Multiple sequence alignment - TraesCS5B01G271500

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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 TraesCS5B01G271500 chr5B 100.000 3638 0 0 1 3638 457127646 457124009 0.000000e+00 6719
1 TraesCS5B01G271500 chr5D 94.021 2007 93 19 1 2001 381028805 381026820 0.000000e+00 3016
2 TraesCS5B01G271500 chr5D 88.440 1263 90 27 2388 3638 381026158 381024940 0.000000e+00 1472
3 TraesCS5B01G271500 chr5D 91.850 319 18 7 2074 2391 381026607 381026296 4.310000e-119 438
4 TraesCS5B01G271500 chr5D 83.234 167 18 6 1995 2159 381026772 381026614 1.050000e-30 145
5 TraesCS5B01G271500 chr5A 92.818 2019 101 19 1 2001 481896178 481894186 0.000000e+00 2885
6 TraesCS5B01G271500 chr5A 88.902 1658 120 35 1998 3638 481894122 481892512 0.000000e+00 1984


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 TraesCS5B01G271500 chr5B 457124009 457127646 3637 True 6719.00 6719 100.00000 1 3638 1 chr5B.!!$R1 3637
1 TraesCS5B01G271500 chr5D 381024940 381028805 3865 True 1267.75 3016 89.38625 1 3638 4 chr5D.!!$R1 3637
2 TraesCS5B01G271500 chr5A 481892512 481896178 3666 True 2434.50 2885 90.86000 1 3638 2 chr5A.!!$R1 3637

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
107 108 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86 F
425 426 2.337170 CGTACACCACGTGCTGGA 59.663 61.111 15.02 3.53 43.95 3.86 F
1276 1293 0.036388 GTGACTTGGCAGGGAATCGA 60.036 55.000 0.44 0.00 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 1272 0.036388 TCGATTCCCTGCCAAGTCAC 60.036 55.0 0.0 0.0 0.00 3.67 R
1366 1383 0.098200 CACAAGCCATCACAGCATCG 59.902 55.0 0.0 0.0 0.00 3.84 R
2658 2968 0.324943 ACGTGTTTGGCTATGGCTCT 59.675 50.0 0.0 0.0 38.73 4.09 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
107 108 2.328589 CCCTCCTCCTCCTCCTCCA 61.329 68.421 0.00 0.00 0.00 3.86
163 164 2.591429 TTCACTGTGGCGGCACTG 60.591 61.111 36.19 36.19 0.00 3.66
425 426 2.337170 CGTACACCACGTGCTGGA 59.663 61.111 15.02 3.53 43.95 3.86
882 895 7.720442 TGTCACCTAGATATCTTCAGAATGTG 58.280 38.462 11.25 6.10 37.40 3.21
1134 1147 2.440409 TGGCTCATCAAAAGGCTTCTC 58.560 47.619 0.00 0.00 39.86 2.87
1203 1217 4.337555 CCTTTGTAGCATTCCTCTTGATGG 59.662 45.833 0.00 0.00 0.00 3.51
1207 1221 2.584236 AGCATTCCTCTTGATGGCATC 58.416 47.619 20.52 20.52 0.00 3.91
1217 1232 6.070596 TCCTCTTGATGGCATCATTATCGTAT 60.071 38.462 29.22 0.00 39.39 3.06
1239 1254 7.743400 CGTATATATCTGCAAGCAAATGAACTG 59.257 37.037 0.00 0.00 0.00 3.16
1240 1255 7.812690 ATATATCTGCAAGCAAATGAACTGA 57.187 32.000 0.00 0.00 0.00 3.41
1241 1256 4.859304 ATCTGCAAGCAAATGAACTGAA 57.141 36.364 0.00 0.00 0.00 3.02
1242 1257 4.859304 TCTGCAAGCAAATGAACTGAAT 57.141 36.364 0.00 0.00 0.00 2.57
1246 1261 6.539464 TCTGCAAGCAAATGAACTGAATTTTT 59.461 30.769 0.00 0.00 0.00 1.94
1247 1262 6.487960 TGCAAGCAAATGAACTGAATTTTTG 58.512 32.000 0.00 0.00 0.00 2.44
1248 1263 6.093771 TGCAAGCAAATGAACTGAATTTTTGT 59.906 30.769 0.00 0.00 31.56 2.83
1249 1264 6.412653 GCAAGCAAATGAACTGAATTTTTGTG 59.587 34.615 0.00 0.00 31.56 3.33
1250 1265 6.607735 AGCAAATGAACTGAATTTTTGTGG 57.392 33.333 0.00 0.00 31.56 4.17
1251 1266 6.347696 AGCAAATGAACTGAATTTTTGTGGA 58.652 32.000 0.00 0.00 31.56 4.02
1253 1268 7.499895 AGCAAATGAACTGAATTTTTGTGGATT 59.500 29.630 0.00 0.00 31.56 3.01
1255 1270 9.654417 CAAATGAACTGAATTTTTGTGGATTTC 57.346 29.630 0.00 0.00 0.00 2.17
1257 1272 8.597662 ATGAACTGAATTTTTGTGGATTTCTG 57.402 30.769 0.00 0.00 0.00 3.02
1260 1275 7.111247 ACTGAATTTTTGTGGATTTCTGTGA 57.889 32.000 0.00 0.00 0.00 3.58
1261 1276 6.980397 ACTGAATTTTTGTGGATTTCTGTGAC 59.020 34.615 0.00 0.00 0.00 3.67
1276 1293 0.036388 GTGACTTGGCAGGGAATCGA 60.036 55.000 0.44 0.00 0.00 3.59
1303 1320 2.065899 TGGGACACCTTTGGAAACTG 57.934 50.000 0.00 0.00 37.76 3.16
1366 1383 0.693049 TGGAGGAAGGGAGCTTTGAC 59.307 55.000 0.00 0.00 0.00 3.18
1390 1407 1.303561 TGTGATGGCTTGTGAGGGC 60.304 57.895 0.00 0.00 0.00 5.19
1402 1419 0.741221 GTGAGGGCGTCTTCCACATC 60.741 60.000 8.82 0.00 0.00 3.06
1408 1425 1.920051 CGTCTTCCACATCGCATCG 59.080 57.895 0.00 0.00 0.00 3.84
1426 1443 1.153147 GCCTGTCCTCGGGAAATCC 60.153 63.158 0.00 0.00 42.46 3.01
1443 1460 0.400213 TCCGACTCCAATTGCAAGGT 59.600 50.000 4.94 0.00 0.00 3.50
1472 1489 3.257933 GCTTCAAGCACCCGACTG 58.742 61.111 3.89 0.00 41.89 3.51
1489 1506 5.874810 CCCGACTGTATTATCATTACCATGG 59.125 44.000 11.19 11.19 0.00 3.66
1495 1512 7.175467 ACTGTATTATCATTACCATGGCATGTG 59.825 37.037 24.80 18.13 0.00 3.21
1592 1609 2.476997 GTGCAAGAAGAGTCCGTTTCTC 59.523 50.000 0.00 0.00 32.71 2.87
1596 1613 4.035208 GCAAGAAGAGTCCGTTTCTCAAAA 59.965 41.667 0.00 0.00 32.71 2.44
1646 1663 2.500504 GGTGAGGATTAGGGACGAAACT 59.499 50.000 0.00 0.00 0.00 2.66
1736 1753 3.552604 ATGCGGAACATTGTAACACAC 57.447 42.857 0.00 0.00 34.40 3.82
1737 1754 1.261885 TGCGGAACATTGTAACACACG 59.738 47.619 0.00 0.00 0.00 4.49
1738 1755 1.262151 GCGGAACATTGTAACACACGT 59.738 47.619 0.00 0.00 0.00 4.49
1739 1756 2.286536 GCGGAACATTGTAACACACGTT 60.287 45.455 0.00 0.00 39.24 3.99
1792 1809 9.195411 TGCATAAAACTTTGATCTGAAATTGTC 57.805 29.630 0.00 0.00 0.00 3.18
1970 1987 3.548770 TGCTTCTGATATCCTTGGCTTG 58.451 45.455 0.00 0.00 0.00 4.01
1976 1993 3.548770 TGATATCCTTGGCTTGCTTCAG 58.451 45.455 0.00 0.00 0.00 3.02
1989 2006 4.513318 GCTTGCTTCAGGGTATGTAAGATC 59.487 45.833 0.00 0.00 0.00 2.75
2003 2086 8.198109 GGTATGTAAGATCTTTCTAGCTCAACA 58.802 37.037 14.36 8.72 0.00 3.33
2009 2092 8.627208 AAGATCTTTCTAGCTCAACATTTTCA 57.373 30.769 0.88 0.00 0.00 2.69
2011 2094 8.728833 AGATCTTTCTAGCTCAACATTTTCAAG 58.271 33.333 0.00 0.00 0.00 3.02
2012 2095 6.672147 TCTTTCTAGCTCAACATTTTCAAGC 58.328 36.000 0.00 0.00 0.00 4.01
2017 2100 7.491682 TCTAGCTCAACATTTTCAAGCTTTTT 58.508 30.769 0.00 0.00 42.88 1.94
2050 2133 3.037549 AGTCCCTGGCTTCAGATCTAAG 58.962 50.000 0.00 1.43 40.86 2.18
2079 2248 1.452110 TGCACCATTCAGATCGTTGG 58.548 50.000 5.17 5.17 35.31 3.77
2080 2249 0.099436 GCACCATTCAGATCGTTGGC 59.901 55.000 6.28 0.00 32.26 4.52
2083 2252 0.379669 CCATTCAGATCGTTGGCTGC 59.620 55.000 0.00 0.00 32.27 5.25
2085 2254 1.741706 CATTCAGATCGTTGGCTGCTT 59.258 47.619 0.00 0.00 32.27 3.91
2086 2255 1.442769 TTCAGATCGTTGGCTGCTTC 58.557 50.000 0.00 0.00 32.27 3.86
2099 2268 2.096762 GGCTGCTTCGTTTTTCAAATGC 60.097 45.455 0.00 0.00 0.00 3.56
2108 2277 5.064558 TCGTTTTTCAAATGCTGTACCCTA 58.935 37.500 0.00 0.00 0.00 3.53
2112 2281 6.509418 TTTTCAAATGCTGTACCCTATGTC 57.491 37.500 0.00 0.00 0.00 3.06
2113 2282 4.150897 TCAAATGCTGTACCCTATGTCC 57.849 45.455 0.00 0.00 0.00 4.02
2114 2283 2.872245 CAAATGCTGTACCCTATGTCCG 59.128 50.000 0.00 0.00 0.00 4.79
2116 2285 1.108776 TGCTGTACCCTATGTCCGTC 58.891 55.000 0.00 0.00 0.00 4.79
2117 2286 0.030369 GCTGTACCCTATGTCCGTCG 59.970 60.000 0.00 0.00 0.00 5.12
2118 2287 0.666913 CTGTACCCTATGTCCGTCGG 59.333 60.000 4.39 4.39 0.00 4.79
2120 2289 1.076850 TACCCTATGTCCGTCGGCA 60.077 57.895 6.34 8.67 0.00 5.69
2121 2290 0.468585 TACCCTATGTCCGTCGGCAT 60.469 55.000 20.08 20.08 0.00 4.40
2122 2291 0.468585 ACCCTATGTCCGTCGGCATA 60.469 55.000 20.14 20.14 0.00 3.14
2123 2292 0.243907 CCCTATGTCCGTCGGCATAG 59.756 60.000 29.55 29.55 42.34 2.23
2124 2293 0.959553 CCTATGTCCGTCGGCATAGT 59.040 55.000 31.44 15.10 41.58 2.12
2125 2294 1.340248 CCTATGTCCGTCGGCATAGTT 59.660 52.381 31.44 14.86 41.58 2.24
2144 2313 8.292448 GCATAGTTGCTAAATGCTGTTATATGT 58.708 33.333 8.75 0.00 45.77 2.29
2235 2404 3.031736 ACGGAGCCACATTCTAGTGTAT 58.968 45.455 0.00 0.00 37.82 2.29
2313 2482 3.826524 TGAATTGGTTGGCTTACTCACA 58.173 40.909 0.00 0.00 0.00 3.58
2348 2517 4.908481 AGTATTCCCTATTCCAAGGAGGTC 59.092 45.833 0.00 0.00 39.15 3.85
2353 2522 3.107601 CCTATTCCAAGGAGGTCAGTCA 58.892 50.000 0.00 0.00 39.15 3.41
2428 2738 8.791675 TGCTGTGAACATACATATTTTTCTTCA 58.208 29.630 0.00 0.00 0.00 3.02
2445 2755 4.897025 CTTCAATCCATCTCTTGAAGCC 57.103 45.455 10.92 0.00 46.52 4.35
2447 2757 3.882444 TCAATCCATCTCTTGAAGCCAG 58.118 45.455 0.00 0.00 0.00 4.85
2448 2758 2.345124 ATCCATCTCTTGAAGCCAGC 57.655 50.000 0.00 0.00 0.00 4.85
2449 2759 0.986527 TCCATCTCTTGAAGCCAGCA 59.013 50.000 0.00 0.00 0.00 4.41
2451 2761 2.025605 TCCATCTCTTGAAGCCAGCATT 60.026 45.455 0.00 0.00 0.00 3.56
2452 2762 2.758979 CCATCTCTTGAAGCCAGCATTT 59.241 45.455 0.00 0.00 0.00 2.32
2453 2763 3.194968 CCATCTCTTGAAGCCAGCATTTT 59.805 43.478 0.00 0.00 0.00 1.82
2454 2764 3.928727 TCTCTTGAAGCCAGCATTTTG 57.071 42.857 0.00 0.00 0.00 2.44
2455 2765 3.489355 TCTCTTGAAGCCAGCATTTTGA 58.511 40.909 0.00 0.00 0.00 2.69
2456 2766 4.084287 TCTCTTGAAGCCAGCATTTTGAT 58.916 39.130 0.00 0.00 0.00 2.57
2457 2767 4.157289 TCTCTTGAAGCCAGCATTTTGATC 59.843 41.667 0.00 0.00 0.00 2.92
2458 2768 3.194116 TCTTGAAGCCAGCATTTTGATCC 59.806 43.478 0.00 0.00 0.00 3.36
2477 2787 5.184864 TGATCCAAATGCGTACCTTGAAATT 59.815 36.000 0.00 0.00 0.00 1.82
2492 2802 1.542915 GAAATTGCTCTGCAGGCTCAA 59.457 47.619 22.36 18.65 40.61 3.02
2493 2803 0.886563 AATTGCTCTGCAGGCTCAAC 59.113 50.000 22.36 5.48 40.61 3.18
2502 2812 0.960861 GCAGGCTCAACAACCCCTAC 60.961 60.000 0.00 0.00 0.00 3.18
2523 2833 1.202533 GGAAAGCAGGCGTATCAGCTA 60.203 52.381 0.00 0.00 36.07 3.32
2653 2963 5.130519 CGTTGTGAAAATAGAGACAACACG 58.869 41.667 12.77 0.00 45.52 4.49
2658 2968 6.314152 TGTGAAAATAGAGACAACACGAACAA 59.686 34.615 0.00 0.00 0.00 2.83
2659 2969 6.846283 GTGAAAATAGAGACAACACGAACAAG 59.154 38.462 0.00 0.00 0.00 3.16
2749 3059 9.967346 CTCTTCAAATAATTCCTATGTCGTCTA 57.033 33.333 0.00 0.00 0.00 2.59
2807 3117 3.991605 ATGCGACTACACGAAATGTTC 57.008 42.857 0.00 0.00 43.19 3.18
2896 3206 5.789710 ACTTTTATCATGCATTTTGCTGC 57.210 34.783 0.00 0.00 45.31 5.25
2897 3207 5.484715 ACTTTTATCATGCATTTTGCTGCT 58.515 33.333 0.00 0.00 45.31 4.24
2902 3212 0.391130 ATGCATTTTGCTGCTGCCTG 60.391 50.000 13.47 6.64 45.31 4.85
2910 3220 2.746671 CTGCTGCCTGACTGCCTG 60.747 66.667 0.00 0.00 42.24 4.85
2916 3226 2.263741 GCCTGACTGCCTGGTGTTG 61.264 63.158 0.00 0.00 36.37 3.33
2917 3227 2.263741 CCTGACTGCCTGGTGTTGC 61.264 63.158 0.00 0.00 0.00 4.17
2918 3228 1.228063 CTGACTGCCTGGTGTTGCT 60.228 57.895 0.00 0.00 0.00 3.91
2919 3229 1.512996 CTGACTGCCTGGTGTTGCTG 61.513 60.000 0.00 0.00 0.00 4.41
2920 3230 1.227943 GACTGCCTGGTGTTGCTGA 60.228 57.895 0.00 0.00 0.00 4.26
2921 3231 1.510480 GACTGCCTGGTGTTGCTGAC 61.510 60.000 0.00 0.00 0.00 3.51
2922 3232 1.526686 CTGCCTGGTGTTGCTGACA 60.527 57.895 0.00 0.00 35.42 3.58
2923 3233 1.077140 TGCCTGGTGTTGCTGACAA 60.077 52.632 0.00 0.00 40.65 3.18
2999 3309 9.997482 TTATTTATTTATTTCAACTCCGCACTC 57.003 29.630 0.00 0.00 0.00 3.51
3000 3310 4.965119 ATTTATTTCAACTCCGCACTCC 57.035 40.909 0.00 0.00 0.00 3.85
3009 3319 1.888436 CTCCGCACTCCTGCCACTTA 61.888 60.000 0.00 0.00 40.73 2.24
3015 3325 2.616510 GCACTCCTGCCACTTACTTCAT 60.617 50.000 0.00 0.00 37.45 2.57
3017 3327 2.906389 ACTCCTGCCACTTACTTCATCA 59.094 45.455 0.00 0.00 0.00 3.07
3021 3331 3.181493 CCTGCCACTTACTTCATCATTGC 60.181 47.826 0.00 0.00 0.00 3.56
3022 3332 2.754552 TGCCACTTACTTCATCATTGCC 59.245 45.455 0.00 0.00 0.00 4.52
3028 3338 5.587443 CACTTACTTCATCATTGCCAGATCA 59.413 40.000 0.00 0.00 0.00 2.92
3030 3340 4.232188 ACTTCATCATTGCCAGATCACT 57.768 40.909 0.00 0.00 0.00 3.41
3031 3341 4.197750 ACTTCATCATTGCCAGATCACTC 58.802 43.478 0.00 0.00 0.00 3.51
3040 3350 1.065199 GCCAGATCACTCCCACAATGA 60.065 52.381 0.00 0.00 0.00 2.57
3064 3374 9.077885 TGAAAAGCCAAATTACTAGACAAATCT 57.922 29.630 0.00 0.00 39.15 2.40
3102 3413 9.611284 TGAATTTCATCTTAATTTCGAAGTGTG 57.389 29.630 0.00 0.00 0.00 3.82
3104 3415 5.545658 TCATCTTAATTTCGAAGTGTGGC 57.454 39.130 0.00 0.00 0.00 5.01
3105 3416 4.092821 TCATCTTAATTTCGAAGTGTGGCG 59.907 41.667 0.00 0.00 0.00 5.69
3109 3420 1.156736 ATTTCGAAGTGTGGCGAAGG 58.843 50.000 0.00 0.00 45.71 3.46
3121 3432 2.166270 GCGAAGGCCAGACTGAAAG 58.834 57.895 5.01 0.00 42.29 2.62
3137 3448 5.640189 CTGAAAGTTTTCTCTGATGCCAT 57.360 39.130 6.21 0.00 38.02 4.40
3140 3451 5.302568 TGAAAGTTTTCTCTGATGCCATTGT 59.697 36.000 6.21 0.00 38.02 2.71
3146 3457 3.538591 TCTCTGATGCCATTGTCATCAC 58.461 45.455 6.29 0.00 43.63 3.06
3166 3477 1.202110 CGTCAATTCTGGATGCACAGC 60.202 52.381 0.00 0.00 38.36 4.40
3181 3492 3.511182 CAGCTGACTGGAGTGAGTG 57.489 57.895 8.42 0.00 40.48 3.51
3198 3509 3.933879 TGGTACACATCACAGGCAG 57.066 52.632 0.00 0.00 0.00 4.85
3211 3524 2.746362 CACAGGCAGAATGAGAAGGTTC 59.254 50.000 0.00 0.00 39.69 3.62
3223 3536 4.389374 TGAGAAGGTTCCACAATTCAGAC 58.611 43.478 0.00 0.00 0.00 3.51
3230 3543 0.883833 CCACAATTCAGACCACCAGC 59.116 55.000 0.00 0.00 0.00 4.85
3340 3660 5.483583 ACCCGGTAACTACTTACACCATAAA 59.516 40.000 0.00 0.00 34.88 1.40
3357 3677 5.652891 ACCATAAAAACAAAACCCAAAACCC 59.347 36.000 0.00 0.00 0.00 4.11
3358 3678 5.652452 CCATAAAAACAAAACCCAAAACCCA 59.348 36.000 0.00 0.00 0.00 4.51
3359 3679 6.152831 CCATAAAAACAAAACCCAAAACCCAA 59.847 34.615 0.00 0.00 0.00 4.12
3360 3680 7.309805 CCATAAAAACAAAACCCAAAACCCAAA 60.310 33.333 0.00 0.00 0.00 3.28
3361 3681 6.479972 AAAAACAAAACCCAAAACCCAAAA 57.520 29.167 0.00 0.00 0.00 2.44
3362 3682 5.455056 AAACAAAACCCAAAACCCAAAAC 57.545 34.783 0.00 0.00 0.00 2.43
3363 3683 3.422796 ACAAAACCCAAAACCCAAAACC 58.577 40.909 0.00 0.00 0.00 3.27
3364 3684 2.404923 AAACCCAAAACCCAAAACCG 57.595 45.000 0.00 0.00 0.00 4.44
3619 3944 2.032681 GGCCTGCTTCTTCACCGT 59.967 61.111 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 2.285743 GGAGAGGGGAAGCTGGGT 60.286 66.667 0.00 0.00 0.00 4.51
133 134 4.162690 GTGAAGGGGAGCGCGGAT 62.163 66.667 8.83 0.00 0.00 4.18
170 171 4.436998 GTCCAGGAGGTCGGCGTG 62.437 72.222 6.85 0.00 35.89 5.34
193 194 2.125350 CAGAGCCTGGCGAGGAAC 60.125 66.667 20.35 10.98 42.93 3.62
481 482 0.172578 CCGAGCTGGTGAACACGATA 59.827 55.000 0.00 0.00 0.00 2.92
762 775 8.922676 GTGACTCGAAGAAAGAATGTTTACATA 58.077 33.333 0.00 0.00 32.60 2.29
771 784 7.872993 TGATAACTTGTGACTCGAAGAAAGAAT 59.127 33.333 0.00 0.00 34.09 2.40
882 895 5.449177 GGTTGGTAGAATGCAGATTTACAGC 60.449 44.000 0.00 0.00 0.00 4.40
1128 1141 3.717400 TGATATCCACACTCGAGAAGC 57.283 47.619 21.68 0.00 0.00 3.86
1134 1147 5.405797 CCTATCACATGATATCCACACTCG 58.594 45.833 0.00 0.00 36.53 4.18
1203 1217 8.219769 GCTTGCAGATATATACGATAATGATGC 58.780 37.037 0.00 0.00 0.00 3.91
1217 1232 7.628769 TTCAGTTCATTTGCTTGCAGATATA 57.371 32.000 0.00 0.00 0.00 0.86
1239 1254 7.042523 CCAAGTCACAGAAATCCACAAAAATTC 60.043 37.037 0.00 0.00 0.00 2.17
1240 1255 6.762661 CCAAGTCACAGAAATCCACAAAAATT 59.237 34.615 0.00 0.00 0.00 1.82
1241 1256 6.282930 CCAAGTCACAGAAATCCACAAAAAT 58.717 36.000 0.00 0.00 0.00 1.82
1242 1257 5.659463 CCAAGTCACAGAAATCCACAAAAA 58.341 37.500 0.00 0.00 0.00 1.94
1246 1261 2.229792 GCCAAGTCACAGAAATCCACA 58.770 47.619 0.00 0.00 0.00 4.17
1247 1262 2.227388 CTGCCAAGTCACAGAAATCCAC 59.773 50.000 0.00 0.00 35.90 4.02
1248 1263 2.507484 CTGCCAAGTCACAGAAATCCA 58.493 47.619 0.00 0.00 35.90 3.41
1249 1264 1.815003 CCTGCCAAGTCACAGAAATCC 59.185 52.381 0.00 0.00 35.90 3.01
1250 1265 1.815003 CCCTGCCAAGTCACAGAAATC 59.185 52.381 0.00 0.00 35.90 2.17
1251 1266 1.425066 TCCCTGCCAAGTCACAGAAAT 59.575 47.619 0.00 0.00 35.90 2.17
1253 1268 0.843309 TTCCCTGCCAAGTCACAGAA 59.157 50.000 0.00 0.00 35.90 3.02
1255 1270 1.457346 GATTCCCTGCCAAGTCACAG 58.543 55.000 0.00 0.00 0.00 3.66
1257 1272 0.036388 TCGATTCCCTGCCAAGTCAC 60.036 55.000 0.00 0.00 0.00 3.67
1260 1275 2.286365 TTTTCGATTCCCTGCCAAGT 57.714 45.000 0.00 0.00 0.00 3.16
1285 1302 0.673985 GCAGTTTCCAAAGGTGTCCC 59.326 55.000 0.00 0.00 0.00 4.46
1303 1320 1.941999 GCCTCTCATTTGCACCAGGC 61.942 60.000 0.00 0.00 45.13 4.85
1366 1383 0.098200 CACAAGCCATCACAGCATCG 59.902 55.000 0.00 0.00 0.00 3.84
1390 1407 1.920051 CGATGCGATGTGGAAGACG 59.080 57.895 0.00 0.00 0.00 4.18
1408 1425 1.153147 GGATTTCCCGAGGACAGGC 60.153 63.158 0.00 0.00 0.00 4.85
1426 1443 3.680642 CATACCTTGCAATTGGAGTCG 57.319 47.619 11.47 0.00 0.00 4.18
1443 1460 2.883574 GCTTGAAGCAAATGCAGCATA 58.116 42.857 13.09 0.00 45.16 3.14
1466 1483 5.351465 GCCATGGTAATGATAATACAGTCGG 59.649 44.000 14.67 0.00 35.67 4.79
1470 1487 7.532571 CACATGCCATGGTAATGATAATACAG 58.467 38.462 26.85 6.44 35.67 2.74
1471 1488 6.072008 GCACATGCCATGGTAATGATAATACA 60.072 38.462 26.85 9.09 35.67 2.29
1472 1489 6.324819 GCACATGCCATGGTAATGATAATAC 58.675 40.000 26.85 11.55 35.67 1.89
1489 1506 4.216902 TGAATAGCATATTCAGGCACATGC 59.783 41.667 7.89 0.00 43.24 4.06
1495 1512 5.159209 GCAACATGAATAGCATATTCAGGC 58.841 41.667 18.83 14.02 41.76 4.85
1592 1609 5.067674 TGAAGATGTGAGAACAACCCTTTTG 59.932 40.000 0.00 0.00 0.00 2.44
1596 1613 4.583871 GATGAAGATGTGAGAACAACCCT 58.416 43.478 0.00 0.00 0.00 4.34
1646 1663 0.181114 ACAACAGTTCTGGCTGCTGA 59.819 50.000 0.00 0.00 39.96 4.26
1718 1735 1.262151 ACGTGTGTTACAATGTTCCGC 59.738 47.619 0.00 0.00 0.00 5.54
1728 1745 6.291796 GGAGTACAGTTTACAACGTGTGTTAC 60.292 42.308 8.33 7.70 41.98 2.50
1729 1746 5.748152 GGAGTACAGTTTACAACGTGTGTTA 59.252 40.000 8.33 0.00 41.98 2.41
1730 1747 4.567959 GGAGTACAGTTTACAACGTGTGTT 59.432 41.667 8.33 0.00 41.98 3.32
1731 1748 4.114794 GGAGTACAGTTTACAACGTGTGT 58.885 43.478 0.00 8.15 44.82 3.72
1732 1749 4.114073 TGGAGTACAGTTTACAACGTGTG 58.886 43.478 0.00 0.00 36.23 3.82
1733 1750 4.365723 CTGGAGTACAGTTTACAACGTGT 58.634 43.478 0.00 0.00 42.42 4.49
1734 1751 4.966850 CTGGAGTACAGTTTACAACGTG 57.033 45.455 0.00 0.00 42.42 4.49
1792 1809 0.107214 TTTGGGCGCATAGAAGAGGG 60.107 55.000 10.83 0.00 0.00 4.30
1970 1987 6.587273 AGAAAGATCTTACATACCCTGAAGC 58.413 40.000 8.75 0.00 29.15 3.86
1976 1993 7.291411 TGAGCTAGAAAGATCTTACATACCC 57.709 40.000 8.75 0.00 38.98 3.69
1989 2006 6.675987 AGCTTGAAAATGTTGAGCTAGAAAG 58.324 36.000 0.00 0.00 41.54 2.62
2017 2100 1.272092 CCAGGGACTTGCATTCAGGAA 60.272 52.381 0.00 0.00 34.60 3.36
2060 2143 1.452110 CCAACGATCTGAATGGTGCA 58.548 50.000 0.00 0.00 0.00 4.57
2064 2147 0.379669 GCAGCCAACGATCTGAATGG 59.620 55.000 0.00 1.36 36.00 3.16
2069 2152 1.016130 ACGAAGCAGCCAACGATCTG 61.016 55.000 9.82 0.00 0.00 2.90
2070 2153 0.320771 AACGAAGCAGCCAACGATCT 60.321 50.000 9.82 0.00 0.00 2.75
2079 2248 2.796593 AGCATTTGAAAAACGAAGCAGC 59.203 40.909 0.00 0.00 0.00 5.25
2080 2249 3.798337 ACAGCATTTGAAAAACGAAGCAG 59.202 39.130 0.00 0.00 0.00 4.24
2083 2252 4.679654 GGGTACAGCATTTGAAAAACGAAG 59.320 41.667 0.00 0.00 0.00 3.79
2085 2254 3.886505 AGGGTACAGCATTTGAAAAACGA 59.113 39.130 0.00 0.00 0.00 3.85
2086 2255 4.237349 AGGGTACAGCATTTGAAAAACG 57.763 40.909 0.00 0.00 0.00 3.60
2099 2268 0.666913 CCGACGGACATAGGGTACAG 59.333 60.000 8.64 0.00 0.00 2.74
2108 2277 3.362581 CAACTATGCCGACGGACAT 57.637 52.632 20.50 21.29 0.00 3.06
2131 2300 5.066893 CACCTGCAAGAACATATAACAGCAT 59.933 40.000 0.00 0.00 34.07 3.79
2144 2313 0.531974 GTCCGTGTCACCTGCAAGAA 60.532 55.000 0.00 0.00 34.07 2.52
2235 2404 1.228124 CCTTGCCTCGGGTGTTTCA 60.228 57.895 0.00 0.00 0.00 2.69
2313 2482 4.388577 AGGGAATACTGGAAACTGCTTT 57.611 40.909 0.00 0.00 0.00 3.51
2392 2702 3.358707 TGTTCACAGCAAAAGCAGATG 57.641 42.857 0.00 0.00 0.00 2.90
2400 2710 9.979578 AAGAAAAATATGTATGTTCACAGCAAA 57.020 25.926 0.00 0.00 0.00 3.68
2428 2738 2.025605 TGCTGGCTTCAAGAGATGGATT 60.026 45.455 0.00 0.00 0.00 3.01
2431 2741 2.054232 ATGCTGGCTTCAAGAGATGG 57.946 50.000 0.00 0.00 0.00 3.51
2440 2750 3.598019 TTGGATCAAAATGCTGGCTTC 57.402 42.857 0.00 0.00 0.00 3.86
2441 2751 4.258543 CATTTGGATCAAAATGCTGGCTT 58.741 39.130 20.09 0.00 39.83 4.35
2442 2752 3.869065 CATTTGGATCAAAATGCTGGCT 58.131 40.909 20.09 0.00 39.83 4.75
2448 2758 4.997565 AGGTACGCATTTGGATCAAAATG 58.002 39.130 25.44 25.44 46.03 2.32
2449 2759 5.184864 TCAAGGTACGCATTTGGATCAAAAT 59.815 36.000 1.92 1.92 36.90 1.82
2451 2761 4.075682 TCAAGGTACGCATTTGGATCAAA 58.924 39.130 0.00 0.00 37.75 2.69
2452 2762 3.680490 TCAAGGTACGCATTTGGATCAA 58.320 40.909 0.00 0.00 0.00 2.57
2453 2763 3.342377 TCAAGGTACGCATTTGGATCA 57.658 42.857 0.00 0.00 0.00 2.92
2454 2764 4.695217 TTTCAAGGTACGCATTTGGATC 57.305 40.909 0.00 0.00 0.00 3.36
2455 2765 5.410067 CAATTTCAAGGTACGCATTTGGAT 58.590 37.500 0.00 0.00 0.00 3.41
2456 2766 4.804108 CAATTTCAAGGTACGCATTTGGA 58.196 39.130 0.00 0.00 0.00 3.53
2457 2767 3.367630 GCAATTTCAAGGTACGCATTTGG 59.632 43.478 0.00 0.00 0.00 3.28
2458 2768 4.236935 AGCAATTTCAAGGTACGCATTTG 58.763 39.130 0.00 0.00 0.00 2.32
2477 2787 1.148949 TTGTTGAGCCTGCAGAGCA 59.851 52.632 23.46 12.85 36.92 4.26
2502 2812 1.766143 GCTGATACGCCTGCTTTCCG 61.766 60.000 0.00 0.00 0.00 4.30
2523 2833 1.548582 CCCTGGAGCTTGGATGTGTTT 60.549 52.381 0.00 0.00 0.00 2.83
2550 2860 2.575532 TGCACTCCTTTGAACTTGAGG 58.424 47.619 0.00 0.00 0.00 3.86
2653 2963 2.819608 TGTTTGGCTATGGCTCTTGTTC 59.180 45.455 0.00 0.00 38.73 3.18
2658 2968 0.324943 ACGTGTTTGGCTATGGCTCT 59.675 50.000 0.00 0.00 38.73 4.09
2659 2969 0.727398 GACGTGTTTGGCTATGGCTC 59.273 55.000 0.00 0.00 38.73 4.70
2722 3032 7.928706 AGACGACATAGGAATTATTTGAAGAGG 59.071 37.037 0.00 0.00 0.00 3.69
2749 3059 9.216117 GACAGTTGATGTTTGGTAATAGTAACT 57.784 33.333 0.00 0.00 44.17 2.24
2807 3117 5.361427 TGAATCAATTGCAAAGCATATGGG 58.639 37.500 1.71 0.00 38.76 4.00
2890 3200 2.981909 GCAGTCAGGCAGCAGCAA 60.982 61.111 2.65 0.00 44.61 3.91
2902 3212 1.227943 TCAGCAACACCAGGCAGTC 60.228 57.895 0.00 0.00 0.00 3.51
2916 3226 1.807142 GGAAGTTAGCCAGTTGTCAGC 59.193 52.381 0.00 0.00 0.00 4.26
2917 3227 3.330267 GAGGAAGTTAGCCAGTTGTCAG 58.670 50.000 0.00 0.00 0.00 3.51
2918 3228 2.038557 GGAGGAAGTTAGCCAGTTGTCA 59.961 50.000 0.00 0.00 0.00 3.58
2919 3229 2.615747 GGGAGGAAGTTAGCCAGTTGTC 60.616 54.545 0.00 0.00 0.00 3.18
2920 3230 1.351350 GGGAGGAAGTTAGCCAGTTGT 59.649 52.381 0.00 0.00 0.00 3.32
2921 3231 1.630878 AGGGAGGAAGTTAGCCAGTTG 59.369 52.381 0.00 0.00 0.00 3.16
2922 3232 1.630878 CAGGGAGGAAGTTAGCCAGTT 59.369 52.381 0.00 0.00 0.00 3.16
2923 3233 1.280457 CAGGGAGGAAGTTAGCCAGT 58.720 55.000 0.00 0.00 0.00 4.00
2924 3234 0.543749 CCAGGGAGGAAGTTAGCCAG 59.456 60.000 0.00 0.00 41.22 4.85
2925 3235 0.914417 CCCAGGGAGGAAGTTAGCCA 60.914 60.000 0.00 0.00 41.22 4.75
2926 3236 0.914902 ACCCAGGGAGGAAGTTAGCC 60.915 60.000 14.54 0.00 41.22 3.93
2927 3237 0.992695 AACCCAGGGAGGAAGTTAGC 59.007 55.000 14.54 0.00 41.22 3.09
2928 3238 2.237392 CTCAACCCAGGGAGGAAGTTAG 59.763 54.545 14.54 0.00 41.22 2.34
2929 3239 2.266279 CTCAACCCAGGGAGGAAGTTA 58.734 52.381 14.54 0.00 41.22 2.24
2930 3240 1.068121 CTCAACCCAGGGAGGAAGTT 58.932 55.000 14.54 0.00 41.22 2.66
2931 3241 1.492993 GCTCAACCCAGGGAGGAAGT 61.493 60.000 14.54 0.00 41.22 3.01
2932 3242 1.301293 GCTCAACCCAGGGAGGAAG 59.699 63.158 14.54 5.03 41.22 3.46
2974 3284 8.617809 GGAGTGCGGAGTTGAAATAAATAAATA 58.382 33.333 0.00 0.00 0.00 1.40
2975 3285 7.339466 AGGAGTGCGGAGTTGAAATAAATAAAT 59.661 33.333 0.00 0.00 0.00 1.40
2976 3286 6.657541 AGGAGTGCGGAGTTGAAATAAATAAA 59.342 34.615 0.00 0.00 0.00 1.40
2977 3287 6.093495 CAGGAGTGCGGAGTTGAAATAAATAA 59.907 38.462 0.00 0.00 0.00 1.40
2978 3288 5.584649 CAGGAGTGCGGAGTTGAAATAAATA 59.415 40.000 0.00 0.00 0.00 1.40
2979 3289 4.396166 CAGGAGTGCGGAGTTGAAATAAAT 59.604 41.667 0.00 0.00 0.00 1.40
2980 3290 3.751175 CAGGAGTGCGGAGTTGAAATAAA 59.249 43.478 0.00 0.00 0.00 1.40
2981 3291 3.334691 CAGGAGTGCGGAGTTGAAATAA 58.665 45.455 0.00 0.00 0.00 1.40
2982 3292 2.935238 GCAGGAGTGCGGAGTTGAAATA 60.935 50.000 0.00 0.00 40.71 1.40
2983 3293 1.813513 CAGGAGTGCGGAGTTGAAAT 58.186 50.000 0.00 0.00 0.00 2.17
2984 3294 0.884704 GCAGGAGTGCGGAGTTGAAA 60.885 55.000 0.00 0.00 40.71 2.69
2985 3295 1.301716 GCAGGAGTGCGGAGTTGAA 60.302 57.895 0.00 0.00 40.71 2.69
2986 3296 2.343758 GCAGGAGTGCGGAGTTGA 59.656 61.111 0.00 0.00 40.71 3.18
2997 3307 3.616956 TGATGAAGTAAGTGGCAGGAG 57.383 47.619 0.00 0.00 0.00 3.69
2999 3309 3.181493 GCAATGATGAAGTAAGTGGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
3000 3310 3.181493 GGCAATGATGAAGTAAGTGGCAG 60.181 47.826 0.00 0.00 0.00 4.85
3009 3319 4.197750 GAGTGATCTGGCAATGATGAAGT 58.802 43.478 0.00 0.00 0.00 3.01
3015 3325 1.065199 GTGGGAGTGATCTGGCAATGA 60.065 52.381 0.00 0.00 0.00 2.57
3017 3327 0.994247 TGTGGGAGTGATCTGGCAAT 59.006 50.000 0.00 0.00 0.00 3.56
3021 3331 3.354948 TTCATTGTGGGAGTGATCTGG 57.645 47.619 0.00 0.00 0.00 3.86
3022 3332 4.380233 GCTTTTCATTGTGGGAGTGATCTG 60.380 45.833 0.00 0.00 0.00 2.90
3028 3338 2.380064 TGGCTTTTCATTGTGGGAGT 57.620 45.000 0.00 0.00 0.00 3.85
3030 3340 4.703379 AATTTGGCTTTTCATTGTGGGA 57.297 36.364 0.00 0.00 0.00 4.37
3031 3341 5.550290 AGTAATTTGGCTTTTCATTGTGGG 58.450 37.500 0.00 0.00 0.00 4.61
3085 3396 3.655486 TCGCCACACTTCGAAATTAAGA 58.345 40.909 0.00 0.00 0.00 2.10
3088 3399 2.739913 CCTTCGCCACACTTCGAAATTA 59.260 45.455 0.00 0.00 42.99 1.40
3104 3415 1.884235 AACTTTCAGTCTGGCCTTCG 58.116 50.000 3.32 0.00 0.00 3.79
3105 3416 3.885901 AGAAAACTTTCAGTCTGGCCTTC 59.114 43.478 3.32 0.00 39.61 3.46
3109 3420 4.130118 TCAGAGAAAACTTTCAGTCTGGC 58.870 43.478 15.79 0.00 38.75 4.85
3110 3421 5.334724 GCATCAGAGAAAACTTTCAGTCTGG 60.335 44.000 15.79 7.14 38.75 3.86
3111 3422 5.334724 GGCATCAGAGAAAACTTTCAGTCTG 60.335 44.000 12.13 12.13 39.19 3.51
3116 3427 5.302568 ACAATGGCATCAGAGAAAACTTTCA 59.697 36.000 0.00 0.00 39.61 2.69
3119 3430 4.828939 TGACAATGGCATCAGAGAAAACTT 59.171 37.500 0.00 0.00 0.00 2.66
3121 3432 4.771590 TGACAATGGCATCAGAGAAAAC 57.228 40.909 0.00 0.00 0.00 2.43
3130 3441 2.009051 TGACGTGATGACAATGGCATC 58.991 47.619 21.56 21.56 41.87 3.91
3132 3443 1.889545 TTGACGTGATGACAATGGCA 58.110 45.000 0.00 0.00 0.00 4.92
3133 3444 3.127548 AGAATTGACGTGATGACAATGGC 59.872 43.478 0.00 0.40 41.13 4.40
3134 3445 4.437794 CCAGAATTGACGTGATGACAATGG 60.438 45.833 0.00 0.00 41.13 3.16
3135 3446 4.392754 TCCAGAATTGACGTGATGACAATG 59.607 41.667 0.00 0.00 41.13 2.82
3136 3447 4.578871 TCCAGAATTGACGTGATGACAAT 58.421 39.130 0.00 0.00 43.28 2.71
3137 3448 4.001618 TCCAGAATTGACGTGATGACAA 57.998 40.909 0.00 0.00 36.70 3.18
3140 3451 2.938451 GCATCCAGAATTGACGTGATGA 59.062 45.455 11.20 0.00 33.20 2.92
3146 3457 1.202110 GCTGTGCATCCAGAATTGACG 60.202 52.381 8.43 0.00 34.23 4.35
3166 3477 2.029828 GTGTACCACTCACTCCAGTCAG 60.030 54.545 0.00 0.00 33.59 3.51
3173 3484 3.579709 CTGTGATGTGTACCACTCACTC 58.420 50.000 18.62 5.08 40.08 3.51
3174 3485 2.300152 CCTGTGATGTGTACCACTCACT 59.700 50.000 18.62 0.00 40.08 3.41
3175 3486 2.688507 CCTGTGATGTGTACCACTCAC 58.311 52.381 14.51 14.51 39.96 3.51
3180 3491 1.347062 TCTGCCTGTGATGTGTACCA 58.653 50.000 0.00 0.00 0.00 3.25
3181 3492 2.472695 TTCTGCCTGTGATGTGTACC 57.527 50.000 0.00 0.00 0.00 3.34
3189 3500 1.980765 ACCTTCTCATTCTGCCTGTGA 59.019 47.619 0.00 0.00 0.00 3.58
3195 3506 2.783135 TGTGGAACCTTCTCATTCTGC 58.217 47.619 0.00 0.00 34.36 4.26
3196 3507 5.474532 TGAATTGTGGAACCTTCTCATTCTG 59.525 40.000 0.00 0.00 34.36 3.02
3197 3508 5.634118 TGAATTGTGGAACCTTCTCATTCT 58.366 37.500 0.00 0.00 34.36 2.40
3198 3509 5.707298 TCTGAATTGTGGAACCTTCTCATTC 59.293 40.000 0.00 0.00 34.36 2.67
3211 3524 0.883833 GCTGGTGGTCTGAATTGTGG 59.116 55.000 0.00 0.00 0.00 4.17
3230 3543 2.506957 GGTTTTGGGGCTGGGTGTG 61.507 63.158 0.00 0.00 0.00 3.82
3340 3660 4.281182 GGTTTTGGGTTTTGGGTTTTGTTT 59.719 37.500 0.00 0.00 0.00 2.83
3357 3677 1.847390 CGGTTTTCGGTTTCGGTTTTG 59.153 47.619 0.00 0.00 36.95 2.44
3358 3678 2.191815 CGGTTTTCGGTTTCGGTTTT 57.808 45.000 0.00 0.00 36.95 2.43
3359 3679 3.922190 CGGTTTTCGGTTTCGGTTT 57.078 47.368 0.00 0.00 36.95 3.27
3619 3944 1.757949 TTCATCCAGGCCAACGTCA 59.242 52.632 5.01 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.