458 148889104 646 False 979.0 979 94.4530 1738 2366 1 chr6A.!!$F2 628
6 TraesCS7A01G063500 chr6A 606660712 606661357 645 True 966.0 966 94.1450 1738 2366 1 chr6A.!!$R2 628
7 TraesCS7A01G063500 chr6A 28272861 28273498 637 False 854.0 854 91.1900 1738 2366 1 chr6A.!!$F1 628
8 TraesCS7A01G063500 chr5A 694635477 694636119 642 True 970.0 970 94.2720 1738 2366 1 chr5A.!!$R2 628
9 TraesCS7A01G063500 chr5A 17561885 17562535 650 True 902.0 902 92.1780 1736 2366 1 chr5A.!!$R1 630
10 TraesCS7A01G063500 chr1A 590203226 590203868 642 True 848.0 848 90.9510 1738 2366 1 chr1A.!!$R1 628
11 TraesCS7A01G063500 chr4A 600954269 600954918 649 False 843.0 843 90.6440 1738 2366 1 chr4A.!!$F1 628
12 TraesCS7A01G063500 chr4A 634168537 634169174 637 False 822.0 822 90.3370 1737 2366 1 chr4A.!!$F2 629
13 TraesCS7A01G063500 chr4A 34677916 34680470 2554 False 214.0 228 77.7985 131 1361 2 chr4A.!!$F4 1230
14 TraesCS7A01G063500 chr4D 433365476 433366861 1385 False 234.0 248 76.8405 130 1361 2 chr4D.!!$F1 1231

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
108 109 0.535797 AATTCTTCGTCGTCTCCCCC 59.464 55.0 0.00 0.0 0.00 5.40 F
605 1848 0.807667 TCGCCGACTCGAGGTACTAC 60.808 60.0 18.41 0.0 41.55 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 2708 0.322456 TCTGGACCGGCAATTCTTGG 60.322 55.000 0.0 0.0 0.0 3.61 R
1774 3398 1.002502 GAACCGGCACTAAAGGGCT 60.003 57.895 0.0 0.0 0.0 5.19 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
28 29 4.241681 GCGAAGACTTGAGAAGACTTGAT 58.758 43.478 5.91 0.00 42.13 2.57
54 55 2.158561 AAATGCAGTTGCTTCGCCCC 62.159 55.000 0.00 0.00 42.66 5.80
64 65 2.451490 TGCTTCGCCCCAAATGAAATA 58.549 42.857 0.00 0.00 0.00 1.40
65 66 2.426738 TGCTTCGCCCCAAATGAAATAG 59.573 45.455 0.00 0.00 0.00 1.73
76 77 6.461509 CCCCAAATGAAATAGATTTCCTTCCG 60.462 42.308 11.51 4.75 44.16 4.30
79 80 7.702348 CCAAATGAAATAGATTTCCTTCCGTTC 59.298 37.037 11.51 0.00 44.16 3.95
81 82 6.062258 TGAAATAGATTTCCTTCCGTTCCT 57.938 37.500 11.51 0.00 44.16 3.36
82 83 7.190335 TGAAATAGATTTCCTTCCGTTCCTA 57.810 36.000 11.51 0.00 44.16 2.94
86 87 5.087391 AGATTTCCTTCCGTTCCTACTTC 57.913 43.478 0.00 0.00 0.00 3.01
90 91 2.974099 TCCTTCCGTTCCTACTTCCAAA 59.026 45.455 0.00 0.00 0.00 3.28
92 93 4.042435 TCCTTCCGTTCCTACTTCCAAATT 59.958 41.667 0.00 0.00 0.00 1.82
101 102 4.021719 TCCTACTTCCAAATTCTTCGTCGT 60.022 41.667 0.00 0.00 0.00 4.34
102 103 4.326548 CCTACTTCCAAATTCTTCGTCGTC 59.673 45.833 0.00 0.00 0.00 4.20
103 104 3.991367 ACTTCCAAATTCTTCGTCGTCT 58.009 40.909 0.00 0.00 0.00 4.18
104 105 3.988517 ACTTCCAAATTCTTCGTCGTCTC 59.011 43.478 0.00 0.00 0.00 3.36
105 106 2.955614 TCCAAATTCTTCGTCGTCTCC 58.044 47.619 0.00 0.00 0.00 3.71
107 108 2.000447 CAAATTCTTCGTCGTCTCCCC 59.000 52.381 0.00 0.00 0.00 4.81
108 109 0.535797 AATTCTTCGTCGTCTCCCCC 59.464 55.000 0.00 0.00 0.00 5.40
116 136 1.001181 CGTCGTCTCCCCCAAAACTAA 59.999 52.381 0.00 0.00 0.00 2.24
122 142 4.412843 GTCTCCCCCAAAACTAAATGGAA 58.587 43.478 0.00 0.00 39.12 3.53
180 209 2.503061 CGATGGAGGCCTGTGAGG 59.497 66.667 12.00 0.00 38.80 3.86
194 223 4.329545 GAGGTCACCCGCCTGCAA 62.330 66.667 0.00 0.00 36.29 4.08
204 233 2.988800 GCCTGCAAGAGGAGCTCT 59.011 61.111 14.64 0.00 46.33 4.09
218 247 3.429141 CTCTTGTGGGCAGCGCTG 61.429 66.667 32.83 32.83 0.00 5.18
233 262 2.737180 CTGTCCAGCACGTCACCT 59.263 61.111 0.00 0.00 0.00 4.00
354 383 3.805307 CGCTCGCTGACGGAGAGT 61.805 66.667 15.41 0.00 42.58 3.24
460 498 2.041922 TAGCCGGATCACCCAGCT 60.042 61.111 5.05 0.00 42.48 4.24
467 505 1.679944 CGGATCACCCAGCTCAACAAT 60.680 52.381 0.00 0.00 34.14 2.71
491 532 5.675684 AATTTGGTTTTCGGGCTAATCAT 57.324 34.783 0.00 0.00 0.00 2.45
492 533 6.783708 AATTTGGTTTTCGGGCTAATCATA 57.216 33.333 0.00 0.00 0.00 2.15
493 534 5.570234 TTTGGTTTTCGGGCTAATCATAC 57.430 39.130 0.00 0.00 0.00 2.39
494 535 4.497291 TGGTTTTCGGGCTAATCATACT 57.503 40.909 0.00 0.00 0.00 2.12
495 536 4.850680 TGGTTTTCGGGCTAATCATACTT 58.149 39.130 0.00 0.00 0.00 2.24
578 1791 1.402896 GGGAGCTGTCCATCGGATGA 61.403 60.000 19.30 3.05 46.07 2.92
582 1795 1.825341 CTGTCCATCGGATGAGGCA 59.175 57.895 19.30 14.73 32.73 4.75
604 1847 1.517361 TCGCCGACTCGAGGTACTA 59.483 57.895 18.41 0.00 41.55 1.82
605 1848 0.807667 TCGCCGACTCGAGGTACTAC 60.808 60.000 18.41 0.00 41.55 2.73
623 1866 4.296056 ACTACCTTCCCTCATTCCGTTAT 58.704 43.478 0.00 0.00 0.00 1.89
629 1872 4.837093 TCCCTCATTCCGTTATTCTGTT 57.163 40.909 0.00 0.00 0.00 3.16
633 1876 5.294552 CCCTCATTCCGTTATTCTGTTCTTC 59.705 44.000 0.00 0.00 0.00 2.87
683 1930 3.419943 TCAATGAACAATGGTGCTAGCA 58.580 40.909 14.93 14.93 0.00 3.49
684 1931 3.191162 TCAATGAACAATGGTGCTAGCAC 59.809 43.478 34.99 34.99 45.49 4.40
703 1970 8.867935 GCTAGCACATATATAGTCAGAACATTG 58.132 37.037 10.63 0.00 0.00 2.82
777 2354 8.854614 AAACTATCATGAAAGAAAGTAGCAGT 57.145 30.769 0.00 0.00 0.00 4.40
779 2356 9.944376 AACTATCATGAAAGAAAGTAGCAGTTA 57.056 29.630 0.00 0.00 0.00 2.24
798 2420 6.017605 GCAGTTATTAGTTCCCATCATCAGTG 60.018 42.308 0.00 0.00 0.00 3.66
818 2440 4.082026 AGTGAGCTTTGCAACTTTTGTTCT 60.082 37.500 0.00 0.00 41.35 3.01
827 2449 3.181497 GCAACTTTTGTTCTCTCTGTGCA 60.181 43.478 0.00 0.00 41.35 4.57
828 2450 4.346129 CAACTTTTGTTCTCTCTGTGCAC 58.654 43.478 10.75 10.75 41.35 4.57
829 2451 3.609853 ACTTTTGTTCTCTCTGTGCACA 58.390 40.909 20.37 20.37 0.00 4.57
830 2452 4.202441 ACTTTTGTTCTCTCTGTGCACAT 58.798 39.130 22.00 0.00 0.00 3.21
832 2454 5.126061 ACTTTTGTTCTCTCTGTGCACATTT 59.874 36.000 22.00 0.00 0.00 2.32
833 2455 5.581126 TTTGTTCTCTCTGTGCACATTTT 57.419 34.783 22.00 0.00 0.00 1.82
836 2458 5.122519 TGTTCTCTCTGTGCACATTTTGTA 58.877 37.500 22.00 2.27 0.00 2.41
837 2459 5.237127 TGTTCTCTCTGTGCACATTTTGTAG 59.763 40.000 22.00 11.94 0.00 2.74
839 2461 2.480037 TCTCTGTGCACATTTTGTAGCG 59.520 45.455 22.00 5.23 30.65 4.26
840 2462 2.480037 CTCTGTGCACATTTTGTAGCGA 59.520 45.455 22.00 9.65 30.65 4.93
841 2463 3.073678 TCTGTGCACATTTTGTAGCGAT 58.926 40.909 22.00 0.00 30.65 4.58
842 2464 3.120234 TCTGTGCACATTTTGTAGCGATG 60.120 43.478 22.00 3.63 30.65 3.84
843 2465 1.913403 GTGCACATTTTGTAGCGATGC 59.087 47.619 13.17 0.00 30.65 3.91
844 2466 1.811965 TGCACATTTTGTAGCGATGCT 59.188 42.857 0.00 0.00 43.41 3.79
845 2467 3.006247 TGCACATTTTGTAGCGATGCTA 58.994 40.909 0.00 0.00 40.44 3.49
846 2468 3.627123 TGCACATTTTGTAGCGATGCTAT 59.373 39.130 1.38 0.00 43.30 2.97
847 2469 4.214437 GCACATTTTGTAGCGATGCTATC 58.786 43.478 1.38 0.00 43.30 2.08
848 2470 4.024556 GCACATTTTGTAGCGATGCTATCT 60.025 41.667 1.38 0.00 43.30 1.98
849 2471 5.177511 GCACATTTTGTAGCGATGCTATCTA 59.822 40.000 1.38 0.00 43.30 1.98
850 2472 6.617317 GCACATTTTGTAGCGATGCTATCTAG 60.617 42.308 1.38 0.00 43.30 2.43
921 2543 9.283768 TCGTTATGAATCCTAAACCTATACGTA 57.716 33.333 0.00 0.00 0.00 3.57
965 2587 4.877282 AGTGCTCAACTCAGACTAGTTTC 58.123 43.478 0.00 0.00 37.61 2.78
971 2593 2.609747 ACTCAGACTAGTTTCCTGGCA 58.390 47.619 9.50 0.00 0.00 4.92
1026 2648 0.835941 CCCAAGGCTCAGCATACTCT 59.164 55.000 0.00 0.00 0.00 3.24
1069 2691 2.948979 GCCAACGATTCATATGGGTTGA 59.051 45.455 20.97 0.00 40.16 3.18
1088 2710 2.699768 CCGACGGTTACTACGGCCA 61.700 63.158 5.48 0.00 38.98 5.36
1190 2812 4.245660 CAAAGAAGCATGAGACGGAACTA 58.754 43.478 0.00 0.00 0.00 2.24
1230 2852 3.428589 GCAAAAGAGCTGATGGTTGGATC 60.429 47.826 0.00 0.00 0.00 3.36
1252 2874 1.596934 CTGGAGCTGGGCGAGTTTA 59.403 57.895 0.00 0.00 0.00 2.01
1278 2900 1.302511 GGGGCACGAATATGGCGAT 60.303 57.895 5.38 0.00 45.84 4.58
1305 2927 3.131933 CCTTCGGTCTGTCAGAGATGAAT 59.868 47.826 1.75 0.00 31.32 2.57
1383 3005 2.187946 GGAGGCATCCACACCGAG 59.812 66.667 13.69 0.00 45.87 4.63
1384 3006 2.660064 GGAGGCATCCACACCGAGT 61.660 63.158 13.69 0.00 45.87 4.18
1385 3007 1.153549 GAGGCATCCACACCGAGTC 60.154 63.158 0.00 0.00 0.00 3.36
1398 3020 3.462678 GAGTCCCGAGCCAGTCCC 61.463 72.222 0.00 0.00 0.00 4.46
1424 3047 2.517402 GGGCGACACACAACCCAA 60.517 61.111 0.00 0.00 42.33 4.12
1432 3055 1.114722 CACACAACCCAATGGCTGGT 61.115 55.000 0.00 0.00 44.76 4.00
1435 3058 0.827507 ACAACCCAATGGCTGGTGAC 60.828 55.000 0.56 0.00 44.76 3.67
1454 3078 2.359169 GGCCTCCACCGAGTGATGA 61.359 63.158 0.00 0.00 35.23 2.92
1479 3103 1.675483 TGTTTTTGCGCTCATCACACT 59.325 42.857 9.73 0.00 0.00 3.55
1481 3105 0.040157 TTTTGCGCTCATCACACTGC 60.040 50.000 9.73 0.00 0.00 4.40
1485 3109 1.964290 GCGCTCATCACACTGCTGTC 61.964 60.000 0.00 0.00 0.00 3.51
1497 3121 6.935167 TCACACTGCTGTCTAAATCAGATAA 58.065 36.000 0.00 0.00 35.17 1.75
1498 3122 7.559486 TCACACTGCTGTCTAAATCAGATAAT 58.441 34.615 0.00 0.00 35.17 1.28
1499 3123 8.043113 TCACACTGCTGTCTAAATCAGATAATT 58.957 33.333 0.00 0.00 35.17 1.40
1506 3130 9.160496 GCTGTCTAAATCAGATAATTATCCCAG 57.840 37.037 19.67 11.51 35.17 4.45
1571 3195 3.243877 CGAATGCGAGAGATCGTGAAATT 59.756 43.478 0.00 0.00 40.82 1.82
1630 3254 7.230747 TGGAAAGAAAACATCACTTATGAGGA 58.769 34.615 0.00 0.00 39.01 3.71
1671 3295 3.052338 AGGAATGAAGGAATTGGAGGCAT 60.052 43.478 0.00 0.00 0.00 4.40
1695 3319 1.602311 AAGCAACCAGAGTGCAAGAG 58.398 50.000 0.00 0.00 0.00 2.85
1696 3320 0.471617 AGCAACCAGAGTGCAAGAGT 59.528 50.000 0.00 0.00 0.00 3.24
1727 3351 2.288579 ACGAGTGAATGCTTGTACCGAA 60.289 45.455 0.00 0.00 31.70 4.30
1731 3355 2.092211 GTGAATGCTTGTACCGAACTCG 59.908 50.000 0.00 0.00 39.44 4.18
1774 3398 1.733360 GCAATAGCACCGGTTCGTAAA 59.267 47.619 2.97 0.00 41.58 2.01
1939 3590 2.288518 CCGGTTGGTAAATGTTTGTGGG 60.289 50.000 0.00 0.00 0.00 4.61
2026 3701 5.961843 ACGTTATAATGAGTTGTAGTCGTCG 59.038 40.000 11.69 0.00 0.00 5.12
2044 3722 4.022935 TCGTCGTCATCATCATCATCATCA 60.023 41.667 0.00 0.00 0.00 3.07
2205 3895 9.719355 TCACTTTGTAACAGAAGCAAAGATATA 57.281 29.630 19.01 3.27 46.98 0.86
2236 3926 7.394077 AGTTCAACATAATCATCACCAACATCA 59.606 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.068165 TCAAGTCTTCTCAAGTCTTCGCA 59.932 43.478 0.00 0.00 35.24 5.10
6 7 3.643763 TCAAGTCTTCTCAAGTCTTCGC 58.356 45.455 0.00 0.00 35.24 4.70
7 8 8.472683 AAATATCAAGTCTTCTCAAGTCTTCG 57.527 34.615 0.00 0.00 35.24 3.79
10 11 9.784531 TTGAAAATATCAAGTCTTCTCAAGTCT 57.215 29.630 0.00 0.00 43.08 3.24
54 55 7.702348 GGAACGGAAGGAAATCTATTTCATTTG 59.298 37.037 14.40 12.64 46.69 2.32
64 65 4.081031 GGAAGTAGGAACGGAAGGAAATCT 60.081 45.833 0.00 0.00 0.00 2.40
65 66 4.190001 GGAAGTAGGAACGGAAGGAAATC 58.810 47.826 0.00 0.00 0.00 2.17
76 77 5.163982 CGACGAAGAATTTGGAAGTAGGAAC 60.164 44.000 0.00 0.00 32.29 3.62
79 80 4.243270 ACGACGAAGAATTTGGAAGTAGG 58.757 43.478 0.00 0.00 32.29 3.18
81 82 5.130292 AGACGACGAAGAATTTGGAAGTA 57.870 39.130 0.00 0.00 32.29 2.24
82 83 3.988517 GAGACGACGAAGAATTTGGAAGT 59.011 43.478 0.00 0.00 32.29 3.01
86 87 2.000447 GGGAGACGACGAAGAATTTGG 59.000 52.381 0.00 0.00 32.29 3.28
90 91 0.613853 TGGGGGAGACGACGAAGAAT 60.614 55.000 0.00 0.00 0.00 2.40
92 93 0.828762 TTTGGGGGAGACGACGAAGA 60.829 55.000 0.00 0.00 0.00 2.87
101 102 4.412843 GTTCCATTTAGTTTTGGGGGAGA 58.587 43.478 0.00 0.00 33.62 3.71
102 103 3.513912 GGTTCCATTTAGTTTTGGGGGAG 59.486 47.826 0.00 0.00 33.62 4.30
103 104 3.512496 GGTTCCATTTAGTTTTGGGGGA 58.488 45.455 0.00 0.00 33.62 4.81
104 105 2.232696 CGGTTCCATTTAGTTTTGGGGG 59.767 50.000 0.00 0.00 33.62 5.40
105 106 3.158676 TCGGTTCCATTTAGTTTTGGGG 58.841 45.455 0.00 0.00 33.62 4.96
107 108 4.076394 TCCTCGGTTCCATTTAGTTTTGG 58.924 43.478 0.00 0.00 0.00 3.28
108 109 5.001232 TCTCCTCGGTTCCATTTAGTTTTG 58.999 41.667 0.00 0.00 0.00 2.44
116 136 0.613853 TCGGTCTCCTCGGTTCCATT 60.614 55.000 0.00 0.00 0.00 3.16
122 142 1.977544 CTTGGTCGGTCTCCTCGGT 60.978 63.158 0.00 0.00 0.00 4.69
180 209 2.743928 CTCTTGCAGGCGGGTGAC 60.744 66.667 0.00 0.00 0.00 3.67
194 223 1.537397 TGCCCACAAGAGCTCCTCT 60.537 57.895 10.93 0.00 43.37 3.69
218 247 2.430921 CGAGGTGACGTGCTGGAC 60.431 66.667 0.00 0.00 0.00 4.02
222 251 4.702081 GTCGCGAGGTGACGTGCT 62.702 66.667 10.24 0.00 42.37 4.40
290 319 4.154347 CAGGCCCAGAGAGCGTCC 62.154 72.222 0.00 0.00 0.00 4.79
296 325 1.681666 CAGAAAGCAGGCCCAGAGA 59.318 57.895 0.00 0.00 0.00 3.10
297 326 2.045131 GCAGAAAGCAGGCCCAGAG 61.045 63.158 0.00 0.00 44.79 3.35
354 383 2.125552 CTTCCTGCATGGCGTCGA 60.126 61.111 0.00 0.00 35.26 4.20
355 384 1.699656 CTTCTTCCTGCATGGCGTCG 61.700 60.000 0.00 0.00 35.26 5.12
357 386 1.377725 CCTTCTTCCTGCATGGCGT 60.378 57.895 0.00 0.00 35.26 5.68
358 387 1.078214 TCCTTCTTCCTGCATGGCG 60.078 57.895 0.00 0.00 35.26 5.69
417 455 1.026182 ATACGTACCACGAGTCCGCA 61.026 55.000 5.61 0.00 46.05 5.69
446 484 1.450312 GTTGAGCTGGGTGATCCGG 60.450 63.158 0.00 0.00 44.90 5.14
460 498 5.467063 GCCCGAAAACCAAATTTATTGTTGA 59.533 36.000 0.00 0.00 0.00 3.18
467 505 6.591750 TGATTAGCCCGAAAACCAAATTTA 57.408 33.333 0.00 0.00 0.00 1.40
491 532 0.894835 TGCTCTGGATGCGACAAGTA 59.105 50.000 0.00 0.00 0.00 2.24
492 533 0.251354 ATGCTCTGGATGCGACAAGT 59.749 50.000 0.00 0.00 0.00 3.16
493 534 0.656259 CATGCTCTGGATGCGACAAG 59.344 55.000 0.00 0.00 0.00 3.16
494 535 0.036105 ACATGCTCTGGATGCGACAA 60.036 50.000 0.00 0.00 0.00 3.18
495 536 0.741927 CACATGCTCTGGATGCGACA 60.742 55.000 0.00 0.00 0.00 4.35
603 1846 4.966805 AGAATAACGGAATGAGGGAAGGTA 59.033 41.667 0.00 0.00 0.00 3.08
604 1847 3.780850 AGAATAACGGAATGAGGGAAGGT 59.219 43.478 0.00 0.00 0.00 3.50
605 1848 4.130118 CAGAATAACGGAATGAGGGAAGG 58.870 47.826 0.00 0.00 0.00 3.46
614 1857 5.721232 ACTCGAAGAACAGAATAACGGAAT 58.279 37.500 0.00 0.00 34.09 3.01
623 1866 3.120792 CAACGGAACTCGAAGAACAGAA 58.879 45.455 0.00 0.00 42.43 3.02
629 1872 0.944311 GCTGCAACGGAACTCGAAGA 60.944 55.000 0.00 0.00 42.43 2.87
633 1876 1.687494 GCTAGCTGCAACGGAACTCG 61.687 60.000 7.70 0.00 42.61 4.18
703 1970 6.106648 TGACTCAGTCATGGATCATTATCC 57.893 41.667 2.36 0.00 43.56 2.59
773 2350 6.017605 CACTGATGATGGGAACTAATAACTGC 60.018 42.308 0.00 0.00 0.00 4.40
774 2351 7.275183 TCACTGATGATGGGAACTAATAACTG 58.725 38.462 0.00 0.00 0.00 3.16
775 2352 7.437713 TCACTGATGATGGGAACTAATAACT 57.562 36.000 0.00 0.00 0.00 2.24
776 2353 6.203723 GCTCACTGATGATGGGAACTAATAAC 59.796 42.308 0.00 0.00 33.22 1.89
777 2354 6.100279 AGCTCACTGATGATGGGAACTAATAA 59.900 38.462 0.00 0.00 33.22 1.40
779 2356 4.411540 AGCTCACTGATGATGGGAACTAAT 59.588 41.667 0.00 0.00 33.22 1.73
798 2420 4.676546 AGAGAACAAAAGTTGCAAAGCTC 58.323 39.130 0.00 0.00 0.00 4.09
818 2440 2.480037 CGCTACAAAATGTGCACAGAGA 59.520 45.455 25.84 0.48 0.00 3.10
843 2465 5.615289 AGTTGCACCCATTTAGCTAGATAG 58.385 41.667 0.00 0.00 0.00 2.08
844 2466 5.630415 AGTTGCACCCATTTAGCTAGATA 57.370 39.130 0.00 0.00 0.00 1.98
845 2467 4.510167 AGTTGCACCCATTTAGCTAGAT 57.490 40.909 0.00 0.00 0.00 1.98
846 2468 4.301072 AAGTTGCACCCATTTAGCTAGA 57.699 40.909 0.00 0.00 0.00 2.43
847 2469 6.699575 ATTAAGTTGCACCCATTTAGCTAG 57.300 37.500 0.00 0.00 0.00 3.42
848 2470 8.629158 CATAATTAAGTTGCACCCATTTAGCTA 58.371 33.333 0.00 0.00 0.00 3.32
849 2471 7.341769 TCATAATTAAGTTGCACCCATTTAGCT 59.658 33.333 0.00 0.00 0.00 3.32
850 2472 7.488322 TCATAATTAAGTTGCACCCATTTAGC 58.512 34.615 0.00 0.00 0.00 3.09
901 2523 8.292448 GTCGAATACGTATAGGTTTAGGATTCA 58.708 37.037 8.83 0.00 40.69 2.57
921 2543 4.015084 TCTCGGAAAACCTAGAGTCGAAT 58.985 43.478 0.00 0.00 32.90 3.34
971 2593 2.823747 TGTATCTTGCCGCGGATATACT 59.176 45.455 33.48 10.66 0.00 2.12
1069 2691 2.700773 GGCCGTAGTAACCGTCGGT 61.701 63.158 12.23 12.23 44.07 4.69
1086 2708 0.322456 TCTGGACCGGCAATTCTTGG 60.322 55.000 0.00 0.00 0.00 3.61
1088 2710 1.614317 CCTTCTGGACCGGCAATTCTT 60.614 52.381 0.00 0.00 34.57 2.52
1190 2812 1.886313 CGAGGAAGCGCTGCATGAT 60.886 57.895 19.31 0.00 0.00 2.45
1266 2888 2.154854 AGGACACATCGCCATATTCG 57.845 50.000 0.00 0.00 0.00 3.34
1270 2892 3.659850 CGAAGGACACATCGCCATA 57.340 52.632 0.00 0.00 31.71 2.74
1305 2927 4.040461 AGACCGTTCTTCCTTCTCAAATCA 59.960 41.667 0.00 0.00 0.00 2.57
1377 2999 4.135153 CTGGCTCGGGACTCGGTG 62.135 72.222 0.00 0.00 39.77 4.94
1378 3000 4.680537 ACTGGCTCGGGACTCGGT 62.681 66.667 0.00 0.00 39.77 4.69
1381 3003 3.462678 GGGACTGGCTCGGGACTC 61.463 72.222 0.00 0.00 0.00 3.36
1384 3006 4.458829 ATCGGGACTGGCTCGGGA 62.459 66.667 1.44 0.00 42.04 5.14
1385 3007 4.227134 CATCGGGACTGGCTCGGG 62.227 72.222 1.44 0.00 42.04 5.14
1398 3020 2.509336 GTGTCGCCCTGTCCATCG 60.509 66.667 0.00 0.00 0.00 3.84
1400 3022 2.050836 TTGTGTGTCGCCCTGTCCAT 62.051 55.000 0.00 0.00 0.00 3.41
1410 3032 1.172180 AGCCATTGGGTTGTGTGTCG 61.172 55.000 0.36 0.00 36.17 4.35
1441 3064 1.270305 ACAACACTCATCACTCGGTGG 60.270 52.381 4.52 0.00 33.87 4.61
1454 3078 2.098934 TGATGAGCGCAAAAACAACACT 59.901 40.909 11.47 0.00 0.00 3.55
1479 3103 8.659527 TGGGATAATTATCTGATTTAGACAGCA 58.340 33.333 21.80 0.00 38.49 4.41
1531 3155 8.981164 TCGCATTCGTTAGTCATTAGTGACAAC 61.981 40.741 19.24 17.59 45.36 3.32
1571 3195 7.870445 GTCCTGCAGAAACATATTAAACCAAAA 59.130 33.333 17.39 0.00 0.00 2.44
1593 3217 6.133356 TGTTTTCTTTCCATGTTTAGGTCCT 58.867 36.000 0.00 0.00 0.00 3.85
1647 3271 4.017591 TGCCTCCAATTCCTTCATTCCTTA 60.018 41.667 0.00 0.00 0.00 2.69
1651 3275 5.360714 TGTTATGCCTCCAATTCCTTCATTC 59.639 40.000 0.00 0.00 0.00 2.67
1654 3278 4.314522 TGTTATGCCTCCAATTCCTTCA 57.685 40.909 0.00 0.00 0.00 3.02
1671 3295 2.649190 TGCACTCTGGTTGCTTTGTTA 58.351 42.857 0.00 0.00 0.00 2.41
1695 3319 1.705256 TTCACTCGTACCGAATGCAC 58.295 50.000 0.00 0.00 33.04 4.57
1696 3320 2.267426 CATTCACTCGTACCGAATGCA 58.733 47.619 0.00 0.00 39.51 3.96
1699 3323 2.930040 CAAGCATTCACTCGTACCGAAT 59.070 45.455 0.00 0.00 34.74 3.34
1711 3335 2.029739 TCGAGTTCGGTACAAGCATTCA 60.030 45.455 1.26 0.00 40.29 2.57
1715 3339 1.241165 TCTCGAGTTCGGTACAAGCA 58.759 50.000 13.13 0.00 40.29 3.91
1774 3398 1.002502 GAACCGGCACTAAAGGGCT 60.003 57.895 0.00 0.00 0.00 5.19
1831 3455 1.551883 GCTGAACCGGTACTAAAGGGA 59.448 52.381 8.00 0.00 0.00 4.20
2083 3761 9.494271 AATAGTGGTAATTAGACGACTACGATA 57.506 33.333 5.64 0.00 41.55 2.92
2205 3895 6.823182 TGGTGATGATTATGTTGAACTCGATT 59.177 34.615 0.00 0.00 0.00 3.34
2236 3926 2.104111 TCATGTCCGTGTCCTGAACTTT 59.896 45.455 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.