Multiple sequence alignment - TraesCS4A01G497100

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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 TraesCS4A01G497100 chr4A 100.000 3194 0 0 1 3194 743326630 743323437 0.000000e+00 5899
1 TraesCS4A01G497100 chr4A 94.693 961 34 10 3 949 717041763 717040806 0.000000e+00 1476
2 TraesCS4A01G497100 chr4A 81.587 1852 279 36 1372 3191 743128209 743126388 0.000000e+00 1474
3 TraesCS4A01G497100 chr4A 81.705 1853 258 50 1374 3191 743158614 743156808 0.000000e+00 1469
4 TraesCS4A01G497100 chr4A 81.522 1840 278 34 1374 3191 743153425 743151626 0.000000e+00 1458
5 TraesCS4A01G497100 chr4A 80.939 1831 268 43 1390 3191 743758649 743756871 0.000000e+00 1373
6 TraesCS4A01G497100 chr4A 81.258 1638 242 30 1568 3191 743119260 743117674 0.000000e+00 1264
7 TraesCS4A01G497100 chr4A 77.680 569 85 24 2635 3191 730954827 730955365 3.090000e-80 309
8 TraesCS4A01G497100 chr4A 82.407 324 55 2 998 1320 730953117 730953439 6.750000e-72 281
9 TraesCS4A01G497100 chr4A 80.405 296 43 9 2908 3191 743774723 743774431 8.980000e-51 211
10 TraesCS4A01G497100 chr7D 98.211 1006 18 0 1340 2345 1557633 1558638 0.000000e+00 1759
11 TraesCS4A01G497100 chr7D 81.270 2237 305 52 998 3191 1018407 1016242 0.000000e+00 1705
12 TraesCS4A01G497100 chr7D 82.972 1797 242 37 1413 3191 1258410 1256660 0.000000e+00 1565
13 TraesCS4A01G497100 chr7D 82.852 1802 249 39 1413 3191 1198096 1196332 0.000000e+00 1561
14 TraesCS4A01G497100 chr7D 81.735 1752 256 30 1381 3114 1514182 1515887 0.000000e+00 1404
15 TraesCS4A01G497100 chr7D 81.400 1414 219 27 1413 2819 550073107 550074483 0.000000e+00 1114
16 TraesCS4A01G497100 chr7D 81.687 486 78 8 1400 1875 1571174 1571658 8.300000e-106 394
17 TraesCS4A01G497100 chr7D 87.956 274 33 0 999 1272 1258904 1258631 1.110000e-84 324
18 TraesCS4A01G497100 chr7B 82.991 1852 240 46 1358 3191 59641193 59639399 0.000000e+00 1605
19 TraesCS4A01G497100 chr7B 81.219 1411 228 23 1413 2819 594215791 594217168 0.000000e+00 1103
20 TraesCS4A01G497100 chr7B 82.572 1291 183 23 1410 2685 111322575 111321312 0.000000e+00 1099
21 TraesCS4A01G497100 chr7B 83.481 339 44 7 989 1324 59641529 59641200 4.000000e-79 305
22 TraesCS4A01G497100 chr5B 96.025 956 26 6 3 948 276224684 276223731 0.000000e+00 1544
23 TraesCS4A01G497100 chr1B 95.720 958 30 6 1 948 182641959 182642915 0.000000e+00 1531
24 TraesCS4A01G497100 chr1B 94.885 958 33 9 3 948 684413846 684412893 0.000000e+00 1483
25 TraesCS4A01G497100 chr3B 82.200 1809 254 42 1413 3191 747710653 747712423 0.000000e+00 1495
26 TraesCS4A01G497100 chr3B 94.346 955 44 6 2 949 196184071 196185022 0.000000e+00 1456
27 TraesCS4A01G497100 chr3B 94.148 957 41 13 1 947 228939172 228938221 0.000000e+00 1443
28 TraesCS4A01G497100 chr3B 87.847 288 35 0 999 1286 747709964 747710251 3.950000e-89 339
29 TraesCS4A01G497100 chr7A 82.117 1795 259 34 1415 3191 763553 761803 0.000000e+00 1480
30 TraesCS4A01G497100 chr7A 81.525 1797 256 35 1417 3191 1417506 1419248 0.000000e+00 1410
31 TraesCS4A01G497100 chr7A 81.279 657 101 6 1599 2253 786161 785525 2.200000e-141 512
32 TraesCS4A01G497100 chr2B 93.750 960 42 9 3 958 20670046 20670991 0.000000e+00 1424
33 TraesCS4A01G497100 chr1D 93.626 957 41 14 2 949 220287471 220288416 0.000000e+00 1411
34 TraesCS4A01G497100 chr1D 81.230 309 47 8 2893 3191 491674966 491674659 4.120000e-59 239
35 TraesCS4A01G497100 chr3D 93.103 957 44 16 2 948 9315463 9316407 0.000000e+00 1382
36 TraesCS4A01G497100 chr6D 77.916 806 119 36 2420 3191 433469984 433469204 6.280000e-122 448
37 TraesCS4A01G497100 chr5D 83.861 316 47 4 1004 1315 464451184 464451499 6.700000e-77 298
38 TraesCS4A01G497100 chrUn 78.019 414 68 15 2788 3191 51459428 51459828 4.120000e-59 239
39 TraesCS4A01G497100 chr6B 83.128 243 39 2 2950 3191 654643063 654642822 1.490000e-53 220


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 TraesCS4A01G497100 chr4A 743323437 743326630 3193 True 5899.0 5899 100.0000 1 3194 1 chr4A.!!$R4 3193
1 TraesCS4A01G497100 chr4A 717040806 717041763 957 True 1476.0 1476 94.6930 3 949 1 chr4A.!!$R1 946
2 TraesCS4A01G497100 chr4A 743126388 743128209 1821 True 1474.0 1474 81.5870 1372 3191 1 chr4A.!!$R3 1819
3 TraesCS4A01G497100 chr4A 743151626 743158614 6988 True 1463.5 1469 81.6135 1374 3191 2 chr4A.!!$R7 1817
4 TraesCS4A01G497100 chr4A 743756871 743758649 1778 True 1373.0 1373 80.9390 1390 3191 1 chr4A.!!$R5 1801
5 TraesCS4A01G497100 chr4A 743117674 743119260 1586 True 1264.0 1264 81.2580 1568 3191 1 chr4A.!!$R2 1623
6 TraesCS4A01G497100 chr4A 730953117 730955365 2248 False 295.0 309 80.0435 998 3191 2 chr4A.!!$F1 2193
7 TraesCS4A01G497100 chr7D 1557633 1558638 1005 False 1759.0 1759 98.2110 1340 2345 1 chr7D.!!$F2 1005
8 TraesCS4A01G497100 chr7D 1016242 1018407 2165 True 1705.0 1705 81.2700 998 3191 1 chr7D.!!$R1 2193
9 TraesCS4A01G497100 chr7D 1196332 1198096 1764 True 1561.0 1561 82.8520 1413 3191 1 chr7D.!!$R2 1778
10 TraesCS4A01G497100 chr7D 1514182 1515887 1705 False 1404.0 1404 81.7350 1381 3114 1 chr7D.!!$F1 1733
11 TraesCS4A01G497100 chr7D 550073107 550074483 1376 False 1114.0 1114 81.4000 1413 2819 1 chr7D.!!$F4 1406
12 TraesCS4A01G497100 chr7D 1256660 1258904 2244 True 944.5 1565 85.4640 999 3191 2 chr7D.!!$R3 2192
13 TraesCS4A01G497100 chr7B 594215791 594217168 1377 False 1103.0 1103 81.2190 1413 2819 1 chr7B.!!$F1 1406
14 TraesCS4A01G497100 chr7B 111321312 111322575 1263 True 1099.0 1099 82.5720 1410 2685 1 chr7B.!!$R1 1275
15 TraesCS4A01G497100 chr7B 59639399 59641529 2130 True 955.0 1605 83.2360 989 3191 2 chr7B.!!$R2 2202
16 TraesCS4A01G497100 chr5B 276223731 276224684 953 True 1544.0 1544 96.0250 3 948 1 chr5B.!!$R1 945
17 TraesCS4A01G497100 chr1B 182641959 182642915 956 False 1531.0 1531 95.7200 1 948 1 chr1B.!!$F1 947
18 TraesCS4A01G497100 chr1B 684412893 684413846 953 True 1483.0 1483 94.8850 3 948 1 chr1B.!!$R1 945
19 TraesCS4A01G497100 chr3B 196184071 196185022 951 False 1456.0 1456 94.3460 2 949 1 chr3B.!!$F1 947
20 TraesCS4A01G497100 chr3B 228938221 228939172 951 True 1443.0 1443 94.1480 1 947 1 chr3B.!!$R1 946
21 TraesCS4A01G497100 chr3B 747709964 747712423 2459 False 917.0 1495 85.0235 999 3191 2 chr3B.!!$F2 2192
22 TraesCS4A01G497100 chr7A 761803 763553 1750 True 1480.0 1480 82.1170 1415 3191 1 chr7A.!!$R1 1776
23 TraesCS4A01G497100 chr7A 1417506 1419248 1742 False 1410.0 1410 81.5250 1417 3191 1 chr7A.!!$F1 1774
24 TraesCS4A01G497100 chr7A 785525 786161 636 True 512.0 512 81.2790 1599 2253 1 chr7A.!!$R2 654
25 TraesCS4A01G497100 chr2B 20670046 20670991 945 False 1424.0 1424 93.7500 3 958 1 chr2B.!!$F1 955
26 TraesCS4A01G497100 chr1D 220287471 220288416 945 False 1411.0 1411 93.6260 2 949 1 chr1D.!!$F1 947
27 TraesCS4A01G497100 chr3D 9315463 9316407 944 False 1382.0 1382 93.1030 2 948 1 chr3D.!!$F1 946
28 TraesCS4A01G497100 chr6D 433469204 433469984 780 True 448.0 448 77.9160 2420 3191 1 chr6D.!!$R1 771

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
980 1003 0.250295 TTCTTTCGCACACTCCTGGG 60.25 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2839 3401 0.618458 CCTCCAATCCAACTTCCGGA 59.382 55.0 0.0 0.0 36.84 5.14 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
21 22 0.685097 ACTAGCAAAAGAGCCCGTGA 59.315 50.000 0.00 0.00 34.23 4.35
69 70 2.096909 CACGCTCTTAACTCAACAACCG 60.097 50.000 0.00 0.00 0.00 4.44
257 264 0.930726 TCTTCTCCCTCTCCCTCTCC 59.069 60.000 0.00 0.00 0.00 3.71
282 297 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
354 369 6.089551 GGTATGCATGTGTAGTTATCGATGTC 59.910 42.308 10.16 0.67 0.00 3.06
863 886 2.182732 TAAATCCGGACGGCGGGTTT 62.183 55.000 15.41 14.36 36.04 3.27
872 895 2.078392 GACGGCGGGTTTATTTCAAGA 58.922 47.619 13.24 0.00 0.00 3.02
940 963 8.826710 GGAAACCCAATTTGCTTTATTATTAGC 58.173 33.333 0.00 0.00 35.81 3.09
970 993 9.778741 AGATAAAGATATATTGGTTCTTTCGCA 57.221 29.630 2.32 0.00 39.64 5.10
971 994 9.813080 GATAAAGATATATTGGTTCTTTCGCAC 57.187 33.333 2.32 0.00 39.64 5.34
972 995 7.624360 AAAGATATATTGGTTCTTTCGCACA 57.376 32.000 0.00 0.00 35.36 4.57
973 996 6.604735 AGATATATTGGTTCTTTCGCACAC 57.395 37.500 0.00 0.00 0.00 3.82
974 997 6.349300 AGATATATTGGTTCTTTCGCACACT 58.651 36.000 0.00 0.00 0.00 3.55
975 998 4.946784 ATATTGGTTCTTTCGCACACTC 57.053 40.909 0.00 0.00 0.00 3.51
976 999 1.305201 TTGGTTCTTTCGCACACTCC 58.695 50.000 0.00 0.00 0.00 3.85
977 1000 0.468226 TGGTTCTTTCGCACACTCCT 59.532 50.000 0.00 0.00 0.00 3.69
978 1001 0.868406 GGTTCTTTCGCACACTCCTG 59.132 55.000 0.00 0.00 0.00 3.86
979 1002 0.868406 GTTCTTTCGCACACTCCTGG 59.132 55.000 0.00 0.00 0.00 4.45
980 1003 0.250295 TTCTTTCGCACACTCCTGGG 60.250 55.000 0.00 0.00 0.00 4.45
981 1004 2.281484 TTTCGCACACTCCTGGGC 60.281 61.111 0.00 0.00 44.22 5.36
982 1005 2.738213 CTTTCGCACACTCCTGGGCT 62.738 60.000 0.00 0.00 45.65 5.19
983 1006 1.476845 TTTCGCACACTCCTGGGCTA 61.477 55.000 0.00 0.00 45.65 3.93
984 1007 1.476845 TTCGCACACTCCTGGGCTAA 61.477 55.000 0.00 0.00 45.65 3.09
985 1008 1.741770 CGCACACTCCTGGGCTAAC 60.742 63.158 0.00 0.00 45.65 2.34
986 1009 1.741770 GCACACTCCTGGGCTAACG 60.742 63.158 0.00 0.00 44.28 3.18
987 1010 1.741770 CACACTCCTGGGCTAACGC 60.742 63.158 0.00 0.00 0.00 4.84
1008 1031 1.000993 ACCGTCTGAGATGGGCTCT 59.999 57.895 23.68 0.60 42.60 4.09
1039 1062 4.960866 TGCTGGGCAGTGTGGCAG 62.961 66.667 2.66 0.00 45.76 4.85
1102 1134 4.660938 GGTTGGCCAAGTCCCGCT 62.661 66.667 21.21 0.00 34.09 5.52
1175 1207 2.056906 GCCAGGAGTCACACCAACCT 62.057 60.000 0.00 0.00 0.00 3.50
1178 1210 1.004918 GGAGTCACACCAACCTCGG 60.005 63.158 0.00 0.00 0.00 4.63
1208 1240 4.197750 CAATGGATCAAGGACCTCAAGAG 58.802 47.826 0.00 0.00 0.00 2.85
1215 1247 2.811317 GACCTCAAGAGTGCCGCG 60.811 66.667 0.00 0.00 0.00 6.46
1234 1266 2.260154 TACCAAGCCGACGACGTCA 61.260 57.895 26.26 2.57 37.88 4.35
1286 1324 4.032452 TGCTGCCAAGATCCGCCA 62.032 61.111 0.00 0.00 0.00 5.69
1289 1327 4.424711 TGCCAAGATCCGCCACCC 62.425 66.667 0.00 0.00 0.00 4.61
1329 1409 2.269241 CCTCGCCCAACCTTCTCC 59.731 66.667 0.00 0.00 0.00 3.71
1332 1412 3.646715 CGCCCAACCTTCTCCCCA 61.647 66.667 0.00 0.00 0.00 4.96
1333 1413 2.035783 GCCCAACCTTCTCCCCAC 59.964 66.667 0.00 0.00 0.00 4.61
1334 1414 2.840753 GCCCAACCTTCTCCCCACA 61.841 63.158 0.00 0.00 0.00 4.17
1337 1417 0.771127 CCAACCTTCTCCCCACAGAA 59.229 55.000 0.00 0.00 0.00 3.02
1338 1418 1.144913 CCAACCTTCTCCCCACAGAAA 59.855 52.381 0.00 0.00 31.86 2.52
1388 1796 7.662258 TGTTTTCGGTATAAGGTCTTGATTTGA 59.338 33.333 0.00 0.00 0.00 2.69
1546 2025 5.063204 TCGTTGTGGAGATGAACAATTTCT 58.937 37.500 0.00 0.00 38.47 2.52
1653 2132 4.974645 AGATGACAAGGAACAAGTGGTA 57.025 40.909 0.00 0.00 0.00 3.25
1773 2277 2.498078 TGTGCACAATGATCGTAGGGTA 59.502 45.455 19.28 0.00 0.00 3.69
2191 2695 4.184649 AGGGAAGTGGAACAACAAGAAT 57.815 40.909 0.00 0.00 44.16 2.40
2367 2877 2.743636 TTGTACCTGCACTACAGCTC 57.256 50.000 0.00 0.00 45.78 4.09
2393 2903 5.871524 GCTACAATCACTTGTCATCAGAAGA 59.128 40.000 0.00 0.00 44.43 2.87
2394 2904 6.369890 GCTACAATCACTTGTCATCAGAAGAA 59.630 38.462 0.00 0.00 44.43 2.52
2446 2957 2.283145 CCAAAGGATAGCCTGATGGG 57.717 55.000 19.70 7.89 46.28 4.00
2462 2973 6.770785 GCCTGATGGGTAAAGACATGTTAATA 59.229 38.462 0.00 0.00 37.43 0.98
2558 3072 4.580580 AGATGTTTCCTCCAAGTTGTGAAC 59.419 41.667 1.45 0.61 0.00 3.18
2567 3081 6.098124 TCCTCCAAGTTGTGAACATTCAAAAT 59.902 34.615 1.45 0.00 36.83 1.82
2578 3092 8.024865 TGTGAACATTCAAAATAATGAGCTCTG 58.975 33.333 16.19 2.72 38.84 3.35
2618 3174 3.196901 TCATGCACCGACCAACTACTTAT 59.803 43.478 0.00 0.00 0.00 1.73
2620 3176 4.380841 TGCACCGACCAACTACTTATAG 57.619 45.455 0.00 0.00 34.25 1.31
2648 3204 1.607628 GATCTCATGCATGACCTTGCC 59.392 52.381 25.42 7.93 42.06 4.52
2701 3257 4.569564 TCTGCAAGAATCTTCATCATGTCG 59.430 41.667 0.00 0.00 42.31 4.35
2725 3281 2.431954 ATTCTGCAAGGATCCACAGG 57.568 50.000 22.21 8.18 0.00 4.00
2757 3313 1.609208 ACAGCATGAGGTTCAACACC 58.391 50.000 0.00 0.00 43.21 4.16
2837 3399 3.331150 CCGAGCCCGCACAATATTATTA 58.669 45.455 0.00 0.00 0.00 0.98
2838 3400 3.370978 CCGAGCCCGCACAATATTATTAG 59.629 47.826 0.00 0.00 0.00 1.73
2839 3401 3.994392 CGAGCCCGCACAATATTATTAGT 59.006 43.478 0.00 0.00 0.00 2.24
2858 3420 0.618458 TCCGGAAGTTGGATTGGAGG 59.382 55.000 0.00 0.00 0.00 4.30
2860 3422 1.004277 CCGGAAGTTGGATTGGAGGAA 59.996 52.381 0.00 0.00 0.00 3.36
2861 3423 2.084546 CGGAAGTTGGATTGGAGGAAC 58.915 52.381 0.00 0.00 0.00 3.62
2869 3440 3.437213 TGGATTGGAGGAACGAGACTTA 58.563 45.455 0.00 0.00 0.00 2.24
2885 3456 6.323996 ACGAGACTTATCTGGATATGGTCAAA 59.676 38.462 17.49 0.00 34.34 2.69
2975 3555 4.764172 ACTTGAAGCATCTTCGCTATCTT 58.236 39.130 0.00 0.00 42.89 2.40
2981 3561 3.497640 AGCATCTTCGCTATCTTGATTGC 59.502 43.478 6.91 6.91 41.55 3.56
3068 3648 2.568062 TCTCACGGGTTGTAAATGCCTA 59.432 45.455 0.00 0.00 0.00 3.93
3128 3708 0.615331 GGCACATCTTCCTCACTGGA 59.385 55.000 0.00 0.00 44.51 3.86
3137 8899 0.970937 TCCTCACTGGAGCTAACCGG 60.971 60.000 0.00 0.00 40.56 5.28
3142 8904 0.608640 ACTGGAGCTAACCGGTTGAG 59.391 55.000 30.08 21.39 46.02 3.02
3168 8930 1.423541 TGCCACAAGGTATTGGTCAGT 59.576 47.619 0.00 0.00 40.97 3.41
3173 8935 4.582656 CCACAAGGTATTGGTCAGTTGAAA 59.417 41.667 0.00 0.00 40.97 2.69
3181 8943 7.989741 AGGTATTGGTCAGTTGAAATCTCTATG 59.010 37.037 0.00 0.00 0.00 2.23
3191 8953 6.825721 AGTTGAAATCTCTATGGACATTGACC 59.174 38.462 0.00 0.00 0.00 4.02
3192 8954 5.359756 TGAAATCTCTATGGACATTGACCG 58.640 41.667 0.80 0.00 0.00 4.79
3193 8955 5.128663 TGAAATCTCTATGGACATTGACCGA 59.871 40.000 0.80 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.947456 GTTTTCTCTCCCGTTGCAACT 59.053 47.619 26.09 0.00 0.00 3.16
69 70 4.273148 ACCTATTGTGGTCTTGAGTGAC 57.727 45.455 0.00 0.00 34.86 3.67
216 217 1.285373 AGGGAGAGAGAACGCCTTAGA 59.715 52.381 0.00 0.00 0.00 2.10
257 264 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
354 369 9.726438 CCACTATAACCATATAGGGAAAAGAAG 57.274 37.037 11.11 2.58 44.92 2.85
540 561 9.596677 TTAAACCGTAACTTCGATTTTAACATG 57.403 29.630 0.00 0.00 29.05 3.21
863 886 8.533569 AAAGTCCCTGTCTTTTTCTTGAAATA 57.466 30.769 0.00 0.00 32.14 1.40
950 973 6.349300 AGTGTGCGAAAGAACCAATATATCT 58.651 36.000 0.00 0.00 39.64 1.98
951 974 6.292919 GGAGTGTGCGAAAGAACCAATATATC 60.293 42.308 0.00 0.00 39.64 1.63
952 975 5.527582 GGAGTGTGCGAAAGAACCAATATAT 59.472 40.000 0.00 0.00 39.64 0.86
953 976 4.873827 GGAGTGTGCGAAAGAACCAATATA 59.126 41.667 0.00 0.00 39.64 0.86
954 977 3.689649 GGAGTGTGCGAAAGAACCAATAT 59.310 43.478 0.00 0.00 39.64 1.28
955 978 3.071479 GGAGTGTGCGAAAGAACCAATA 58.929 45.455 0.00 0.00 39.64 1.90
956 979 1.880027 GGAGTGTGCGAAAGAACCAAT 59.120 47.619 0.00 0.00 39.64 3.16
957 980 1.134220 AGGAGTGTGCGAAAGAACCAA 60.134 47.619 0.00 0.00 39.64 3.67
958 981 0.468226 AGGAGTGTGCGAAAGAACCA 59.532 50.000 0.00 0.00 39.64 3.67
959 982 0.868406 CAGGAGTGTGCGAAAGAACC 59.132 55.000 0.00 0.00 39.64 3.62
960 983 0.868406 CCAGGAGTGTGCGAAAGAAC 59.132 55.000 0.00 0.00 41.28 3.01
961 984 0.250295 CCCAGGAGTGTGCGAAAGAA 60.250 55.000 0.00 0.00 0.00 2.52
962 985 1.371183 CCCAGGAGTGTGCGAAAGA 59.629 57.895 0.00 0.00 0.00 2.52
963 986 2.328099 GCCCAGGAGTGTGCGAAAG 61.328 63.158 0.00 0.00 0.00 2.62
964 987 1.476845 TAGCCCAGGAGTGTGCGAAA 61.477 55.000 0.00 0.00 0.00 3.46
965 988 1.476845 TTAGCCCAGGAGTGTGCGAA 61.477 55.000 0.00 0.00 0.00 4.70
966 989 1.911269 TTAGCCCAGGAGTGTGCGA 60.911 57.895 0.00 0.00 0.00 5.10
967 990 1.741770 GTTAGCCCAGGAGTGTGCG 60.742 63.158 0.00 0.00 0.00 5.34
968 991 1.741770 CGTTAGCCCAGGAGTGTGC 60.742 63.158 0.00 0.00 0.00 4.57
969 992 1.741770 GCGTTAGCCCAGGAGTGTG 60.742 63.158 0.00 0.00 37.42 3.82
970 993 2.663196 GCGTTAGCCCAGGAGTGT 59.337 61.111 0.00 0.00 37.42 3.55
980 1003 2.879462 CAGACGGTCGGCGTTAGC 60.879 66.667 6.85 0.00 44.18 3.09
981 1004 1.226323 CTCAGACGGTCGGCGTTAG 60.226 63.158 6.85 1.45 0.00 2.34
982 1005 1.028330 ATCTCAGACGGTCGGCGTTA 61.028 55.000 6.85 0.00 0.00 3.18
983 1006 2.341101 ATCTCAGACGGTCGGCGTT 61.341 57.895 6.85 0.00 0.00 4.84
984 1007 2.750637 ATCTCAGACGGTCGGCGT 60.751 61.111 6.85 0.00 0.00 5.68
985 1008 2.278206 CATCTCAGACGGTCGGCG 60.278 66.667 0.00 0.00 0.00 6.46
986 1009 2.105128 CCATCTCAGACGGTCGGC 59.895 66.667 3.24 0.00 0.00 5.54
987 1010 2.808315 CCCATCTCAGACGGTCGG 59.192 66.667 1.89 1.73 0.00 4.79
1008 1031 4.091939 AGCAGCGGCATGAGCAGA 62.092 61.111 12.44 0.00 44.61 4.26
1087 1119 4.659172 CCAGCGGGACTTGGCCAA 62.659 66.667 19.25 19.25 35.59 4.52
1091 1123 2.747855 GCTTCCAGCGGGACTTGG 60.748 66.667 4.56 0.00 44.89 3.61
1102 1134 2.669569 GTGGCGCTCAAGCTTCCA 60.670 61.111 7.64 0.00 38.41 3.53
1160 1192 1.004918 CCGAGGTTGGTGTGACTCC 60.005 63.158 0.00 0.00 0.00 3.85
1178 1210 2.051804 CTTGATCCATTGGCGGACGC 62.052 60.000 8.39 8.39 38.07 5.19
1187 1219 3.848975 ACTCTTGAGGTCCTTGATCCATT 59.151 43.478 0.00 0.00 0.00 3.16
1215 1247 1.799121 GACGTCGTCGGCTTGGTAC 60.799 63.158 10.05 0.00 42.52 3.34
1234 1266 3.003897 GCCTCGTAGAAGAAGTCATCGAT 59.996 47.826 0.00 0.00 34.71 3.59
1289 1327 0.960364 AACCTTGCACGCCATGTAGG 60.960 55.000 0.00 0.00 37.91 3.18
1329 1409 1.530323 CGGGGTACTTTTTCTGTGGG 58.470 55.000 0.00 0.00 0.00 4.61
1332 1412 0.251033 GGGCGGGGTACTTTTTCTGT 60.251 55.000 0.00 0.00 0.00 3.41
1333 1413 0.037734 AGGGCGGGGTACTTTTTCTG 59.962 55.000 0.00 0.00 0.00 3.02
1334 1414 0.037734 CAGGGCGGGGTACTTTTTCT 59.962 55.000 0.00 0.00 0.00 2.52
1337 1417 1.722110 AACCAGGGCGGGGTACTTTT 61.722 55.000 0.00 0.00 37.77 2.27
1338 1418 2.158130 AACCAGGGCGGGGTACTTT 61.158 57.895 0.00 0.00 37.77 2.66
1546 2025 0.821301 TCGGCATGTTGTTGGAAGCA 60.821 50.000 0.00 0.00 0.00 3.91
1653 2132 8.229253 TGCTATTGTGATCAAGCAATATCTTT 57.771 30.769 15.71 0.00 37.08 2.52
1773 2277 9.976511 CATAATACCAGCTCAAAATGATGATTT 57.023 29.630 0.00 0.00 32.87 2.17
2367 2877 5.173664 TCTGATGACAAGTGATTGTAGCTG 58.826 41.667 0.00 0.00 34.90 4.24
2409 2920 5.404466 TTTGGGAAAATAGCACAGAATGG 57.596 39.130 0.00 0.00 43.62 3.16
2462 2973 4.603131 AGTCATTTGCCATCCATAACTGT 58.397 39.130 0.00 0.00 0.00 3.55
2558 3072 9.582431 AATTCACAGAGCTCATTATTTTGAATG 57.418 29.630 17.77 2.99 38.03 2.67
2567 3081 7.825761 TCATCTTGAAATTCACAGAGCTCATTA 59.174 33.333 17.77 0.00 0.00 1.90
2578 3092 6.307318 GTGCATGAACTCATCTTGAAATTCAC 59.693 38.462 0.00 0.00 35.61 3.18
2648 3204 2.876091 TCATTTCCGCTTACAGAGTCG 58.124 47.619 0.00 0.00 0.00 4.18
2701 3257 4.012374 TGTGGATCCTTGCAGAATTTCTC 58.988 43.478 14.23 0.00 0.00 2.87
2725 3281 2.749076 TCATGCTGTAATGAACTGGTGC 59.251 45.455 0.00 0.00 33.63 5.01
2769 3325 7.201732 GGCTGCAATAGTATTGTAACTCACATT 60.202 37.037 21.15 0.00 36.90 2.71
2837 3399 1.279271 CTCCAATCCAACTTCCGGACT 59.721 52.381 1.83 0.00 34.69 3.85
2838 3400 1.679032 CCTCCAATCCAACTTCCGGAC 60.679 57.143 1.83 0.00 34.69 4.79
2839 3401 0.618458 CCTCCAATCCAACTTCCGGA 59.382 55.000 0.00 0.00 36.84 5.14
2858 3420 6.016192 TGACCATATCCAGATAAGTCTCGTTC 60.016 42.308 16.17 0.00 34.43 3.95
2860 3422 5.386060 TGACCATATCCAGATAAGTCTCGT 58.614 41.667 16.17 0.00 34.43 4.18
2861 3423 5.966742 TGACCATATCCAGATAAGTCTCG 57.033 43.478 16.17 0.00 34.43 4.04
2869 3440 6.100859 ACTCACAGATTTGACCATATCCAGAT 59.899 38.462 0.00 0.00 0.00 2.90
2885 3456 1.137086 GACGTGGCCATACTCACAGAT 59.863 52.381 9.72 0.00 33.83 2.90
2948 3525 3.316308 AGCGAAGATGCTTCAAGTTTGTT 59.684 39.130 7.81 0.00 44.46 2.83
2981 3561 6.985645 GCAGCCCAGATATATGAGAATAAGAG 59.014 42.308 0.00 0.00 0.00 2.85
3068 3648 5.190528 TCTCATGCCTTCTGGTAATTTCTCT 59.809 40.000 0.00 0.00 35.27 3.10
3128 3708 2.264794 CGCCTCAACCGGTTAGCT 59.735 61.111 21.79 0.00 0.00 3.32
3129 3709 3.497031 GCGCCTCAACCGGTTAGC 61.497 66.667 21.79 21.05 0.00 3.09
3168 8930 5.817296 CGGTCAATGTCCATAGAGATTTCAA 59.183 40.000 0.00 0.00 33.90 2.69


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

AutoCloner maintained by Alex Coulton.