Multiple sequence alignment - TraesCS3B01G258100

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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 TraesCS3B01G258100 chr3B 100.000 3433 0 0 1 3433 416034930 416031498 0.000000e+00 6340.0
1 TraesCS3B01G258100 chr3B 74.930 359 76 14 2571 2925 42569484 42569832 5.930000e-33 152.0
2 TraesCS3B01G258100 chr3B 74.167 360 77 16 2571 2925 793521403 793521751 5.980000e-28 135.0
3 TraesCS3B01G258100 chr3B 73.669 357 85 9 2558 2911 588412696 588413046 2.780000e-26 130.0
4 TraesCS3B01G258100 chr3A 89.563 1945 108 38 1 1895 423706339 423708238 0.000000e+00 2379.0
5 TraesCS3B01G258100 chr3A 89.968 1256 93 16 2188 3432 423709077 423710310 0.000000e+00 1591.0
6 TraesCS3B01G258100 chr3A 94.118 289 13 1 1908 2192 423708487 423708775 1.460000e-118 436.0
7 TraesCS3B01G258100 chr3D 91.114 1598 101 20 1864 3433 305746537 305748121 0.000000e+00 2126.0
8 TraesCS3B01G258100 chr3D 93.137 1326 47 18 573 1863 305745125 305746441 0.000000e+00 1905.0
9 TraesCS3B01G258100 chr3D 83.871 341 33 10 204 536 305744422 305744748 4.300000e-79 305.0
10 TraesCS3B01G258100 chr3D 97.015 134 1 1 33 166 305744292 305744422 4.460000e-54 222.0
11 TraesCS3B01G258100 chr7D 82.946 387 36 14 57 427 127503528 127503156 4.270000e-84 322.0
12 TraesCS3B01G258100 chr7D 82.817 355 30 14 89 427 127213117 127213456 4.330000e-74 289.0
13 TraesCS3B01G258100 chr7D 85.484 62 4 1 37 93 127208084 127208145 3.700000e-05 60.2
14 TraesCS3B01G258100 chr6A 75.871 373 75 15 2558 2926 495110504 495110143 3.520000e-40 176.0
15 TraesCS3B01G258100 chr7A 80.000 220 18 12 1 204 127861209 127861418 4.620000e-29 139.0
16 TraesCS3B01G258100 chr7A 85.507 138 8 3 290 427 127861878 127862003 2.150000e-27 134.0
17 TraesCS3B01G258100 chr7A 90.361 83 4 3 200 280 127861695 127861775 4.690000e-19 106.0
18 TraesCS3B01G258100 chr7B 77.500 240 42 12 2690 2926 630132342 630132112 2.150000e-27 134.0
19 TraesCS3B01G258100 chr4B 73.590 390 76 19 2571 2950 372826269 372825897 1.290000e-24 124.0
20 TraesCS3B01G258100 chr1A 76.978 139 20 10 2602 2735 573722292 573722423 6.150000e-08 69.4


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 TraesCS3B01G258100 chr3B 416031498 416034930 3432 True 6340.000000 6340 100.000000 1 3433 1 chr3B.!!$R1 3432
1 TraesCS3B01G258100 chr3A 423706339 423710310 3971 False 1468.666667 2379 91.216333 1 3432 3 chr3A.!!$F1 3431
2 TraesCS3B01G258100 chr3D 305744292 305748121 3829 False 1139.500000 2126 91.284250 33 3433 4 chr3D.!!$F1 3400

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
976 1368 0.472044 TATAAAGCCATCCGCCTGCA 59.528 50.0 0.00 0.00 38.78 4.41 F
1859 2288 0.027979 CAAACCCGTGCGCATAGATG 59.972 55.0 15.91 4.86 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2774 0.036765 GCTGTATCCGGTGTGGTTCA 60.037 55.0 0.0 0.0 39.52 3.18 R
3187 4292 0.544697 GGCGAGGGTAAAAGATGGGA 59.455 55.0 0.0 0.0 0.00 4.37 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
85 86 1.880027 GTGCAGTCTCAAACCGGAAAT 59.120 47.619 9.46 0.00 0.00 2.17
137 139 6.717084 CCCTCCCTTGATGGATTTCTTAATAC 59.283 42.308 0.00 0.00 38.35 1.89
138 140 7.421853 CCCTCCCTTGATGGATTTCTTAATACT 60.422 40.741 0.00 0.00 38.35 2.12
139 141 8.660435 CCTCCCTTGATGGATTTCTTAATACTA 58.340 37.037 0.00 0.00 38.35 1.82
167 169 0.741221 GGGTCTTCGCTGATGGTGAC 60.741 60.000 0.00 0.00 33.81 3.67
293 304 3.772025 ACTTGTAAGCAGCCTAGTGAGAT 59.228 43.478 0.00 0.00 0.00 2.75
319 330 0.880278 TTCTCTGTGTGAGCCGTTGC 60.880 55.000 0.00 0.00 42.38 4.17
320 331 2.661537 TCTGTGTGAGCCGTTGCG 60.662 61.111 0.00 0.00 44.33 4.85
321 332 2.967076 CTGTGTGAGCCGTTGCGT 60.967 61.111 0.00 0.00 44.33 5.24
322 333 2.512745 TGTGTGAGCCGTTGCGTT 60.513 55.556 0.00 0.00 44.33 4.84
323 334 2.248431 GTGTGAGCCGTTGCGTTC 59.752 61.111 0.00 0.00 44.33 3.95
338 349 3.857052 TGCGTTCGATCTCTATTGGTTT 58.143 40.909 0.00 0.00 0.00 3.27
404 423 5.309323 TGGCAAATAAAAGGTGAATCTCG 57.691 39.130 0.00 0.00 0.00 4.04
406 425 4.142381 GGCAAATAAAAGGTGAATCTCGCT 60.142 41.667 0.00 0.00 0.00 4.93
526 550 9.835389 CAAATTTATTTCCCATACACCATGATT 57.165 29.630 0.00 0.00 36.69 2.57
547 571 2.558378 AGATGGAGTGCATGAACGATG 58.442 47.619 0.12 0.00 34.84 3.84
600 964 7.387948 GTCAGATAGTTTGTTAGCTTTCCTTGA 59.612 37.037 0.00 0.00 0.00 3.02
602 966 8.567948 CAGATAGTTTGTTAGCTTTCCTTGAAA 58.432 33.333 0.00 0.00 0.00 2.69
676 1050 4.870123 AACAATGTGCCATCTAAGCAAA 57.130 36.364 0.00 0.00 43.02 3.68
677 1051 4.870123 ACAATGTGCCATCTAAGCAAAA 57.130 36.364 0.00 0.00 43.02 2.44
678 1052 4.559153 ACAATGTGCCATCTAAGCAAAAC 58.441 39.130 0.00 0.00 43.02 2.43
679 1053 4.281688 ACAATGTGCCATCTAAGCAAAACT 59.718 37.500 0.00 0.00 43.02 2.66
680 1054 5.476599 ACAATGTGCCATCTAAGCAAAACTA 59.523 36.000 0.00 0.00 43.02 2.24
681 1055 5.824904 ATGTGCCATCTAAGCAAAACTAG 57.175 39.130 0.00 0.00 43.02 2.57
682 1056 4.651778 TGTGCCATCTAAGCAAAACTAGT 58.348 39.130 0.00 0.00 43.02 2.57
683 1057 5.070001 TGTGCCATCTAAGCAAAACTAGTT 58.930 37.500 1.12 1.12 43.02 2.24
684 1058 5.181245 TGTGCCATCTAAGCAAAACTAGTTC 59.819 40.000 8.95 0.00 43.02 3.01
685 1059 5.181245 GTGCCATCTAAGCAAAACTAGTTCA 59.819 40.000 8.95 0.00 43.02 3.18
734 1108 2.775911 TCTCTTCCAGGTCAGCAATG 57.224 50.000 0.00 0.00 0.00 2.82
773 1147 6.963805 CGTGATTTCTTTTCTGAAGATAAGGC 59.036 38.462 9.67 0.00 35.00 4.35
779 1153 9.574516 TTTCTTTTCTGAAGATAAGGCTAAAGT 57.425 29.630 9.67 0.00 35.00 2.66
815 1207 6.494893 TTAGGACAACTGTTTATGTGCATC 57.505 37.500 5.60 0.00 39.97 3.91
841 1233 2.363807 GTGAGACATTCACGAGCCG 58.636 57.895 0.00 0.00 46.13 5.52
934 1326 1.522355 CTTGCACCGATCCGCTGAT 60.522 57.895 0.00 0.00 0.00 2.90
956 1348 2.224305 GCACCCTCCACTCCACATATAC 60.224 54.545 0.00 0.00 0.00 1.47
957 1349 3.309296 CACCCTCCACTCCACATATACT 58.691 50.000 0.00 0.00 0.00 2.12
959 1351 5.087323 CACCCTCCACTCCACATATACTAT 58.913 45.833 0.00 0.00 0.00 2.12
960 1352 6.253758 CACCCTCCACTCCACATATACTATA 58.746 44.000 0.00 0.00 0.00 1.31
961 1353 6.724441 CACCCTCCACTCCACATATACTATAA 59.276 42.308 0.00 0.00 0.00 0.98
962 1354 7.234782 CACCCTCCACTCCACATATACTATAAA 59.765 40.741 0.00 0.00 0.00 1.40
963 1355 7.455008 ACCCTCCACTCCACATATACTATAAAG 59.545 40.741 0.00 0.00 0.00 1.85
964 1356 7.324178 CCTCCACTCCACATATACTATAAAGC 58.676 42.308 0.00 0.00 0.00 3.51
965 1357 7.241042 TCCACTCCACATATACTATAAAGCC 57.759 40.000 0.00 0.00 0.00 4.35
966 1358 6.785466 TCCACTCCACATATACTATAAAGCCA 59.215 38.462 0.00 0.00 0.00 4.75
967 1359 7.457852 TCCACTCCACATATACTATAAAGCCAT 59.542 37.037 0.00 0.00 0.00 4.40
969 1361 7.766278 CACTCCACATATACTATAAAGCCATCC 59.234 40.741 0.00 0.00 0.00 3.51
970 1362 6.873997 TCCACATATACTATAAAGCCATCCG 58.126 40.000 0.00 0.00 0.00 4.18
972 1364 5.523916 CACATATACTATAAAGCCATCCGCC 59.476 44.000 0.00 0.00 38.78 6.13
973 1365 5.425539 ACATATACTATAAAGCCATCCGCCT 59.574 40.000 0.00 0.00 38.78 5.52
974 1366 2.550830 ACTATAAAGCCATCCGCCTG 57.449 50.000 0.00 0.00 38.78 4.85
975 1367 1.160137 CTATAAAGCCATCCGCCTGC 58.840 55.000 0.00 0.00 38.78 4.85
976 1368 0.472044 TATAAAGCCATCCGCCTGCA 59.528 50.000 0.00 0.00 38.78 4.41
1016 1421 2.620115 CCTTGATGTTGAATCATCGGGG 59.380 50.000 0.00 0.00 44.82 5.73
1024 1429 4.204012 GTTGAATCATCGGGGGATGTTAA 58.796 43.478 4.21 0.00 34.39 2.01
1114 1519 1.171308 CTACTCTTTCCCCGACGACA 58.829 55.000 0.00 0.00 0.00 4.35
1273 1684 0.181114 CATCCTGATCAAGCCCGGAA 59.819 55.000 0.73 0.00 0.00 4.30
1362 1788 0.883814 GCCTGATCGCCTGGAATCTG 60.884 60.000 0.00 3.84 36.07 2.90
1458 1884 1.078759 GTGATCACCTGGAACGAGCG 61.079 60.000 15.31 0.00 0.00 5.03
1465 1891 2.992689 TGGAACGAGCGCTGGGTA 60.993 61.111 23.76 0.00 0.00 3.69
1468 1894 1.591863 GAACGAGCGCTGGGTATCC 60.592 63.158 23.76 1.26 0.00 2.59
1570 1996 5.000591 TCCATAGTTCGTGATTGCAAAGAA 58.999 37.500 1.71 4.61 0.00 2.52
1579 2005 3.187227 GTGATTGCAAAGAAAGAGCGAGA 59.813 43.478 1.71 0.00 0.00 4.04
1730 2156 1.306642 AAGACACGCTCCTCGACGAT 61.307 55.000 0.00 0.00 41.67 3.73
1829 2258 6.708949 TCTTTGAAGTAAGTACATGTTCACCC 59.291 38.462 2.30 0.00 0.00 4.61
1859 2288 0.027979 CAAACCCGTGCGCATAGATG 59.972 55.000 15.91 4.86 0.00 2.90
1860 2289 0.107897 AAACCCGTGCGCATAGATGA 60.108 50.000 15.91 0.00 0.00 2.92
1861 2290 0.106708 AACCCGTGCGCATAGATGAT 59.893 50.000 15.91 0.00 0.00 2.45
1901 2664 1.892468 GTACGTACGAGAGGTTGCTG 58.108 55.000 24.41 0.00 0.00 4.41
1902 2665 0.169672 TACGTACGAGAGGTTGCTGC 59.830 55.000 24.41 0.00 0.00 5.25
1903 2666 1.805945 CGTACGAGAGGTTGCTGCC 60.806 63.158 10.44 0.00 0.00 4.85
1904 2667 1.292223 GTACGAGAGGTTGCTGCCA 59.708 57.895 0.00 0.00 0.00 4.92
1905 2668 0.320421 GTACGAGAGGTTGCTGCCAA 60.320 55.000 0.00 0.00 0.00 4.52
1906 2669 0.037326 TACGAGAGGTTGCTGCCAAG 60.037 55.000 0.00 0.00 0.00 3.61
1927 2690 5.633830 AGTGCCAAGATCAACTAACAATG 57.366 39.130 0.00 0.00 0.00 2.82
2017 2784 1.219522 CGTCCGAGTTGAACCACACC 61.220 60.000 0.00 0.00 0.00 4.16
2033 2800 0.172578 CACCGGATACAGCTTCGTCA 59.827 55.000 9.46 0.00 0.00 4.35
2196 3269 6.519551 GCCAACCAGAGGTAAACTTAGTCTTA 60.520 42.308 0.00 0.00 33.12 2.10
2327 3405 0.112412 AAGGGGCGAAAACTGATGGT 59.888 50.000 0.00 0.00 0.00 3.55
2359 3437 1.448540 CTCGCAACCTCTCGCCAAT 60.449 57.895 0.00 0.00 0.00 3.16
2399 3477 3.411517 AAGGCCTGGATCGGTGGG 61.412 66.667 5.69 0.00 0.00 4.61
2437 3515 0.251742 CAGCCCCCTTCATGACCAAA 60.252 55.000 0.00 0.00 0.00 3.28
2438 3516 0.486879 AGCCCCCTTCATGACCAAAA 59.513 50.000 0.00 0.00 0.00 2.44
2439 3517 0.897621 GCCCCCTTCATGACCAAAAG 59.102 55.000 0.00 0.00 0.00 2.27
2440 3518 1.560505 CCCCCTTCATGACCAAAAGG 58.439 55.000 0.00 0.00 39.44 3.11
2489 3567 0.307760 CAGAAAACAGTCGGTGGTGC 59.692 55.000 0.00 0.00 0.00 5.01
2590 3680 4.003648 GGATGAATCCGGGAACATATGAC 58.996 47.826 10.38 3.00 37.19 3.06
2592 3682 3.045634 TGAATCCGGGAACATATGACCT 58.954 45.455 10.38 0.00 0.00 3.85
2598 3688 3.370527 CCGGGAACATATGACCTCACTTT 60.371 47.826 10.38 0.00 0.00 2.66
2599 3689 3.871594 CGGGAACATATGACCTCACTTTC 59.128 47.826 10.38 0.00 0.00 2.62
2600 3690 3.871594 GGGAACATATGACCTCACTTTCG 59.128 47.826 10.38 0.00 0.00 3.46
2673 3763 2.804421 TTTCATGTTCTATGTGCGCG 57.196 45.000 0.00 0.00 0.00 6.86
2686 3776 2.248431 GCGCGCAGAAAGTTTCGT 59.752 55.556 29.10 0.00 34.02 3.85
2687 3777 1.216298 TGCGCGCAGAAAGTTTCGTA 61.216 50.000 33.09 1.22 34.02 3.43
2761 3854 9.334693 GTCATTGAACTTTATTTAGAAGCACTG 57.665 33.333 0.00 0.00 0.00 3.66
2762 3855 8.514594 TCATTGAACTTTATTTAGAAGCACTGG 58.485 33.333 0.00 0.00 0.00 4.00
2773 3866 6.560253 TTAGAAGCACTGGAATTTGTCTTC 57.440 37.500 0.00 0.00 0.00 2.87
2775 3868 4.759183 AGAAGCACTGGAATTTGTCTTCTC 59.241 41.667 0.00 0.00 35.29 2.87
2777 3870 4.070716 AGCACTGGAATTTGTCTTCTCTG 58.929 43.478 0.00 0.00 0.00 3.35
2809 3902 7.641802 GCAAAATAAAAAGACATTTTTCCGCAA 59.358 29.630 2.22 0.00 43.51 4.85
2871 3967 9.356929 GTTCACGTGAAATTTCATTTTGATTTC 57.643 29.630 31.20 9.85 39.73 2.17
3117 4214 2.432146 AGCGATTGAGGCTACTGATTCA 59.568 45.455 0.00 0.00 39.39 2.57
3130 4227 6.753744 GGCTACTGATTCATTTTGTCATTTCC 59.246 38.462 0.00 0.00 0.00 3.13
3157 4262 0.616395 TCCCCTCGCATGTCCTTACA 60.616 55.000 0.00 0.00 40.69 2.41
3168 4273 6.436218 TCGCATGTCCTTACATAGGTGTATAT 59.564 38.462 0.00 0.00 44.70 0.86
3187 4292 8.765219 GTGTATATATGTCATTGACTCGCTTTT 58.235 33.333 17.26 0.70 33.15 2.27
3198 4303 4.647611 TGACTCGCTTTTCCCATCTTTTA 58.352 39.130 0.00 0.00 0.00 1.52
3220 4325 4.717629 CGCCTCGCACGGTCTCAA 62.718 66.667 0.00 0.00 0.00 3.02
3221 4326 2.811317 GCCTCGCACGGTCTCAAG 60.811 66.667 0.00 0.00 0.00 3.02
3243 4356 5.799213 AGCACTCTAGATATACCAAATGCC 58.201 41.667 0.00 0.00 0.00 4.40
3281 4394 0.251564 CCCACAATTGCCAGGGTGTA 60.252 55.000 18.44 0.00 36.52 2.90
3286 4399 1.942657 CAATTGCCAGGGTGTAGATCG 59.057 52.381 0.00 0.00 0.00 3.69
3413 4526 5.109210 CAAATGATCTTGAATGTGCTGCAT 58.891 37.500 5.27 0.00 40.03 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.665848 GCGCGCACTTGTACAATCTTTAA 60.666 43.478 29.10 0.00 0.00 1.52
21 22 2.159761 GCGCGCACTTGTACAATCTTTA 60.160 45.455 29.10 0.00 0.00 1.85
22 23 1.399727 GCGCGCACTTGTACAATCTTT 60.400 47.619 29.10 0.00 0.00 2.52
23 24 0.165944 GCGCGCACTTGTACAATCTT 59.834 50.000 29.10 0.00 0.00 2.40
24 25 0.948623 TGCGCGCACTTGTACAATCT 60.949 50.000 33.09 0.00 0.00 2.40
85 86 2.102420 TGACAAGCTTTCTGACGAAGGA 59.898 45.455 0.00 0.00 0.00 3.36
137 139 3.074412 AGCGAAGACCCAAAACACATAG 58.926 45.455 0.00 0.00 0.00 2.23
138 140 2.811431 CAGCGAAGACCCAAAACACATA 59.189 45.455 0.00 0.00 0.00 2.29
139 141 1.608590 CAGCGAAGACCCAAAACACAT 59.391 47.619 0.00 0.00 0.00 3.21
257 259 4.083324 GCTTACAAGTTACAAGCTCATGCA 60.083 41.667 11.52 0.00 41.14 3.96
262 264 3.120165 GGCTGCTTACAAGTTACAAGCTC 60.120 47.826 17.04 10.95 43.98 4.09
263 265 2.814336 GGCTGCTTACAAGTTACAAGCT 59.186 45.455 17.04 0.00 43.98 3.74
264 266 2.814336 AGGCTGCTTACAAGTTACAAGC 59.186 45.455 11.78 11.78 43.92 4.01
265 267 5.120830 CACTAGGCTGCTTACAAGTTACAAG 59.879 44.000 0.00 0.00 0.00 3.16
266 268 4.994852 CACTAGGCTGCTTACAAGTTACAA 59.005 41.667 0.00 0.00 0.00 2.41
267 269 4.282449 TCACTAGGCTGCTTACAAGTTACA 59.718 41.667 0.00 0.00 0.00 2.41
268 270 4.817517 TCACTAGGCTGCTTACAAGTTAC 58.182 43.478 0.00 0.00 0.00 2.50
269 271 4.770531 TCTCACTAGGCTGCTTACAAGTTA 59.229 41.667 0.00 0.00 0.00 2.24
319 330 4.267928 GGTCAAACCAATAGAGATCGAACG 59.732 45.833 0.00 0.00 38.42 3.95
320 331 5.720261 GGTCAAACCAATAGAGATCGAAC 57.280 43.478 0.00 0.00 38.42 3.95
352 363 9.762933 CCCAAATTTAGTTTTCTTCTTCATTCA 57.237 29.630 0.00 0.00 0.00 2.57
353 364 9.981114 TCCCAAATTTAGTTTTCTTCTTCATTC 57.019 29.630 0.00 0.00 0.00 2.67
375 386 2.158234 ACCTTTTATTTGCCAGGTCCCA 60.158 45.455 0.00 0.00 34.27 4.37
377 388 3.161866 TCACCTTTTATTTGCCAGGTCC 58.838 45.455 0.00 0.00 37.56 4.46
404 423 0.036388 TTGAACGGGAGATGGTCAGC 60.036 55.000 0.00 0.00 0.00 4.26
406 425 2.187958 AGATTGAACGGGAGATGGTCA 58.812 47.619 0.00 0.00 0.00 4.02
470 494 8.229253 TGAATTGAACTTTGGATATCTCATGG 57.771 34.615 2.05 0.00 0.00 3.66
526 550 3.721035 CATCGTTCATGCACTCCATCTA 58.279 45.455 0.00 0.00 29.71 1.98
547 571 3.330720 ACTGCCCCTAGGGTGTGC 61.331 66.667 26.66 21.96 46.51 4.57
565 589 6.867662 AACAAACTATCTGACCAGTTTCAG 57.132 37.500 13.45 8.43 41.78 3.02
600 964 4.990526 TCCAAGAGCTGAAGAAATCCTTT 58.009 39.130 0.00 0.00 34.68 3.11
602 966 4.219264 CTCCAAGAGCTGAAGAAATCCT 57.781 45.455 0.00 0.00 0.00 3.24
676 1050 8.079211 TGCTTTCTCCTATACATGAACTAGTT 57.921 34.615 8.13 8.13 0.00 2.24
677 1051 7.661536 TGCTTTCTCCTATACATGAACTAGT 57.338 36.000 0.00 0.00 0.00 2.57
678 1052 8.821894 GTTTGCTTTCTCCTATACATGAACTAG 58.178 37.037 0.00 0.00 0.00 2.57
679 1053 8.318412 TGTTTGCTTTCTCCTATACATGAACTA 58.682 33.333 0.00 0.00 0.00 2.24
680 1054 7.119846 GTGTTTGCTTTCTCCTATACATGAACT 59.880 37.037 0.00 0.00 0.00 3.01
681 1055 7.244192 GTGTTTGCTTTCTCCTATACATGAAC 58.756 38.462 0.00 0.00 0.00 3.18
682 1056 6.374333 GGTGTTTGCTTTCTCCTATACATGAA 59.626 38.462 0.00 0.00 0.00 2.57
683 1057 5.880332 GGTGTTTGCTTTCTCCTATACATGA 59.120 40.000 0.00 0.00 0.00 3.07
684 1058 5.066505 GGGTGTTTGCTTTCTCCTATACATG 59.933 44.000 0.00 0.00 0.00 3.21
685 1059 5.044846 AGGGTGTTTGCTTTCTCCTATACAT 60.045 40.000 0.00 0.00 0.00 2.29
734 1108 9.774742 AAAAGAAATCACGTAAGATAATTGCTC 57.225 29.630 0.00 0.00 43.62 4.26
773 1147 6.001460 TCCTAAATGTGGTTGGTGACTTTAG 58.999 40.000 0.00 0.00 0.00 1.85
779 1153 3.866703 TGTCCTAAATGTGGTTGGTGA 57.133 42.857 0.00 0.00 0.00 4.02
841 1233 1.486726 ACCCCTCCATCACGAGAAATC 59.513 52.381 0.00 0.00 30.97 2.17
934 1326 0.546507 TATGTGGAGTGGAGGGTGCA 60.547 55.000 0.00 0.00 0.00 4.57
964 1356 2.745884 TTCGTTGCAGGCGGATGG 60.746 61.111 11.79 0.00 0.00 3.51
965 1357 2.480555 GTTCGTTGCAGGCGGATG 59.519 61.111 11.79 0.00 0.00 3.51
966 1358 3.118454 CGTTCGTTGCAGGCGGAT 61.118 61.111 11.79 0.00 0.00 4.18
970 1362 3.702334 GATCGCGTTCGTTGCAGGC 62.702 63.158 5.77 0.00 36.96 4.85
972 1364 1.057822 CTGATCGCGTTCGTTGCAG 59.942 57.895 5.77 0.00 36.96 4.41
973 1365 3.010585 GCTGATCGCGTTCGTTGCA 62.011 57.895 5.77 0.00 36.96 4.08
974 1366 2.276058 GCTGATCGCGTTCGTTGC 60.276 61.111 5.77 9.70 36.96 4.17
992 1392 3.488047 CCGATGATTCAACATCAAGGCAC 60.488 47.826 0.00 0.00 44.57 5.01
1016 1421 3.541516 CGAGTTGACGCGATTTAACATCC 60.542 47.826 15.93 5.15 41.67 3.51
1024 1429 3.179265 CGCCGAGTTGACGCGATT 61.179 61.111 15.93 0.00 41.67 3.34
1273 1684 1.191535 TGCGGTACTTGCCTGTAGAT 58.808 50.000 7.92 0.00 0.00 1.98
1362 1788 1.646189 GATCTTCTCCCTGCAACGAC 58.354 55.000 0.00 0.00 0.00 4.34
1441 1867 2.167861 GCGCTCGTTCCAGGTGATC 61.168 63.158 0.00 0.00 0.00 2.92
1465 1891 0.325296 TAGGGGAAGTGTCGCTGGAT 60.325 55.000 0.00 0.00 36.92 3.41
1468 1894 1.218316 GGTAGGGGAAGTGTCGCTG 59.782 63.158 0.00 0.00 36.92 5.18
1579 2005 3.750373 AAACTGTCAGCACCCGCGT 62.750 57.895 4.92 0.00 45.49 6.01
1584 2010 1.312815 AGCAAGAAACTGTCAGCACC 58.687 50.000 0.00 0.00 33.35 5.01
1588 2014 6.794158 CGAGAAAATTAGCAAGAAACTGTCAG 59.206 38.462 0.00 0.00 0.00 3.51
1652 2078 4.147449 CCCATGACTCTCGCCGCA 62.147 66.667 0.00 0.00 0.00 5.69
1657 2083 0.743688 CCTGTCTCCCATGACTCTCG 59.256 60.000 0.00 0.00 37.79 4.04
1730 2156 1.113788 AGTAGTAATGGCGCCCGTTA 58.886 50.000 26.77 19.88 34.27 3.18
1829 2258 0.535102 ACGGGTTTGCTGGTGAGAAG 60.535 55.000 0.00 0.00 0.00 2.85
1859 2288 5.645497 ACGGGGTAAGTACGTATGATCTATC 59.355 44.000 0.00 0.00 39.30 2.08
1860 2289 5.564550 ACGGGGTAAGTACGTATGATCTAT 58.435 41.667 0.00 0.00 39.30 1.98
1861 2290 4.973168 ACGGGGTAAGTACGTATGATCTA 58.027 43.478 0.00 0.00 39.30 1.98
1901 2664 1.251251 AGTTGATCTTGGCACTTGGC 58.749 50.000 0.00 0.00 43.74 4.52
1902 2665 3.820467 TGTTAGTTGATCTTGGCACTTGG 59.180 43.478 0.00 0.00 0.00 3.61
1903 2666 5.437289 TTGTTAGTTGATCTTGGCACTTG 57.563 39.130 0.00 0.00 0.00 3.16
1904 2667 5.047802 CCATTGTTAGTTGATCTTGGCACTT 60.048 40.000 0.00 0.00 0.00 3.16
1905 2668 4.460382 CCATTGTTAGTTGATCTTGGCACT 59.540 41.667 0.00 0.00 0.00 4.40
1906 2669 4.218417 ACCATTGTTAGTTGATCTTGGCAC 59.782 41.667 0.00 0.00 0.00 5.01
2007 2774 0.036765 GCTGTATCCGGTGTGGTTCA 60.037 55.000 0.00 0.00 39.52 3.18
2017 2784 0.456221 ACCTGACGAAGCTGTATCCG 59.544 55.000 0.00 0.00 0.00 4.18
2196 3269 1.678970 GGGAAAATGGCAGCGGAGT 60.679 57.895 0.00 0.00 0.00 3.85
2327 3405 0.905809 TGCGAGCCCACTTAACCCTA 60.906 55.000 0.00 0.00 0.00 3.53
2359 3437 2.300967 ATGAAGGGGGCTGCTTCGA 61.301 57.895 0.00 0.00 0.00 3.71
2437 3515 1.299976 GTCCACCGATCCAAGCCTT 59.700 57.895 0.00 0.00 0.00 4.35
2438 3516 1.903877 CTGTCCACCGATCCAAGCCT 61.904 60.000 0.00 0.00 0.00 4.58
2439 3517 1.450312 CTGTCCACCGATCCAAGCC 60.450 63.158 0.00 0.00 0.00 4.35
2440 3518 2.109126 GCTGTCCACCGATCCAAGC 61.109 63.158 0.00 0.00 0.00 4.01
2468 3546 1.330521 CACCACCGACTGTTTTCTGTG 59.669 52.381 0.00 0.00 32.21 3.66
2469 3547 1.663695 CACCACCGACTGTTTTCTGT 58.336 50.000 0.00 0.00 34.75 3.41
2470 3548 0.307760 GCACCACCGACTGTTTTCTG 59.692 55.000 0.00 0.00 0.00 3.02
2526 3604 9.349713 ACTTGTATCCTTCAAATGAAAACACTA 57.650 29.630 0.00 0.00 33.07 2.74
2527 3605 8.237811 ACTTGTATCCTTCAAATGAAAACACT 57.762 30.769 0.00 0.00 33.07 3.55
2528 3606 8.871686 AACTTGTATCCTTCAAATGAAAACAC 57.128 30.769 0.00 0.00 33.07 3.32
2533 3611 9.581289 TCCTTTAACTTGTATCCTTCAAATGAA 57.419 29.630 0.00 0.00 0.00 2.57
2534 3612 9.581289 TTCCTTTAACTTGTATCCTTCAAATGA 57.419 29.630 0.00 0.00 0.00 2.57
2578 3668 3.871594 CGAAAGTGAGGTCATATGTTCCC 59.128 47.826 1.90 1.95 0.00 3.97
2590 3680 5.821204 AGAAATGTGTTTTCGAAAGTGAGG 58.179 37.500 10.98 0.00 46.89 3.86
2592 3682 9.232082 CATTTAGAAATGTGTTTTCGAAAGTGA 57.768 29.630 10.98 0.00 45.72 3.41
2598 3688 6.078202 TGGCATTTAGAAATGTGTTTTCGA 57.922 33.333 14.72 0.00 46.89 3.71
2599 3689 6.761731 TTGGCATTTAGAAATGTGTTTTCG 57.238 33.333 14.72 0.00 46.89 3.46
2638 3728 5.889219 ACATGAAAATATATGCGTGCAACA 58.111 33.333 0.00 0.00 35.74 3.33
2644 3734 8.017373 GCACATAGAACATGAAAATATATGCGT 58.983 33.333 0.00 0.00 0.00 5.24
2646 3736 7.007725 GCGCACATAGAACATGAAAATATATGC 59.992 37.037 0.30 2.78 0.00 3.14
2648 3738 7.236474 CGCGCACATAGAACATGAAAATATAT 58.764 34.615 8.75 0.00 0.00 0.86
2651 3741 4.785025 GCGCGCACATAGAACATGAAAATA 60.785 41.667 29.10 0.00 0.00 1.40
2695 3785 2.891580 TGCACGGGCCAAATAAAAAGTA 59.108 40.909 7.46 0.00 40.13 2.24
2700 3790 2.910688 TTTTGCACGGGCCAAATAAA 57.089 40.000 7.46 0.00 40.13 1.40
2722 3812 8.776376 AAAGTTCAATGACACATTTTCTGTTT 57.224 26.923 0.00 0.00 35.29 2.83
2738 3831 8.635765 TCCAGTGCTTCTAAATAAAGTTCAAT 57.364 30.769 0.00 0.00 0.00 2.57
2761 3854 2.675348 CTCCGCAGAGAAGACAAATTCC 59.325 50.000 0.00 0.00 43.39 3.01
2762 3855 2.675348 CCTCCGCAGAGAAGACAAATTC 59.325 50.000 0.00 0.00 43.39 2.17
2777 3870 3.908213 TGTCTTTTTATTTTGCCTCCGC 58.092 40.909 0.00 0.00 0.00 5.54
2907 4004 5.120399 TCGGGTACATATGAAATCGCTTTT 58.880 37.500 10.38 0.00 0.00 2.27
2914 4011 5.454755 CCCTGAACTCGGGTACATATGAAAT 60.455 44.000 10.38 0.00 40.86 2.17
2989 4086 4.376225 ACTAATTTTCCTCCCCGTGAAA 57.624 40.909 0.00 0.00 0.00 2.69
2990 4087 5.013391 ACTTACTAATTTTCCTCCCCGTGAA 59.987 40.000 0.00 0.00 0.00 3.18
3008 4105 9.342308 TCAATTCAGACTTTTGATGAACTTACT 57.658 29.630 0.00 0.00 35.89 2.24
3117 4214 6.340522 GGGATCGAAATGGAAATGACAAAAT 58.659 36.000 0.00 0.00 0.00 1.82
3157 4262 8.191446 GCGAGTCAATGACATATATACACCTAT 58.809 37.037 16.38 0.00 34.60 2.57
3168 4273 3.938963 GGGAAAAGCGAGTCAATGACATA 59.061 43.478 16.38 0.00 34.60 2.29
3187 4292 0.544697 GGCGAGGGTAAAAGATGGGA 59.455 55.000 0.00 0.00 0.00 4.37
3219 4324 6.183361 TGGCATTTGGTATATCTAGAGTGCTT 60.183 38.462 0.00 0.00 0.00 3.91
3220 4325 5.307976 TGGCATTTGGTATATCTAGAGTGCT 59.692 40.000 0.00 0.00 0.00 4.40
3221 4326 5.409826 GTGGCATTTGGTATATCTAGAGTGC 59.590 44.000 0.00 0.00 0.00 4.40
3243 4356 2.292267 GGGAATGCTATCAGGTGTGTG 58.708 52.381 0.00 0.00 0.00 3.82
3281 4394 5.089970 TGATTCCATGAGTTCAACGATCT 57.910 39.130 0.00 0.00 0.00 2.75
3363 4476 6.982899 TCCACTAAACTCTTATACTCCTCCT 58.017 40.000 0.00 0.00 0.00 3.69
3406 4519 7.864108 AGTTATTAGATGTGTTTATGCAGCA 57.136 32.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.