Multiple sequence alignment - TraesCS1B01G172500

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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 TraesCS1B01G172500 chr1B 100.000 3262 0 0 1 3262 307483741 307480480 0.000000e+00 6024.0
1 TraesCS1B01G172500 chr1B 100.000 170 0 0 3594 3763 307480148 307479979 7.850000e-82 315.0
2 TraesCS1B01G172500 chr1B 84.564 298 38 7 205 498 307483388 307483095 4.760000e-74 289.0
3 TraesCS1B01G172500 chr1B 84.564 298 38 7 354 647 307483537 307483244 4.760000e-74 289.0
4 TraesCS1B01G172500 chr1D 93.575 2070 99 21 1 2046 214603158 214601099 0.000000e+00 3055.0
5 TraesCS1B01G172500 chr1D 91.599 988 47 12 2098 3070 214601102 214600136 0.000000e+00 1332.0
6 TraesCS1B01G172500 chr1D 82.119 302 43 7 205 498 214602807 214602509 8.070000e-62 248.0
7 TraesCS1B01G172500 chr1D 100.000 39 0 0 3152 3190 214600022 214599984 5.210000e-09 73.1
8 TraesCS1B01G172500 chr1A 92.322 2123 97 26 703 2800 272985894 272983813 0.000000e+00 2957.0
9 TraesCS1B01G172500 chr1A 93.056 720 48 2 1 719 272986626 272985908 0.000000e+00 1051.0
10 TraesCS1B01G172500 chr1A 92.373 236 17 1 3006 3240 272983408 272983173 6.020000e-88 335.0
11 TraesCS1B01G172500 chr1A 85.121 289 37 5 354 639 272986422 272986137 1.320000e-74 291.0
12 TraesCS1B01G172500 chr1A 83.557 298 43 5 205 499 272986273 272985979 1.330000e-69 274.0
13 TraesCS1B01G172500 chr1A 90.431 209 13 2 2798 3006 272983732 272983531 6.200000e-68 268.0
14 TraesCS1B01G172500 chr1A 91.176 170 15 0 3594 3763 272982775 272982606 8.130000e-57 231.0
15 TraesCS1B01G172500 chr1A 77.703 148 27 5 503 647 272986422 272986278 6.700000e-13 86.1
16 TraesCS1B01G172500 chr2B 81.579 152 28 0 3598 3749 43049001 43048850 3.950000e-25 126.0
17 TraesCS1B01G172500 chr6D 100.000 38 0 0 3115 3152 93538524 93538487 1.880000e-08 71.3
18 TraesCS1B01G172500 chr4D 95.349 43 1 1 3115 3156 507778226 507778268 2.430000e-07 67.6
19 TraesCS1B01G172500 chr5A 95.122 41 1 1 3115 3154 580938266 580938306 3.140000e-06 63.9
20 TraesCS1B01G172500 chr3B 95.122 41 1 1 3115 3154 688162638 688162678 3.140000e-06 63.9
21 TraesCS1B01G172500 chr7D 94.872 39 1 1 3119 3156 33818038 33818076 4.060000e-05 60.2
22 TraesCS1B01G172500 chr7D 94.737 38 2 0 3119 3156 56996681 56996718 4.060000e-05 60.2
23 TraesCS1B01G172500 chr7D 87.500 48 6 0 3118 3165 41698048 41698001 5.250000e-04 56.5
24 TraesCS1B01G172500 chr3D 94.872 39 1 1 3116 3153 522308238 522308276 4.060000e-05 60.2


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 TraesCS1B01G172500 chr1B 307479979 307483741 3762 True 1729.2500 6024 92.282000 1 3763 4 chr1B.!!$R1 3762
1 TraesCS1B01G172500 chr1D 214599984 214603158 3174 True 1177.0250 3055 91.823250 1 3190 4 chr1D.!!$R1 3189
2 TraesCS1B01G172500 chr1A 272982606 272986626 4020 True 686.6375 2957 88.217375 1 3763 8 chr1A.!!$R1 3762

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
578 583 0.250166 GTCTAACGGTTGTGCCCTGT 60.250 55.0 3.07 0.0 0.0 4.00 F
1943 1998 0.107456 ACTTCTGCTGGACCACACTG 59.893 55.0 0.00 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2118 0.254638 TTCTCCCCCTCCTCCTCCTA 60.255 60.0 0.00 0.00 0.00 2.94 R
3617 4021 0.106894 AAGGTAGATAAGCCGGCAGC 59.893 55.0 31.54 16.56 44.25 5.25 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
40 41 7.721842 TCCTGTACAATTCTTGAACCATTGTAA 59.278 33.333 0.00 0.00 42.32 2.41
124 125 9.201989 TCACTCTACAATCTCATAACTTACCAT 57.798 33.333 0.00 0.00 0.00 3.55
141 142 7.380536 ACTTACCATACTATTTGTTGACGTCA 58.619 34.615 15.76 15.76 0.00 4.35
242 243 9.654663 GAAGTCTTTATTCTTGTAGGCTTCTTA 57.345 33.333 0.00 0.00 42.90 2.10
281 282 5.652994 TTGATTTAATGGTTGTGCCCTAC 57.347 39.130 0.00 0.00 36.04 3.18
308 309 4.786292 GCGCAATCACATTCATGTAATCGT 60.786 41.667 0.30 0.00 39.39 3.73
331 332 3.181575 GCAGTAAACCACGCAATTTTCAC 59.818 43.478 0.00 0.00 0.00 3.18
356 357 6.263168 CCAACATAAATCCTTACATGACCTCC 59.737 42.308 0.00 0.00 0.00 4.30
357 358 5.611374 ACATAAATCCTTACATGACCTCCG 58.389 41.667 0.00 0.00 0.00 4.63
431 436 1.455248 TTAACGGTTGTGCCCTATGC 58.545 50.000 3.07 0.00 41.77 3.14
447 452 3.058160 GCAGCGGCAATCACACCT 61.058 61.111 3.18 0.00 40.72 4.00
461 466 1.024046 ACACCTATGCAATTGCGCGA 61.024 50.000 24.58 8.69 45.83 5.87
467 472 0.523072 ATGCAATTGCGCGAGAAACT 59.477 45.000 24.58 0.00 45.83 2.66
495 500 9.311916 CACAGTTTTCATCAACAAAAATCCTTA 57.688 29.630 0.00 0.00 0.00 2.69
520 525 3.952323 TGACCTCCATACCTAAGAAGTCG 59.048 47.826 0.00 0.00 0.00 4.18
577 582 0.953960 GGTCTAACGGTTGTGCCCTG 60.954 60.000 3.07 0.00 0.00 4.45
578 583 0.250166 GTCTAACGGTTGTGCCCTGT 60.250 55.000 3.07 0.00 0.00 4.00
583 588 1.369692 CGGTTGTGCCCTGTGTAGA 59.630 57.895 0.00 0.00 0.00 2.59
589 594 2.124942 GCCCTGTGTAGAGCCAGC 60.125 66.667 0.00 0.00 0.00 4.85
598 603 2.592993 TAGAGCCAGCCACACCCAC 61.593 63.158 0.00 0.00 0.00 4.61
742 778 2.361230 CCAACGCCTTTCCCCCTC 60.361 66.667 0.00 0.00 0.00 4.30
743 779 2.434331 CAACGCCTTTCCCCCTCA 59.566 61.111 0.00 0.00 0.00 3.86
744 780 1.228429 CAACGCCTTTCCCCCTCAA 60.228 57.895 0.00 0.00 0.00 3.02
745 781 1.228459 AACGCCTTTCCCCCTCAAC 60.228 57.895 0.00 0.00 0.00 3.18
943 980 1.566211 CCATCTCCTCTCACACAGGT 58.434 55.000 0.00 0.00 32.20 4.00
1154 1191 2.071540 TGAGTTTCGCATCTTGCTGAG 58.928 47.619 0.00 0.00 42.25 3.35
1262 1299 1.758440 TTCTGCTGTGCGGGAAGAGT 61.758 55.000 0.00 0.00 35.34 3.24
1295 1332 2.685202 GGTCAACTACCTCAGCCCT 58.315 57.895 0.00 0.00 45.75 5.19
1379 1416 3.181454 CCCTCGGCAACAGGTAGAATAAT 60.181 47.826 0.00 0.00 34.28 1.28
1380 1417 4.058817 CCTCGGCAACAGGTAGAATAATC 58.941 47.826 0.00 0.00 32.28 1.75
1514 1553 7.078249 TGTACTCCATATATTGCCTTCATGT 57.922 36.000 0.00 0.00 0.00 3.21
1585 1640 1.142870 ACTGTCTTGCCAGCCTACAAA 59.857 47.619 0.00 0.00 35.83 2.83
1822 1877 2.771943 AGATTCCATCTCGTTTGGCCTA 59.228 45.455 3.32 0.00 33.42 3.93
1943 1998 0.107456 ACTTCTGCTGGACCACACTG 59.893 55.000 0.00 0.00 0.00 3.66
1991 2046 4.074970 AGCGCCTCCATTAATCCTTATTG 58.925 43.478 2.29 0.00 0.00 1.90
2024 2079 0.462047 CGATCAGTACCCCAGTTGCC 60.462 60.000 0.00 0.00 0.00 4.52
2050 2105 9.559958 CGAATTCAAGAGCATTTGTAAATTACT 57.440 29.630 6.22 0.00 0.00 2.24
2070 2125 9.710818 AATTACTAAGTATCACAAGTAGGAGGA 57.289 33.333 0.00 0.00 0.00 3.71
2071 2126 8.749026 TTACTAAGTATCACAAGTAGGAGGAG 57.251 38.462 0.00 0.00 0.00 3.69
2072 2127 6.130569 ACTAAGTATCACAAGTAGGAGGAGG 58.869 44.000 0.00 0.00 0.00 4.30
2073 2128 4.883021 AGTATCACAAGTAGGAGGAGGA 57.117 45.455 0.00 0.00 0.00 3.71
2074 2129 4.798882 AGTATCACAAGTAGGAGGAGGAG 58.201 47.826 0.00 0.00 0.00 3.69
2075 2130 2.534042 TCACAAGTAGGAGGAGGAGG 57.466 55.000 0.00 0.00 0.00 4.30
2076 2131 1.007238 TCACAAGTAGGAGGAGGAGGG 59.993 57.143 0.00 0.00 0.00 4.30
2085 2140 0.397957 GAGGAGGAGGGGGAGAAGTC 60.398 65.000 0.00 0.00 0.00 3.01
2117 2172 7.606456 TCAGATTAAACCATCTCTACGCTTTTT 59.394 33.333 0.00 0.00 30.50 1.94
2118 2173 7.905493 CAGATTAAACCATCTCTACGCTTTTTC 59.095 37.037 0.00 0.00 30.50 2.29
2119 2174 4.663636 AAACCATCTCTACGCTTTTTCG 57.336 40.909 0.00 0.00 0.00 3.46
2120 2175 2.000447 ACCATCTCTACGCTTTTTCGC 59.000 47.619 0.00 0.00 0.00 4.70
2152 2207 3.550437 ACATCTCTACCCTGTGCATTC 57.450 47.619 0.00 0.00 0.00 2.67
2181 2236 5.882557 TCAAATCTTTGAAGTATCTGAGGCC 59.117 40.000 0.00 0.00 43.62 5.19
2198 2253 0.744874 GCCTGCATGCAGTTGATGAT 59.255 50.000 38.22 0.00 42.15 2.45
2201 2256 2.623416 CCTGCATGCAGTTGATGATGAT 59.377 45.455 38.22 0.00 42.15 2.45
2230 2285 3.637998 ACAGTTGCAGCTCTGAATTTG 57.362 42.857 19.76 2.45 35.84 2.32
2357 2415 4.408821 AAGCCAGCCGCCGATCAA 62.409 61.111 0.00 0.00 38.78 2.57
2434 2492 4.700365 CGTCGACGCTGGTGAGCA 62.700 66.667 26.59 0.00 46.62 4.26
2436 2494 3.295273 TCGACGCTGGTGAGCAGT 61.295 61.111 13.65 0.00 46.62 4.40
2450 2508 4.710695 CAGTACACGTCGCCGCCA 62.711 66.667 0.00 0.00 37.70 5.69
2658 2725 1.524621 GGTGCCATGGACGAGGATG 60.525 63.158 18.40 0.00 0.00 3.51
2768 2835 3.877508 ACTTGCCAGAGTTGTAACAGTTC 59.122 43.478 0.00 0.00 0.00 3.01
2773 2840 4.552184 GCCAGAGTTGTAACAGTTCGAAAC 60.552 45.833 0.00 0.00 0.00 2.78
2851 3001 1.177401 GGTGAGAAATTGAGGTGCCC 58.823 55.000 0.00 0.00 0.00 5.36
2903 3053 2.029288 CAGTCGGCAGTCGCAACAT 61.029 57.895 0.00 0.00 41.24 2.71
2906 3056 0.793861 GTCGGCAGTCGCAACATTTA 59.206 50.000 0.00 0.00 41.24 1.40
2907 3057 1.396996 GTCGGCAGTCGCAACATTTAT 59.603 47.619 0.00 0.00 41.24 1.40
2911 3067 3.059306 CGGCAGTCGCAACATTTATTTTG 59.941 43.478 0.00 0.00 41.24 2.44
2971 3127 4.887655 GGTATTAGCCACAACTATTTGCCT 59.112 41.667 0.00 0.00 36.00 4.75
3053 3334 9.152595 GTCTCCTCGTATTTTAGTCAGATTTTT 57.847 33.333 0.00 0.00 0.00 1.94
3077 3358 9.542462 TTTATCATGATTTTAAGTACTCCTCCG 57.458 33.333 14.65 0.00 0.00 4.63
3078 3359 6.540438 TCATGATTTTAAGTACTCCTCCGT 57.460 37.500 0.00 0.00 0.00 4.69
3080 3361 8.070034 TCATGATTTTAAGTACTCCTCCGTTA 57.930 34.615 0.00 0.00 0.00 3.18
3193 3553 4.141135 TCAAAACATTGGGTCACCTCCTAA 60.141 41.667 0.00 0.00 37.76 2.69
3201 3561 2.509964 GGGTCACCTCCTAATGGAATGT 59.490 50.000 0.00 0.00 42.66 2.71
3212 3572 5.719563 TCCTAATGGAATGTGTCTACACTCA 59.280 40.000 13.95 7.84 42.40 3.41
3214 3574 3.297830 TGGAATGTGTCTACACTCACG 57.702 47.619 13.95 0.00 46.55 4.35
3219 3579 1.335810 TGTGTCTACACTCACGTCACC 59.664 52.381 13.95 0.00 46.55 4.02
3221 3581 1.878088 TGTCTACACTCACGTCACCTC 59.122 52.381 0.00 0.00 0.00 3.85
3232 3592 0.652592 CGTCACCTCGCATGAAATCC 59.347 55.000 0.00 0.00 0.00 3.01
3240 3600 0.933097 CGCATGAAATCCTCTCGTGG 59.067 55.000 0.00 0.00 31.61 4.94
3241 3601 1.740380 CGCATGAAATCCTCTCGTGGT 60.740 52.381 0.00 0.00 31.61 4.16
3242 3602 1.667724 GCATGAAATCCTCTCGTGGTG 59.332 52.381 0.00 0.00 31.61 4.17
3243 3603 1.667724 CATGAAATCCTCTCGTGGTGC 59.332 52.381 0.00 0.00 0.00 5.01
3244 3604 0.036388 TGAAATCCTCTCGTGGTGCC 60.036 55.000 0.00 0.00 0.00 5.01
3245 3605 1.079127 AAATCCTCTCGTGGTGCCG 60.079 57.895 0.00 0.00 0.00 5.69
3246 3606 2.521958 AAATCCTCTCGTGGTGCCGG 62.522 60.000 0.00 0.00 0.00 6.13
3247 3607 3.957435 ATCCTCTCGTGGTGCCGGA 62.957 63.158 5.05 0.00 0.00 5.14
3248 3608 3.461773 CCTCTCGTGGTGCCGGAT 61.462 66.667 5.05 0.00 0.00 4.18
3249 3609 2.579201 CTCTCGTGGTGCCGGATT 59.421 61.111 5.05 0.00 0.00 3.01
3250 3610 1.811266 CTCTCGTGGTGCCGGATTG 60.811 63.158 5.05 0.00 0.00 2.67
3251 3611 3.499737 CTCGTGGTGCCGGATTGC 61.500 66.667 5.05 0.00 0.00 3.56
3254 3614 3.747976 GTGGTGCCGGATTGCCAC 61.748 66.667 5.05 13.41 43.52 5.01
3257 3617 4.740822 GTGCCGGATTGCCACCCT 62.741 66.667 5.05 0.00 0.00 4.34
3258 3618 4.424711 TGCCGGATTGCCACCCTC 62.425 66.667 5.05 0.00 0.00 4.30
3260 3620 4.506255 CCGGATTGCCACCCTCCC 62.506 72.222 0.00 0.00 0.00 4.30
3261 3621 4.506255 CGGATTGCCACCCTCCCC 62.506 72.222 0.00 0.00 0.00 4.81
3617 4021 3.365291 TACTAGGCAAGCGTGGGCG 62.365 63.158 0.79 0.00 46.35 6.13
3650 4054 8.154856 GCTTATCTACCTTTATCCATGTAACCA 58.845 37.037 0.00 0.00 0.00 3.67
3651 4055 9.712305 CTTATCTACCTTTATCCATGTAACCAG 57.288 37.037 0.00 0.00 0.00 4.00
3658 4062 5.772393 TTATCCATGTAACCAGGTGTTCT 57.228 39.130 0.00 0.00 38.42 3.01
3678 4082 1.377333 GTACTGGGGCTGAGCAACC 60.377 63.158 6.82 8.73 0.00 3.77
3690 4094 1.846712 GAGCAACCCCTCCTCTGCTT 61.847 60.000 0.00 0.00 44.93 3.91
3695 4099 1.062488 ACCCCTCCTCTGCTTGTTGT 61.062 55.000 0.00 0.00 0.00 3.32
3710 4114 3.485947 TGTTGTGTTTCTCTGTTGCAC 57.514 42.857 0.00 0.00 0.00 4.57
3718 4122 0.319728 TCTCTGTTGCACCTCTCAGC 59.680 55.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.703328 ACAACAATAGAACAAGACGACAAAAT 58.297 30.769 0.00 0.00 0.00 1.82
47 48 6.043327 TCACAACAACAATAGAACAAGACG 57.957 37.500 0.00 0.00 0.00 4.18
124 125 6.864685 ACGATTCTTGACGTCAACAAATAGTA 59.135 34.615 27.49 15.52 38.34 1.82
141 142 2.948315 GGGGTACTCTACGACGATTCTT 59.052 50.000 0.00 0.00 0.00 2.52
242 243 2.355197 TCAATGTGAATGCCGATCGTT 58.645 42.857 15.09 1.20 0.00 3.85
281 282 2.030823 ACATGAATGTGATTGCGCTACG 59.969 45.455 9.73 0.00 40.03 3.51
308 309 3.181486 TGAAAATTGCGTGGTTTACTGCA 60.181 39.130 0.00 0.00 37.16 4.41
321 322 7.671495 AAGGATTTATGTTGGTGAAAATTGC 57.329 32.000 0.00 0.00 0.00 3.56
331 332 6.263168 GGAGGTCATGTAAGGATTTATGTTGG 59.737 42.308 0.00 0.00 0.00 3.77
431 436 0.659427 CATAGGTGTGATTGCCGCTG 59.341 55.000 0.00 0.00 0.00 5.18
447 452 1.737236 AGTTTCTCGCGCAATTGCATA 59.263 42.857 28.77 12.89 42.21 3.14
467 472 8.474025 AGGATTTTTGTTGATGAAAACTGTGTA 58.526 29.630 0.00 0.00 0.00 2.90
495 500 5.281314 ACTTCTTAGGTATGGAGGTCATGT 58.719 41.667 0.00 0.00 37.30 3.21
520 525 5.828747 TCGTCAAGAAGCCTATGTATACAC 58.171 41.667 7.96 0.00 0.00 2.90
577 582 1.376037 GGTGTGGCTGGCTCTACAC 60.376 63.158 12.88 12.88 41.90 2.90
578 583 2.592993 GGGTGTGGCTGGCTCTACA 61.593 63.158 2.00 0.00 0.00 2.74
589 594 2.049248 GCAATTGCGTGGGTGTGG 60.049 61.111 15.87 0.00 0.00 4.17
627 633 3.571571 GGTGTAAGGATTTTTCGTTGCC 58.428 45.455 0.00 0.00 0.00 4.52
783 820 1.041726 CGTTGTTGCCGATTTCGTTG 58.958 50.000 0.00 0.00 37.74 4.10
1154 1191 4.222847 GGGAGTCCATCGTCGGCC 62.223 72.222 12.30 0.00 0.00 6.13
1249 1286 1.300620 CGACAACTCTTCCCGCACA 60.301 57.895 0.00 0.00 0.00 4.57
1295 1332 1.971167 GTTGCCCCGCTTGATGTCA 60.971 57.895 0.00 0.00 0.00 3.58
1534 1573 9.407380 TGTTCATAGCAATTTATGGAGTACAAT 57.593 29.630 0.00 0.00 32.95 2.71
1535 1574 8.800370 TGTTCATAGCAATTTATGGAGTACAA 57.200 30.769 0.00 0.00 32.95 2.41
1585 1640 1.705186 ACTGACTAGGCCCACAACAAT 59.295 47.619 0.00 0.00 0.00 2.71
1680 1735 6.858478 GCTTTTGTCTTCTTTGGAGTATTGTC 59.142 38.462 0.00 0.00 0.00 3.18
1822 1877 3.385749 CTCCACTGGCCGCCGTTAT 62.386 63.158 4.58 0.00 0.00 1.89
1943 1998 1.066787 GTAGCCTGGACTCTTGGACAC 60.067 57.143 0.00 0.00 0.00 3.67
1972 2027 6.623767 GCGATTCAATAAGGATTAATGGAGGC 60.624 42.308 0.00 0.00 32.42 4.70
1991 2046 3.055591 ACTGATCGATCATGTGCGATTC 58.944 45.455 27.43 15.32 46.13 2.52
2024 2079 9.559958 AGTAATTTACAAATGCTCTTGAATTCG 57.440 29.630 9.15 0.00 0.00 3.34
2050 2105 6.337185 TCCTCCTCCTACTTGTGATACTTA 57.663 41.667 0.00 0.00 0.00 2.24
2051 2106 5.205056 CTCCTCCTCCTACTTGTGATACTT 58.795 45.833 0.00 0.00 0.00 2.24
2052 2107 4.386986 CCTCCTCCTCCTACTTGTGATACT 60.387 50.000 0.00 0.00 0.00 2.12
2053 2108 3.892588 CCTCCTCCTCCTACTTGTGATAC 59.107 52.174 0.00 0.00 0.00 2.24
2054 2109 3.117093 CCCTCCTCCTCCTACTTGTGATA 60.117 52.174 0.00 0.00 0.00 2.15
2055 2110 2.359781 CCCTCCTCCTCCTACTTGTGAT 60.360 54.545 0.00 0.00 0.00 3.06
2056 2111 1.007238 CCCTCCTCCTCCTACTTGTGA 59.993 57.143 0.00 0.00 0.00 3.58
2057 2112 1.490574 CCCTCCTCCTCCTACTTGTG 58.509 60.000 0.00 0.00 0.00 3.33
2058 2113 0.340208 CCCCTCCTCCTCCTACTTGT 59.660 60.000 0.00 0.00 0.00 3.16
2059 2114 0.399233 CCCCCTCCTCCTCCTACTTG 60.399 65.000 0.00 0.00 0.00 3.16
2061 2116 1.002242 CTCCCCCTCCTCCTCCTACT 61.002 65.000 0.00 0.00 0.00 2.57
2062 2117 1.000041 TCTCCCCCTCCTCCTCCTAC 61.000 65.000 0.00 0.00 0.00 3.18
2063 2118 0.254638 TTCTCCCCCTCCTCCTCCTA 60.255 60.000 0.00 0.00 0.00 2.94
2064 2119 1.550374 TTCTCCCCCTCCTCCTCCT 60.550 63.158 0.00 0.00 0.00 3.69
2065 2120 1.074850 CTTCTCCCCCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
2066 2121 0.397957 GACTTCTCCCCCTCCTCCTC 60.398 65.000 0.00 0.00 0.00 3.71
2067 2122 1.707200 GACTTCTCCCCCTCCTCCT 59.293 63.158 0.00 0.00 0.00 3.69
2068 2123 1.758906 CGACTTCTCCCCCTCCTCC 60.759 68.421 0.00 0.00 0.00 4.30
2069 2124 1.000612 ACGACTTCTCCCCCTCCTC 59.999 63.158 0.00 0.00 0.00 3.71
2070 2125 1.305381 CACGACTTCTCCCCCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
2071 2126 3.020237 GCACGACTTCTCCCCCTCC 62.020 68.421 0.00 0.00 0.00 4.30
2072 2127 1.545706 AAGCACGACTTCTCCCCCTC 61.546 60.000 0.00 0.00 30.77 4.30
2073 2128 1.536662 AAGCACGACTTCTCCCCCT 60.537 57.895 0.00 0.00 30.77 4.79
2074 2129 3.069778 AAGCACGACTTCTCCCCC 58.930 61.111 0.00 0.00 30.77 5.40
2085 2140 4.872691 AGAGATGGTTTAATCTGAAGCACG 59.127 41.667 0.00 0.00 37.03 5.34
2139 2194 1.557371 TGATTCCGAATGCACAGGGTA 59.443 47.619 0.00 0.00 0.00 3.69
2140 2195 0.327924 TGATTCCGAATGCACAGGGT 59.672 50.000 0.00 0.00 0.00 4.34
2142 2197 3.379372 AGATTTGATTCCGAATGCACAGG 59.621 43.478 0.00 0.00 0.00 4.00
2152 2207 8.201554 TCAGATACTTCAAAGATTTGATTCCG 57.798 34.615 8.72 2.08 45.65 4.30
2270 2328 4.980805 TCGTTGTCAGTGCGCCCC 62.981 66.667 4.18 0.00 0.00 5.80
2379 2437 1.510480 GCCTGCTTGCGTGACTTCTT 61.510 55.000 0.00 0.00 0.00 2.52
2427 2485 2.087009 GCGACGTGTACTGCTCACC 61.087 63.158 0.00 0.00 32.86 4.02
2499 2557 4.873129 CGAGGATGACACCGCCGG 62.873 72.222 0.00 0.00 34.73 6.13
2658 2725 1.601171 AGCTCATCACCAGGCTCAC 59.399 57.895 0.00 0.00 0.00 3.51
2851 3001 1.257743 TCCCTCGTCAAGAAGGTGAG 58.742 55.000 0.00 0.00 32.21 3.51
2928 3084 7.744087 ATACCGCTGCATTTGATTAATTCTA 57.256 32.000 0.00 0.00 0.00 2.10
2940 3096 1.308998 GTGGCTAATACCGCTGCATT 58.691 50.000 0.00 0.00 37.24 3.56
2971 3127 5.165961 ACTAGTGCAGAAAGGCAAGAATA 57.834 39.130 0.00 0.00 46.93 1.75
3005 3286 5.757988 ACTAGTAAAGGAGGACTGAGGTAG 58.242 45.833 0.00 0.00 0.00 3.18
3006 3287 5.491800 AGACTAGTAAAGGAGGACTGAGGTA 59.508 44.000 0.00 0.00 0.00 3.08
3053 3334 8.246430 ACGGAGGAGTACTTAAAATCATGATA 57.754 34.615 9.04 0.00 0.00 2.15
3077 3358 6.354362 GTCTAAAACGCCGTACAAAAGTTAAC 59.646 38.462 0.00 0.00 0.00 2.01
3078 3359 6.036517 TGTCTAAAACGCCGTACAAAAGTTAA 59.963 34.615 0.00 0.00 0.00 2.01
3080 3361 4.332268 TGTCTAAAACGCCGTACAAAAGTT 59.668 37.500 0.00 0.00 0.00 2.66
3092 3374 4.756502 ACTCCCTCTAATGTCTAAAACGC 58.243 43.478 0.00 0.00 0.00 4.84
3212 3572 1.359848 GATTTCATGCGAGGTGACGT 58.640 50.000 0.00 0.00 35.59 4.34
3214 3574 1.936547 GAGGATTTCATGCGAGGTGAC 59.063 52.381 0.00 0.00 0.00 3.67
3219 3579 1.857217 CACGAGAGGATTTCATGCGAG 59.143 52.381 0.00 0.00 0.00 5.03
3221 3581 0.933097 CCACGAGAGGATTTCATGCG 59.067 55.000 0.00 0.00 0.00 4.73
3232 3592 1.811266 CAATCCGGCACCACGAGAG 60.811 63.158 0.00 0.00 35.47 3.20
3243 3603 4.506255 GGGAGGGTGGCAATCCGG 62.506 72.222 0.00 0.00 33.68 5.14
3244 3604 4.506255 GGGGAGGGTGGCAATCCG 62.506 72.222 8.15 0.00 33.68 4.18
3617 4021 0.106894 AAGGTAGATAAGCCGGCAGC 59.893 55.000 31.54 16.56 44.25 5.25
3618 4022 2.622064 AAAGGTAGATAAGCCGGCAG 57.378 50.000 31.54 0.00 0.00 4.85
3619 4023 3.007614 GGATAAAGGTAGATAAGCCGGCA 59.992 47.826 31.54 9.64 0.00 5.69
3650 4054 0.400594 GCCCCAGTACAAGAACACCT 59.599 55.000 0.00 0.00 0.00 4.00
3651 4055 0.400594 AGCCCCAGTACAAGAACACC 59.599 55.000 0.00 0.00 0.00 4.16
3658 4062 0.250727 GTTGCTCAGCCCCAGTACAA 60.251 55.000 0.00 0.00 0.00 2.41
3678 4082 0.109342 ACACAACAAGCAGAGGAGGG 59.891 55.000 0.00 0.00 0.00 4.30
3680 4084 3.209410 AGAAACACAACAAGCAGAGGAG 58.791 45.455 0.00 0.00 0.00 3.69
3690 4094 2.163412 GGTGCAACAGAGAAACACAACA 59.837 45.455 0.00 0.00 39.98 3.33
3695 4099 2.170397 TGAGAGGTGCAACAGAGAAACA 59.830 45.455 3.64 0.00 39.98 2.83
3710 4114 1.085091 ACACTACGTACGCTGAGAGG 58.915 55.000 16.72 10.36 0.00 3.69
3718 4122 2.597305 GGCAAATCTCACACTACGTACG 59.403 50.000 15.01 15.01 0.00 3.67


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

AutoCloner maintained by Alex Coulton.