Multiple sequence alignment - TraesCS3A01G289700

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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 TraesCS3A01G289700 chr3A 100.000 3105 0 0 1 3105 518644265 518641161 0.000000e+00 5734.0
1 TraesCS3A01G289700 chr3A 86.936 421 45 8 930 1350 589913975 589914385 6.060000e-127 464.0
2 TraesCS3A01G289700 chr3A 86.325 117 12 4 1535 1649 510664230 510664344 1.170000e-24 124.0
3 TraesCS3A01G289700 chr3D 89.267 2525 130 60 14 2489 399381983 399379551 0.000000e+00 3031.0
4 TraesCS3A01G289700 chr3D 89.117 634 35 17 2488 3102 399379451 399378833 0.000000e+00 758.0
5 TraesCS3A01G289700 chr3D 84.615 117 14 4 1535 1649 390042179 390042293 2.530000e-21 113.0
6 TraesCS3A01G289700 chr3B 88.131 2536 114 70 8 2489 525243954 525241552 0.000000e+00 2843.0
7 TraesCS3A01G289700 chr3B 90.190 316 22 3 2488 2803 525241452 525241146 1.340000e-108 403.0
8 TraesCS3A01G289700 chr3B 92.444 225 9 4 2881 3105 525241090 525240874 6.460000e-82 315.0
9 TraesCS3A01G289700 chr3B 85.470 117 13 4 1535 1649 507286943 507287057 5.440000e-23 119.0
10 TraesCS3A01G289700 chr1D 87.967 241 21 5 930 1170 405003482 405003714 8.480000e-71 278.0
11 TraesCS3A01G289700 chr1D 91.870 123 10 0 1536 1658 283617842 283617964 4.120000e-39 172.0
12 TraesCS3A01G289700 chr1D 94.737 57 3 0 1360 1416 481603266 481603322 4.260000e-14 89.8
13 TraesCS3A01G289700 chr1A 87.137 241 25 4 930 1170 278372188 278371954 5.100000e-68 268.0
14 TraesCS3A01G289700 chr1A 91.870 123 10 0 1536 1658 355343726 355343848 4.120000e-39 172.0
15 TraesCS3A01G289700 chr4B 87.137 241 24 6 930 1170 616747010 616747243 1.840000e-67 267.0
16 TraesCS3A01G289700 chr7A 92.500 120 9 0 985 1104 68202937 68202818 4.120000e-39 172.0
17 TraesCS3A01G289700 chr1B 91.870 123 10 0 1536 1658 385296794 385296916 4.120000e-39 172.0
18 TraesCS3A01G289700 chr1B 96.552 58 2 0 1359 1416 670202744 670202801 2.550000e-16 97.1
19 TraesCS3A01G289700 chr2A 93.043 115 8 0 985 1099 505417400 505417286 5.330000e-38 169.0
20 TraesCS3A01G289700 chr2A 86.957 69 9 0 1348 1416 686214686 686214618 9.230000e-11 78.7
21 TraesCS3A01G289700 chr2B 86.957 69 9 0 1348 1416 648653144 648653076 9.230000e-11 78.7


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 TraesCS3A01G289700 chr3A 518641161 518644265 3104 True 5734.0 5734 100.000 1 3105 1 chr3A.!!$R1 3104
1 TraesCS3A01G289700 chr3D 399378833 399381983 3150 True 1894.5 3031 89.192 14 3102 2 chr3D.!!$R1 3088
2 TraesCS3A01G289700 chr3B 525240874 525243954 3080 True 1187.0 2843 90.255 8 3105 3 chr3B.!!$R1 3097

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
522 557 0.111061 ACACACACAGCACATCCCAT 59.889 50.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 2561 0.39113 AGTGTGTGTGTGTGCGTCTT 60.391 50.0 0.0 0.0 0.0 3.01 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
63 64 1.066573 AGACATGCACAGAGTGGTAGC 60.067 52.381 0.00 0.00 33.64 3.58
91 92 1.140161 CGTATCCTGGCCGTCGAAA 59.860 57.895 0.00 0.00 0.00 3.46
110 111 4.152045 CGAAATAGAATCTGATGCTCCAGC 59.848 45.833 0.17 0.00 42.50 4.85
151 152 0.249398 GAACCCGACACCTGCTACAT 59.751 55.000 0.00 0.00 0.00 2.29
152 153 1.479323 GAACCCGACACCTGCTACATA 59.521 52.381 0.00 0.00 0.00 2.29
153 154 0.822164 ACCCGACACCTGCTACATAC 59.178 55.000 0.00 0.00 0.00 2.39
214 215 3.251729 GCGGCAAAGTACATCATCATCAT 59.748 43.478 0.00 0.00 0.00 2.45
215 216 4.612259 GCGGCAAAGTACATCATCATCATC 60.612 45.833 0.00 0.00 0.00 2.92
216 217 4.512571 CGGCAAAGTACATCATCATCATCA 59.487 41.667 0.00 0.00 0.00 3.07
217 218 5.180680 CGGCAAAGTACATCATCATCATCAT 59.819 40.000 0.00 0.00 0.00 2.45
218 219 6.609533 GGCAAAGTACATCATCATCATCATC 58.390 40.000 0.00 0.00 0.00 2.92
219 220 6.206048 GGCAAAGTACATCATCATCATCATCA 59.794 38.462 0.00 0.00 0.00 3.07
220 221 7.094334 GGCAAAGTACATCATCATCATCATCAT 60.094 37.037 0.00 0.00 0.00 2.45
221 222 7.963465 GCAAAGTACATCATCATCATCATCATC 59.037 37.037 0.00 0.00 0.00 2.92
222 223 7.829378 AAGTACATCATCATCATCATCATCG 57.171 36.000 0.00 0.00 0.00 3.84
324 331 1.895020 TTGGCCAGATCGGTTAGCGT 61.895 55.000 5.11 0.00 36.97 5.07
361 369 3.059597 CAGCCTCCGCTAATTTAATCGTG 60.060 47.826 0.00 0.00 46.25 4.35
363 371 2.223377 CCTCCGCTAATTTAATCGTGCC 59.777 50.000 0.00 0.00 0.00 5.01
367 375 1.265905 GCTAATTTAATCGTGCCCCCG 59.734 52.381 0.00 0.00 0.00 5.73
401 435 0.961358 CCCTCCTCCTCCTATACGCG 60.961 65.000 3.53 3.53 0.00 6.01
418 452 2.896443 GACAGCGAGGGAGGAAGG 59.104 66.667 0.00 0.00 0.00 3.46
419 453 1.682684 GACAGCGAGGGAGGAAGGA 60.683 63.158 0.00 0.00 0.00 3.36
443 477 1.833630 AGAGCGATCCAATCCAGAACA 59.166 47.619 0.00 0.00 0.00 3.18
512 547 4.654904 CTGCGCGCACACACACAG 62.655 66.667 33.09 14.58 0.00 3.66
516 551 3.875039 GCGCACACACACAGCACA 61.875 61.111 0.30 0.00 0.00 4.57
520 555 1.951510 CACACACACAGCACATCCC 59.048 57.895 0.00 0.00 0.00 3.85
521 556 0.818852 CACACACACAGCACATCCCA 60.819 55.000 0.00 0.00 0.00 4.37
522 557 0.111061 ACACACACAGCACATCCCAT 59.889 50.000 0.00 0.00 0.00 4.00
705 770 4.779733 ATCACTCGACCCGGCCCT 62.780 66.667 0.00 0.00 0.00 5.19
719 784 1.818522 CGGCCCTCCCTGTACTACTAG 60.819 61.905 0.00 0.00 0.00 2.57
731 796 2.049888 ACTACTAGTACACCCCTCGC 57.950 55.000 0.00 0.00 0.00 5.03
751 825 0.540830 CCCCTCCTCCGTCCTGATAG 60.541 65.000 0.00 0.00 0.00 2.08
752 826 0.186386 CCCTCCTCCGTCCTGATAGT 59.814 60.000 0.00 0.00 0.00 2.12
753 827 1.323412 CCTCCTCCGTCCTGATAGTG 58.677 60.000 0.00 0.00 0.00 2.74
771 845 0.249699 TGGTACACTCTGTTGCGGTG 60.250 55.000 0.00 0.00 37.05 4.94
785 859 1.884464 CGGTGGCCAGTGATCATCG 60.884 63.158 5.11 0.00 0.00 3.84
790 864 1.442526 GGCCAGTGATCATCGCCAAG 61.443 60.000 20.01 0.25 39.50 3.61
864 950 2.016393 GCTTTTTATCCGGGGCAGCC 62.016 60.000 1.26 1.26 0.00 4.85
865 951 0.682855 CTTTTTATCCGGGGCAGCCA 60.683 55.000 15.19 0.00 0.00 4.75
866 952 0.682855 TTTTTATCCGGGGCAGCCAG 60.683 55.000 15.19 6.46 0.00 4.85
867 953 2.566111 TTTTATCCGGGGCAGCCAGG 62.566 60.000 15.19 16.23 0.00 4.45
937 1023 0.518195 GCTAGATAGCTCCGTCCGTC 59.482 60.000 4.58 0.00 45.62 4.79
938 1024 1.158434 CTAGATAGCTCCGTCCGTCC 58.842 60.000 0.00 0.00 0.00 4.79
939 1025 0.602106 TAGATAGCTCCGTCCGTCCG 60.602 60.000 0.00 0.00 0.00 4.79
940 1026 2.124403 ATAGCTCCGTCCGTCCGT 60.124 61.111 0.00 0.00 0.00 4.69
941 1027 2.389866 GATAGCTCCGTCCGTCCGTG 62.390 65.000 0.00 0.00 0.00 4.94
1017 1108 2.046892 ATGTCGGACTGCAGCACC 60.047 61.111 15.27 16.54 0.00 5.01
1162 1253 2.179589 GCAGGTACGTACATACACACG 58.820 52.381 26.02 8.26 43.63 4.49
1167 1258 2.933495 ACGTACATACACACGCATCT 57.067 45.000 0.00 0.00 41.80 2.90
1168 1259 2.793933 ACGTACATACACACGCATCTC 58.206 47.619 0.00 0.00 41.80 2.75
1169 1260 2.117137 CGTACATACACACGCATCTCC 58.883 52.381 0.00 0.00 0.00 3.71
1170 1261 2.478879 CGTACATACACACGCATCTCCA 60.479 50.000 0.00 0.00 0.00 3.86
1232 1333 2.306255 TAGGCGGCGGAGGATTGAAC 62.306 60.000 9.78 0.00 0.00 3.18
1242 1343 3.797256 CGGAGGATTGAACGAGTATGTTC 59.203 47.826 0.00 0.00 46.63 3.18
1251 1352 0.247145 CGAGTATGTTCGTTTGGCGC 60.247 55.000 0.00 0.00 41.07 6.53
1255 1356 0.519519 TATGTTCGTTTGGCGCTTGG 59.480 50.000 7.64 0.00 41.07 3.61
1271 1372 2.514824 GGTTGCAGCCGGAGATCC 60.515 66.667 5.05 0.00 0.00 3.36
1416 1517 3.853487 CCCCCTACCCGCGGTAAC 61.853 72.222 26.12 0.00 37.76 2.50
1420 1521 1.356624 CCTACCCGCGGTAACTACG 59.643 63.158 26.12 9.27 37.76 3.51
1428 1529 2.492418 CGGTAACTACGCCTACCCA 58.508 57.895 0.00 0.00 35.13 4.51
1429 1530 0.101219 CGGTAACTACGCCTACCCAC 59.899 60.000 0.00 0.00 35.13 4.61
1430 1531 0.461548 GGTAACTACGCCTACCCACC 59.538 60.000 0.00 0.00 32.83 4.61
1431 1532 1.185315 GTAACTACGCCTACCCACCA 58.815 55.000 0.00 0.00 0.00 4.17
1432 1533 1.758862 GTAACTACGCCTACCCACCAT 59.241 52.381 0.00 0.00 0.00 3.55
1433 1534 2.163810 AACTACGCCTACCCACCATA 57.836 50.000 0.00 0.00 0.00 2.74
1434 1535 1.700955 ACTACGCCTACCCACCATAG 58.299 55.000 0.00 0.00 0.00 2.23
1435 1536 1.216175 ACTACGCCTACCCACCATAGA 59.784 52.381 0.00 0.00 0.00 1.98
1438 1539 2.245582 ACGCCTACCCACCATAGATAC 58.754 52.381 0.00 0.00 0.00 2.24
1441 1542 3.368427 CGCCTACCCACCATAGATACATG 60.368 52.174 0.00 0.00 0.00 3.21
1468 1569 1.340017 TGCAGGACAGGCTGGTAATTC 60.340 52.381 20.34 6.48 0.00 2.17
1469 1570 2.019156 GCAGGACAGGCTGGTAATTCC 61.019 57.143 20.34 15.67 0.00 3.01
1470 1571 1.561542 CAGGACAGGCTGGTAATTCCT 59.438 52.381 20.34 17.72 37.07 3.36
1471 1572 2.025887 CAGGACAGGCTGGTAATTCCTT 60.026 50.000 20.34 3.73 37.07 3.36
1482 1583 3.764434 TGGTAATTCCTTTGCGGCAATTA 59.236 39.130 17.19 8.79 37.07 1.40
1498 1599 6.751888 GCGGCAATTAAAATCATCAGTTACTT 59.248 34.615 0.00 0.00 0.00 2.24
2107 2227 3.461773 GCGCCCTGCTCCTGACTA 61.462 66.667 0.00 0.00 41.73 2.59
2108 2228 2.801631 GCGCCCTGCTCCTGACTAT 61.802 63.158 0.00 0.00 41.73 2.12
2109 2229 1.826024 CGCCCTGCTCCTGACTATT 59.174 57.895 0.00 0.00 0.00 1.73
2238 2363 3.826157 TCAAAGGGATTTCGCTGTTCAAT 59.174 39.130 0.00 0.00 39.23 2.57
2273 2398 4.624604 GCTTATTTTACTCCCTCGGTTCCA 60.625 45.833 0.00 0.00 0.00 3.53
2404 2529 0.388520 GGTTGGCATTTTCAGGCGTC 60.389 55.000 0.00 0.00 0.00 5.19
2441 2566 2.916423 CGCAGCGCAGATAAGACG 59.084 61.111 11.47 0.00 0.00 4.18
2582 2810 2.652530 GACGGACGGCTACACCAA 59.347 61.111 0.00 0.00 39.03 3.67
2583 2811 1.217244 GACGGACGGCTACACCAAT 59.783 57.895 0.00 0.00 39.03 3.16
2584 2812 0.457035 GACGGACGGCTACACCAATA 59.543 55.000 0.00 0.00 39.03 1.90
2596 2824 1.856920 ACACCAATAATCCCCGGGAAT 59.143 47.619 26.32 2.83 34.34 3.01
2631 2860 3.236137 GTCGCGTACGCCGTCTTC 61.236 66.667 32.64 13.60 39.84 2.87
2666 2895 2.365617 TGAATTCGGTCTCTATCCCTGC 59.634 50.000 0.04 0.00 0.00 4.85
2679 2908 1.813753 CCCTGCACCGTATTCGTGG 60.814 63.158 0.00 0.00 35.01 4.94
2719 2948 1.155424 TGCCCGGTCGCGATATTTTC 61.155 55.000 14.06 0.00 0.00 2.29
2766 3000 5.700373 CAGACAAACAAATTATTGGGTTGGG 59.300 40.000 13.91 0.76 41.01 4.12
2767 3001 5.368230 AGACAAACAAATTATTGGGTTGGGT 59.632 36.000 13.91 7.29 41.01 4.51
2768 3002 6.007485 ACAAACAAATTATTGGGTTGGGTT 57.993 33.333 13.91 0.00 41.01 4.11
2769 3003 5.825151 ACAAACAAATTATTGGGTTGGGTTG 59.175 36.000 13.91 4.11 41.01 3.77
2770 3004 4.632327 ACAAATTATTGGGTTGGGTTGG 57.368 40.909 0.00 0.00 41.01 3.77
2794 3028 0.749049 GGCCTGGCATGAAAAGATCC 59.251 55.000 22.05 0.00 0.00 3.36
2807 3041 0.250513 AAGATCCAGCCAACTCGACC 59.749 55.000 0.00 0.00 0.00 4.79
2810 3044 1.330655 ATCCAGCCAACTCGACCGAT 61.331 55.000 0.00 0.00 0.00 4.18
2865 3099 8.997621 AAAAGCGAAATGAATGAGTACTACTA 57.002 30.769 0.00 0.00 0.00 1.82
2867 3101 6.200100 AGCGAAATGAATGAGTACTACTACG 58.800 40.000 0.00 0.00 0.00 3.51
2869 3103 7.011763 AGCGAAATGAATGAGTACTACTACGTA 59.988 37.037 0.00 0.00 0.00 3.57
2870 3104 7.111317 GCGAAATGAATGAGTACTACTACGTAC 59.889 40.741 0.00 0.00 39.97 3.67
2873 3107 8.648557 AATGAATGAGTACTACTACGTACGTA 57.351 34.615 25.41 25.41 43.42 3.57
2874 3108 7.451281 TGAATGAGTACTACTACGTACGTAC 57.549 40.000 23.60 15.90 43.42 3.67
2875 3109 7.258441 TGAATGAGTACTACTACGTACGTACT 58.742 38.462 23.60 19.90 43.62 2.73
2877 3111 5.776850 GAGTACTACTACGTACGTACTCG 57.223 47.826 23.60 16.42 44.83 4.18
2879 3113 5.264712 AGTACTACTACGTACGTACTCGAC 58.735 45.833 23.60 16.47 43.42 4.20
2897 3148 2.202479 GCGAATCCTTGGCGTTGC 60.202 61.111 0.00 0.00 0.00 4.17
2907 3158 4.520846 GGCGTTGCATTCGAGCCG 62.521 66.667 14.40 0.00 38.28 5.52
2908 3159 3.487202 GCGTTGCATTCGAGCCGA 61.487 61.111 14.40 0.00 0.00 5.54
2909 3160 2.813179 GCGTTGCATTCGAGCCGAT 61.813 57.895 14.40 0.00 35.23 4.18
2951 3202 2.296471 CCGATGGATGGTGAGTAGGTAC 59.704 54.545 0.00 0.00 0.00 3.34
2952 3203 3.223435 CGATGGATGGTGAGTAGGTACT 58.777 50.000 0.00 0.00 46.37 2.73
2953 3204 4.395625 CGATGGATGGTGAGTAGGTACTA 58.604 47.826 0.00 0.00 41.75 1.82
2975 3226 1.320344 TTCGTGGTGCTCTCGCCTAT 61.320 55.000 0.00 0.00 43.26 2.57
2976 3227 0.464916 TCGTGGTGCTCTCGCCTATA 60.465 55.000 0.00 0.00 43.26 1.31
2986 3237 2.560542 CTCTCGCCTATAGCACTCCAAT 59.439 50.000 0.00 0.00 44.04 3.16
2992 3243 2.289072 CCTATAGCACTCCAATGGACGG 60.289 54.545 0.00 0.00 0.00 4.79
3012 3263 6.348868 GGACGGTTAACTATCTTATCCTACGG 60.349 46.154 5.42 0.00 0.00 4.02
3027 3278 1.549170 CTACGGGTTAGGAAGCACACT 59.451 52.381 0.00 0.00 0.00 3.55
3047 3298 7.276658 GCACACTCACAGGTATTATATCTATGC 59.723 40.741 0.00 0.00 0.00 3.14
3091 3342 1.117994 ATCGCAGCAGAGATTCTCCA 58.882 50.000 10.09 0.00 29.32 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.261783 CGCAAGCAGAGGATTCTATGAGTA 60.262 45.833 0.00 0.00 34.34 2.59
1 2 3.492309 CGCAAGCAGAGGATTCTATGAGT 60.492 47.826 0.00 0.00 34.34 3.41
3 4 3.103447 CGCAAGCAGAGGATTCTATGA 57.897 47.619 0.00 0.00 34.34 2.15
63 64 0.934901 CCAGGATACGTCGATGCACG 60.935 60.000 4.06 0.00 45.65 5.34
91 92 3.008157 CCAGCTGGAGCATCAGATTCTAT 59.992 47.826 29.88 0.00 45.16 1.98
151 152 0.671796 CCGCCCGTGATCATGTAGTA 59.328 55.000 13.81 0.00 0.00 1.82
152 153 1.441729 CCGCCCGTGATCATGTAGT 59.558 57.895 13.81 0.00 0.00 2.73
153 154 1.956170 GCCGCCCGTGATCATGTAG 60.956 63.158 13.81 6.06 0.00 2.74
214 215 1.649267 CGGAGCGAGACGATGATGA 59.351 57.895 0.00 0.00 0.00 2.92
215 216 1.371022 CCGGAGCGAGACGATGATG 60.371 63.158 0.00 0.00 0.00 3.07
216 217 3.034878 CCGGAGCGAGACGATGAT 58.965 61.111 0.00 0.00 0.00 2.45
217 218 3.889044 GCCGGAGCGAGACGATGA 61.889 66.667 5.05 0.00 0.00 2.92
218 219 3.815569 GAGCCGGAGCGAGACGATG 62.816 68.421 5.05 0.00 46.67 3.84
219 220 3.587933 GAGCCGGAGCGAGACGAT 61.588 66.667 5.05 0.00 46.67 3.73
295 302 0.548031 ATCTGGCCAATCATGTCCGT 59.452 50.000 7.01 0.00 0.00 4.69
375 383 3.827898 GAGGAGGAGGGCGACGTG 61.828 72.222 0.00 0.00 0.00 4.49
401 435 1.671901 CTCCTTCCTCCCTCGCTGTC 61.672 65.000 0.00 0.00 0.00 3.51
415 449 0.325671 TTGGATCGCTCTCCCTCCTT 60.326 55.000 0.00 0.00 34.12 3.36
418 452 0.320050 GGATTGGATCGCTCTCCCTC 59.680 60.000 0.00 0.00 34.12 4.30
419 453 0.399091 TGGATTGGATCGCTCTCCCT 60.399 55.000 0.00 0.00 34.12 4.20
468 502 1.778591 CGCCTGTTTGTTTAGCGTTTG 59.221 47.619 0.00 0.00 41.78 2.93
512 547 1.779221 TGGAATGGAATGGGATGTGC 58.221 50.000 0.00 0.00 0.00 4.57
516 551 5.612688 ACTACTGTATGGAATGGAATGGGAT 59.387 40.000 0.00 0.00 0.00 3.85
520 555 5.934625 GCCTACTACTGTATGGAATGGAATG 59.065 44.000 6.03 0.00 0.00 2.67
521 556 5.279506 CGCCTACTACTGTATGGAATGGAAT 60.280 44.000 6.03 0.00 0.00 3.01
522 557 4.038763 CGCCTACTACTGTATGGAATGGAA 59.961 45.833 6.03 0.00 0.00 3.53
731 796 2.020100 TATCAGGACGGAGGAGGGGG 62.020 65.000 0.00 0.00 0.00 5.40
751 825 0.249741 ACCGCAACAGAGTGTACCAC 60.250 55.000 0.00 0.00 34.10 4.16
752 826 0.249699 CACCGCAACAGAGTGTACCA 60.250 55.000 0.00 0.00 0.00 3.25
753 827 0.949105 CCACCGCAACAGAGTGTACC 60.949 60.000 0.00 0.00 0.00 3.34
771 845 1.442526 CTTGGCGATGATCACTGGCC 61.443 60.000 20.88 20.88 44.00 5.36
898 984 1.211969 TCTGGACGCGTAACAGAGC 59.788 57.895 30.71 11.82 36.41 4.09
900 986 1.880894 CCTCTGGACGCGTAACAGA 59.119 57.895 31.51 31.51 38.80 3.41
901 987 1.805945 GCCTCTGGACGCGTAACAG 60.806 63.158 27.97 27.97 0.00 3.16
1150 1241 3.159353 TGGAGATGCGTGTGTATGTAC 57.841 47.619 0.00 0.00 0.00 2.90
1162 1253 2.355920 GGATGGATGGAGATGGAGATGC 60.356 54.545 0.00 0.00 0.00 3.91
1251 1352 1.372087 GATCTCCGGCTGCAACCAAG 61.372 60.000 6.99 3.14 0.00 3.61
1271 1372 1.293498 CACCACCCTCTTCTCCACG 59.707 63.158 0.00 0.00 0.00 4.94
1416 1517 1.991121 TCTATGGTGGGTAGGCGTAG 58.009 55.000 0.00 0.00 0.00 3.51
1420 1521 3.619979 GCATGTATCTATGGTGGGTAGGC 60.620 52.174 0.00 0.00 0.00 3.93
1421 1522 3.582647 TGCATGTATCTATGGTGGGTAGG 59.417 47.826 0.00 0.00 0.00 3.18
1423 1524 3.007940 GCTGCATGTATCTATGGTGGGTA 59.992 47.826 0.00 0.00 0.00 3.69
1424 1525 2.224621 GCTGCATGTATCTATGGTGGGT 60.225 50.000 0.00 0.00 0.00 4.51
1425 1526 2.039480 AGCTGCATGTATCTATGGTGGG 59.961 50.000 1.02 0.00 0.00 4.61
1426 1527 3.413846 AGCTGCATGTATCTATGGTGG 57.586 47.619 1.02 0.00 0.00 4.61
1427 1528 5.104562 CAAAGCTGCATGTATCTATGGTG 57.895 43.478 1.02 0.00 0.00 4.17
1468 1569 4.869297 TGATGATTTTAATTGCCGCAAAGG 59.131 37.500 10.42 0.00 44.97 3.11
1469 1570 5.577945 ACTGATGATTTTAATTGCCGCAAAG 59.422 36.000 10.42 0.81 0.00 2.77
1470 1571 5.477510 ACTGATGATTTTAATTGCCGCAAA 58.522 33.333 10.42 0.00 0.00 3.68
1471 1572 5.070770 ACTGATGATTTTAATTGCCGCAA 57.929 34.783 8.55 8.55 0.00 4.85
1498 1599 6.402118 GCGACAGCAATTCACAGAAATTAGTA 60.402 38.462 0.00 0.00 44.35 1.82
1502 1619 3.568538 GCGACAGCAATTCACAGAAATT 58.431 40.909 0.00 0.00 44.35 1.82
1507 1624 0.451628 CACGCGACAGCAATTCACAG 60.452 55.000 15.93 0.00 45.49 3.66
1618 1735 1.552337 TCGTAGGAGTAGGTGACGAGT 59.448 52.381 0.00 0.00 37.60 4.18
1699 1816 4.748144 GGCTTGGGCTCCACCAGG 62.748 72.222 0.00 0.00 42.47 4.45
1874 1991 1.869824 AAGCTCTCCTCCTCCTCGGT 61.870 60.000 0.00 0.00 0.00 4.69
2106 2226 4.215742 CGGGAGGCGCGGTGAATA 62.216 66.667 8.83 0.00 36.19 1.75
2273 2398 2.125912 GGATATGGCGAGCGCGAT 60.126 61.111 15.92 16.04 43.06 4.58
2433 2558 2.096909 GTGTGTGTGTGTGCGTCTTATC 60.097 50.000 0.00 0.00 0.00 1.75
2434 2559 1.864711 GTGTGTGTGTGTGCGTCTTAT 59.135 47.619 0.00 0.00 0.00 1.73
2435 2560 1.134936 AGTGTGTGTGTGTGCGTCTTA 60.135 47.619 0.00 0.00 0.00 2.10
2436 2561 0.391130 AGTGTGTGTGTGTGCGTCTT 60.391 50.000 0.00 0.00 0.00 3.01
2440 2565 1.490693 GAGGAGTGTGTGTGTGTGCG 61.491 60.000 0.00 0.00 0.00 5.34
2441 2566 1.490693 CGAGGAGTGTGTGTGTGTGC 61.491 60.000 0.00 0.00 0.00 4.57
2442 2567 1.490693 GCGAGGAGTGTGTGTGTGTG 61.491 60.000 0.00 0.00 0.00 3.82
2515 2742 0.532115 GCCAGGCACCAAATTACCAG 59.468 55.000 6.55 0.00 0.00 4.00
2576 2804 1.300927 TTCCCGGGGATTATTGGTGT 58.699 50.000 23.50 0.00 0.00 4.16
2582 2810 1.960689 CGCAAAATTCCCGGGGATTAT 59.039 47.619 28.00 14.61 0.00 1.28
2583 2811 1.341187 ACGCAAAATTCCCGGGGATTA 60.341 47.619 28.00 7.72 0.00 1.75
2584 2812 0.613572 ACGCAAAATTCCCGGGGATT 60.614 50.000 22.45 22.45 0.00 3.01
2631 2860 2.284684 CGAATTCAAGACATCGCACTCG 60.285 50.000 6.22 0.00 0.00 4.18
2666 2895 1.079405 ACAGGCCACGAATACGGTG 60.079 57.895 5.01 0.00 44.46 4.94
2699 2928 1.157870 AAAATATCGCGACCGGGCAG 61.158 55.000 12.93 0.00 34.56 4.85
2710 2939 9.351432 AGGTAGATTCCTGTCCCGAAAATATCG 62.351 44.444 0.00 0.00 42.76 2.92
2719 2948 2.662866 TGTAGGTAGATTCCTGTCCCG 58.337 52.381 0.00 0.00 38.41 5.14
2724 2953 4.466370 TGTCTGGTTGTAGGTAGATTCCTG 59.534 45.833 0.00 0.00 38.41 3.86
2766 3000 4.932105 TGCCAGGCCCAACCCAAC 62.932 66.667 9.64 0.00 40.58 3.77
2767 3001 3.926214 ATGCCAGGCCCAACCCAA 61.926 61.111 9.64 0.00 40.58 4.12
2768 3002 4.700448 CATGCCAGGCCCAACCCA 62.700 66.667 9.64 0.00 40.58 4.51
2769 3003 3.903281 TTCATGCCAGGCCCAACCC 62.903 63.158 9.64 0.00 40.58 4.11
2770 3004 1.479368 TTTTCATGCCAGGCCCAACC 61.479 55.000 9.64 0.00 39.61 3.77
2794 3028 1.519455 GGATCGGTCGAGTTGGCTG 60.519 63.158 0.00 0.00 0.00 4.85
2807 3041 2.158986 GGATGGCTGGATAGATGGATCG 60.159 54.545 0.00 0.00 0.00 3.69
2810 3044 2.263545 CTGGATGGCTGGATAGATGGA 58.736 52.381 0.00 0.00 0.00 3.41
2838 3072 6.183309 AGTACTCATTCATTTCGCTTTTCC 57.817 37.500 0.00 0.00 0.00 3.13
2873 3107 1.153823 CCAAGGATTCGCGTCGAGT 60.154 57.895 5.77 0.07 37.14 4.18
2874 3108 2.517450 GCCAAGGATTCGCGTCGAG 61.517 63.158 5.77 0.00 37.14 4.04
2875 3109 2.508439 GCCAAGGATTCGCGTCGA 60.508 61.111 5.77 0.00 0.00 4.20
2876 3110 3.913573 CGCCAAGGATTCGCGTCG 61.914 66.667 5.77 0.00 40.99 5.12
2897 3148 2.910205 AGCATCATCGGCTCGAATG 58.090 52.632 1.44 3.80 39.99 2.67
2951 3202 2.112475 CGAGAGCACCACGAATCTAG 57.888 55.000 0.00 0.00 0.00 2.43
2975 3226 0.981183 AACCGTCCATTGGAGTGCTA 59.019 50.000 5.39 0.00 29.39 3.49
2976 3227 0.981183 TAACCGTCCATTGGAGTGCT 59.019 50.000 5.39 0.00 29.39 4.40
2986 3237 6.205464 CGTAGGATAAGATAGTTAACCGTCCA 59.795 42.308 0.88 0.00 0.00 4.02
3012 3263 2.417719 CTGTGAGTGTGCTTCCTAACC 58.582 52.381 0.00 0.00 0.00 2.85
3027 3278 9.314133 AGTTCAGCATAGATATAATACCTGTGA 57.686 33.333 0.00 0.00 0.00 3.58
3047 3298 1.804601 TGTGATGCAGAGCAGTTCAG 58.195 50.000 0.00 0.00 43.65 3.02


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

AutoCloner maintained by Alex Coulton.