Multiple sequence alignment - TraesCS2D01G410400

Loading Multiple Alignment...

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 TraesCS2D01G410400 chr2D 100.000 4123 0 0 1 4123 524967742 524963620 0.000000e+00 7614.0
1 TraesCS2D01G410400 chr2D 94.545 110 3 1 3126 3232 524964510 524964401 2.550000e-37 167.0
2 TraesCS2D01G410400 chr2D 94.545 110 3 1 3233 3342 524964617 524964511 2.550000e-37 167.0
3 TraesCS2D01G410400 chr2A 93.043 3306 142 45 1 3232 670461805 670458514 0.000000e+00 4750.0
4 TraesCS2D01G410400 chr2A 96.782 435 14 0 3689 4123 670458151 670457717 0.000000e+00 726.0
5 TraesCS2D01G410400 chr2A 93.310 284 18 1 3407 3689 670458485 670458202 6.370000e-113 418.0
6 TraesCS2D01G410400 chr2A 92.899 169 8 4 3943 4110 765527804 765527969 4.120000e-60 243.0
7 TraesCS2D01G410400 chr2B 94.588 2975 108 21 1 2939 621065590 621062633 0.000000e+00 4553.0
8 TraesCS2D01G410400 chr2B 91.228 399 21 3 3714 4112 621055708 621055324 7.850000e-147 531.0
9 TraesCS2D01G410400 chr2B 94.426 305 12 3 2933 3232 621062530 621062226 8.070000e-127 464.0
10 TraesCS2D01G410400 chr2B 91.954 261 19 2 3233 3491 621062337 621062077 8.420000e-97 364.0
11 TraesCS2D01G410400 chr2B 90.777 206 16 2 3487 3689 621058281 621058076 5.250000e-69 272.0
12 TraesCS2D01G410400 chr2B 95.000 40 2 0 3689 3728 621058025 621057986 3.440000e-06 63.9
13 TraesCS2D01G410400 chr6D 94.512 164 7 2 3940 4103 431160831 431160670 6.840000e-63 252.0
14 TraesCS2D01G410400 chr6D 87.500 104 13 0 2288 2391 324514843 324514740 2.010000e-23 121.0
15 TraesCS2D01G410400 chr6D 87.838 74 7 1 421 494 14681992 14681921 7.340000e-13 86.1
16 TraesCS2D01G410400 chr7D 94.410 161 8 1 3943 4103 629832195 629832354 3.180000e-61 246.0
17 TraesCS2D01G410400 chr7D 89.855 69 6 1 420 487 80766937 80767005 2.040000e-13 87.9
18 TraesCS2D01G410400 chr6B 93.902 164 8 2 3940 4103 650598703 650598542 3.180000e-61 246.0
19 TraesCS2D01G410400 chr6B 92.442 172 9 4 3934 4103 132353406 132353575 4.120000e-60 243.0
20 TraesCS2D01G410400 chr6B 87.500 104 13 0 2288 2391 499022358 499022461 2.010000e-23 121.0
21 TraesCS2D01G410400 chr3B 93.333 165 9 2 3939 4103 68913642 68913480 4.120000e-60 243.0
22 TraesCS2D01G410400 chr3B 90.960 177 13 3 3928 4103 552226392 552226566 6.890000e-58 235.0
23 TraesCS2D01G410400 chr6A 84.000 125 20 0 2288 2412 461833051 461832927 2.010000e-23 121.0
24 TraesCS2D01G410400 chr3A 79.851 134 24 3 422 555 20556362 20556492 1.220000e-15 95.3
25 TraesCS2D01G410400 chr3A 91.176 68 5 1 426 493 522063857 522063791 1.580000e-14 91.6
26 TraesCS2D01G410400 chr7B 88.889 72 8 0 422 493 623563750 623563679 5.680000e-14 89.8
27 TraesCS2D01G410400 chr1A 91.045 67 5 1 421 487 554214596 554214531 5.680000e-14 89.8
28 TraesCS2D01G410400 chr4D 92.857 56 4 0 421 476 467118662 467118717 9.500000e-12 82.4
29 TraesCS2D01G410400 chr5D 93.182 44 3 0 433 476 352448649 352448606 9.570000e-07 65.8


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 TraesCS2D01G410400 chr2D 524963620 524967742 4122 True 2649.333333 7614 96.363333 1 4123 3 chr2D.!!$R1 4122
1 TraesCS2D01G410400 chr2A 670457717 670461805 4088 True 1964.666667 4750 94.378333 1 4123 3 chr2A.!!$R1 4122
2 TraesCS2D01G410400 chr2B 621055324 621065590 10266 True 1041.316667 4553 92.995500 1 4112 6 chr2B.!!$R1 4111

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
87 88 0.460284 CCTTGCTAAGACCGCGACAT 60.460 55.000 8.23 0.0 0.0 3.06 F
585 615 1.064906 AGCAATCCCAGTCATGGTGAG 60.065 52.381 0.00 0.0 46.1 3.51 F
1176 1253 1.068741 CCCTAACACCGGCTACATCTC 59.931 57.143 0.00 0.0 0.0 2.75 F
1714 1791 1.610873 GAGGACGAGGAGGAGGACT 59.389 63.158 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1098 1175 0.796927 GGTTCAAAGTACGGCTCTGC 59.203 55.000 0.00 0.00 0.00 4.26 R
1473 1550 1.747709 TAGACGAGAACTCCTTCCCG 58.252 55.000 0.00 0.00 34.02 5.14 R
2790 2867 1.304381 AATGCCGACCTGCAACCAT 60.304 52.632 0.00 0.00 45.84 3.55 R
3237 3432 0.465097 CCTGGATGGTGCACCTGATC 60.465 60.000 34.75 27.89 36.82 2.92 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
58 59 1.066143 CAGCCTCGTGGTAATCACCTT 60.066 52.381 5.26 0.00 45.98 3.50
80 81 1.581223 AGGTACCCCTTGCTAAGACC 58.419 55.000 8.74 0.00 38.13 3.85
87 88 0.460284 CCTTGCTAAGACCGCGACAT 60.460 55.000 8.23 0.00 0.00 3.06
97 98 2.494445 CGCGACATGTGGCCTCTA 59.506 61.111 24.71 0.00 0.00 2.43
117 118 2.831685 TATGTGAGCCACTTGACGTT 57.168 45.000 0.00 0.00 35.11 3.99
129 130 4.209288 CCACTTGACGTTAGAAGACAGTTG 59.791 45.833 9.21 0.00 0.00 3.16
209 210 1.532238 GGAATGGGGAGGGTGCTAC 59.468 63.158 0.00 0.00 0.00 3.58
289 297 6.095860 TGCTATGAAATCACAATCCAAAGAGG 59.904 38.462 0.00 0.00 39.47 3.69
352 360 1.552337 TGCAGAAGAGGAACTAGCAGG 59.448 52.381 0.00 0.00 41.55 4.85
358 366 1.896465 AGAGGAACTAGCAGGACACAC 59.104 52.381 0.00 0.00 41.55 3.82
390 406 9.231297 CTTTTCATGGTAGAGAAAAACAGGATA 57.769 33.333 0.00 0.00 41.55 2.59
487 507 5.972935 TCGGTCAAGTGACACAACATATAT 58.027 37.500 13.21 0.00 46.47 0.86
547 577 6.981762 ATATAATATCGACCGAGACTTCGT 57.018 37.500 0.00 0.00 45.28 3.85
585 615 1.064906 AGCAATCCCAGTCATGGTGAG 60.065 52.381 0.00 0.00 46.10 3.51
870 914 3.991051 CCCGACACTGCCGTCACT 61.991 66.667 0.00 0.00 35.54 3.41
1032 1078 2.104967 TCGTCCATGGTTAACGAGGAT 58.895 47.619 19.90 0.00 40.21 3.24
1056 1132 1.754803 CTGAACCGCCCTACTCATGTA 59.245 52.381 0.00 0.00 0.00 2.29
1098 1175 3.328237 ACTTAAGTGTTTGCGTTTCCG 57.672 42.857 7.48 0.00 37.07 4.30
1129 1206 6.401796 CCGTACTTTGAACCCTAAATTTCTCG 60.402 42.308 0.00 0.00 0.00 4.04
1170 1247 1.350071 TGTTTCCCTAACACCGGCTA 58.650 50.000 0.00 0.00 41.73 3.93
1176 1253 1.068741 CCCTAACACCGGCTACATCTC 59.931 57.143 0.00 0.00 0.00 2.75
1352 1429 4.586472 CGACGACGACGATCCCGG 62.586 72.222 15.32 0.00 42.66 5.73
1543 1620 2.756283 CGGGCGAAGAGGAGGACT 60.756 66.667 0.00 0.00 0.00 3.85
1714 1791 1.610873 GAGGACGAGGAGGAGGACT 59.389 63.158 0.00 0.00 0.00 3.85
1864 1941 1.769098 CTTCCCGATCGTCGTAGCGA 61.769 60.000 15.09 2.62 45.32 4.93
2605 2682 4.487412 CGTCCCCGTCGCTGTACC 62.487 72.222 0.00 0.00 0.00 3.34
3069 3262 4.085721 GCTAGCTAGTACGTAATTTGCACG 60.086 45.833 21.62 11.44 44.80 5.34
3160 3355 1.134401 ACCATCCAGGCATCACTTACG 60.134 52.381 0.00 0.00 43.14 3.18
3161 3356 1.134401 CCATCCAGGCATCACTTACGT 60.134 52.381 0.00 0.00 0.00 3.57
3162 3357 2.205074 CATCCAGGCATCACTTACGTC 58.795 52.381 0.00 0.00 0.00 4.34
3163 3358 0.535335 TCCAGGCATCACTTACGTCC 59.465 55.000 0.00 0.00 0.00 4.79
3164 3359 0.462047 CCAGGCATCACTTACGTCCC 60.462 60.000 0.00 0.00 0.00 4.46
3165 3360 0.462047 CAGGCATCACTTACGTCCCC 60.462 60.000 0.00 0.00 0.00 4.81
3166 3361 1.153229 GGCATCACTTACGTCCCCC 60.153 63.158 0.00 0.00 0.00 5.40
3167 3362 1.623542 GGCATCACTTACGTCCCCCT 61.624 60.000 0.00 0.00 0.00 4.79
3168 3363 0.252197 GCATCACTTACGTCCCCCTT 59.748 55.000 0.00 0.00 0.00 3.95
3169 3364 1.483415 GCATCACTTACGTCCCCCTTA 59.517 52.381 0.00 0.00 0.00 2.69
3170 3365 2.483188 GCATCACTTACGTCCCCCTTAG 60.483 54.545 0.00 0.00 0.00 2.18
3171 3366 2.610438 TCACTTACGTCCCCCTTAGT 57.390 50.000 0.00 0.00 0.00 2.24
3172 3367 2.173519 TCACTTACGTCCCCCTTAGTG 58.826 52.381 0.00 0.00 35.51 2.74
3173 3368 0.900421 ACTTACGTCCCCCTTAGTGC 59.100 55.000 0.00 0.00 0.00 4.40
3174 3369 1.192428 CTTACGTCCCCCTTAGTGCT 58.808 55.000 0.00 0.00 0.00 4.40
3175 3370 1.553704 CTTACGTCCCCCTTAGTGCTT 59.446 52.381 0.00 0.00 0.00 3.91
3176 3371 2.530460 TACGTCCCCCTTAGTGCTTA 57.470 50.000 0.00 0.00 0.00 3.09
3177 3372 1.875488 ACGTCCCCCTTAGTGCTTAT 58.125 50.000 0.00 0.00 0.00 1.73
3178 3373 3.036452 ACGTCCCCCTTAGTGCTTATA 57.964 47.619 0.00 0.00 0.00 0.98
3179 3374 3.584294 ACGTCCCCCTTAGTGCTTATAT 58.416 45.455 0.00 0.00 0.00 0.86
3180 3375 3.577415 ACGTCCCCCTTAGTGCTTATATC 59.423 47.826 0.00 0.00 0.00 1.63
3181 3376 3.576982 CGTCCCCCTTAGTGCTTATATCA 59.423 47.826 0.00 0.00 0.00 2.15
3182 3377 4.039973 CGTCCCCCTTAGTGCTTATATCAA 59.960 45.833 0.00 0.00 0.00 2.57
3183 3378 5.280011 CGTCCCCCTTAGTGCTTATATCAAT 60.280 44.000 0.00 0.00 0.00 2.57
3184 3379 6.070995 CGTCCCCCTTAGTGCTTATATCAATA 60.071 42.308 0.00 0.00 0.00 1.90
3185 3380 7.364762 CGTCCCCCTTAGTGCTTATATCAATAT 60.365 40.741 0.00 0.00 0.00 1.28
3186 3381 8.329502 GTCCCCCTTAGTGCTTATATCAATATT 58.670 37.037 0.00 0.00 0.00 1.28
3187 3382 9.569074 TCCCCCTTAGTGCTTATATCAATATTA 57.431 33.333 0.00 0.00 0.00 0.98
3188 3383 9.838339 CCCCCTTAGTGCTTATATCAATATTAG 57.162 37.037 0.00 0.00 0.00 1.73
3189 3384 9.838339 CCCCTTAGTGCTTATATCAATATTAGG 57.162 37.037 0.00 0.00 0.00 2.69
3202 3397 9.692325 ATATCAATATTAGGATCCTTTTGAGGC 57.308 33.333 22.03 0.00 0.00 4.70
3203 3398 5.997746 TCAATATTAGGATCCTTTTGAGGCG 59.002 40.000 22.03 2.59 0.00 5.52
3204 3399 5.825593 ATATTAGGATCCTTTTGAGGCGA 57.174 39.130 22.03 0.00 0.00 5.54
3205 3400 2.981859 TAGGATCCTTTTGAGGCGAC 57.018 50.000 22.03 0.00 0.00 5.19
3206 3401 0.984230 AGGATCCTTTTGAGGCGACA 59.016 50.000 9.02 0.00 0.00 4.35
3207 3402 1.351017 AGGATCCTTTTGAGGCGACAA 59.649 47.619 9.02 0.00 0.00 3.18
3208 3403 2.025887 AGGATCCTTTTGAGGCGACAAT 60.026 45.455 9.02 0.00 0.00 2.71
3209 3404 3.199946 AGGATCCTTTTGAGGCGACAATA 59.800 43.478 9.02 0.00 0.00 1.90
3210 3405 4.137543 GGATCCTTTTGAGGCGACAATAT 58.862 43.478 3.84 0.00 0.00 1.28
3211 3406 4.580580 GGATCCTTTTGAGGCGACAATATT 59.419 41.667 3.84 0.00 0.00 1.28
3212 3407 5.763204 GGATCCTTTTGAGGCGACAATATTA 59.237 40.000 3.84 0.00 0.00 0.98
3213 3408 6.073003 GGATCCTTTTGAGGCGACAATATTAG 60.073 42.308 3.84 0.00 0.00 1.73
3214 3409 5.984725 TCCTTTTGAGGCGACAATATTAGA 58.015 37.500 0.00 0.00 0.00 2.10
3215 3410 6.411376 TCCTTTTGAGGCGACAATATTAGAA 58.589 36.000 0.00 0.00 0.00 2.10
3216 3411 7.054124 TCCTTTTGAGGCGACAATATTAGAAT 58.946 34.615 0.00 0.00 0.00 2.40
3217 3412 7.556275 TCCTTTTGAGGCGACAATATTAGAATT 59.444 33.333 0.00 0.00 0.00 2.17
3218 3413 8.190784 CCTTTTGAGGCGACAATATTAGAATTT 58.809 33.333 0.00 0.00 0.00 1.82
3219 3414 8.909708 TTTTGAGGCGACAATATTAGAATTTG 57.090 30.769 0.00 0.00 0.00 2.32
3220 3415 7.857734 TTGAGGCGACAATATTAGAATTTGA 57.142 32.000 0.00 0.00 0.00 2.69
3221 3416 7.482654 TGAGGCGACAATATTAGAATTTGAG 57.517 36.000 0.00 0.00 0.00 3.02
3222 3417 7.272244 TGAGGCGACAATATTAGAATTTGAGA 58.728 34.615 0.00 0.00 0.00 3.27
3223 3418 7.933577 TGAGGCGACAATATTAGAATTTGAGAT 59.066 33.333 0.00 0.00 0.00 2.75
3224 3419 8.682936 AGGCGACAATATTAGAATTTGAGATT 57.317 30.769 0.00 0.00 0.00 2.40
3225 3420 8.562892 AGGCGACAATATTAGAATTTGAGATTG 58.437 33.333 0.00 0.00 0.00 2.67
3226 3421 7.324616 GGCGACAATATTAGAATTTGAGATTGC 59.675 37.037 0.00 0.00 0.00 3.56
3227 3422 8.072567 GCGACAATATTAGAATTTGAGATTGCT 58.927 33.333 0.00 0.00 0.00 3.91
3243 3438 8.843885 TGAGATTGCTAATCAATAAGATCAGG 57.156 34.615 10.26 0.00 44.95 3.86
3244 3439 8.435187 TGAGATTGCTAATCAATAAGATCAGGT 58.565 33.333 10.26 0.00 44.95 4.00
3245 3440 8.618702 AGATTGCTAATCAATAAGATCAGGTG 57.381 34.615 10.26 0.00 44.95 4.00
3246 3441 6.624352 TTGCTAATCAATAAGATCAGGTGC 57.376 37.500 0.00 0.00 35.39 5.01
3247 3442 5.683681 TGCTAATCAATAAGATCAGGTGCA 58.316 37.500 0.00 0.00 35.39 4.57
3248 3443 5.528690 TGCTAATCAATAAGATCAGGTGCAC 59.471 40.000 8.80 8.80 35.39 4.57
3249 3444 5.049129 GCTAATCAATAAGATCAGGTGCACC 60.049 44.000 29.22 29.22 35.39 5.01
3250 3445 3.998913 TCAATAAGATCAGGTGCACCA 57.001 42.857 36.39 18.76 38.89 4.17
3251 3446 4.508551 TCAATAAGATCAGGTGCACCAT 57.491 40.909 36.39 22.83 38.89 3.55
3252 3447 4.454678 TCAATAAGATCAGGTGCACCATC 58.545 43.478 36.39 28.82 38.89 3.51
3253 3448 3.498774 ATAAGATCAGGTGCACCATCC 57.501 47.619 36.39 21.41 38.89 3.51
3254 3449 0.994247 AAGATCAGGTGCACCATCCA 59.006 50.000 36.39 17.62 38.89 3.41
3255 3450 0.545171 AGATCAGGTGCACCATCCAG 59.455 55.000 36.39 19.92 38.89 3.86
3256 3451 0.465097 GATCAGGTGCACCATCCAGG 60.465 60.000 36.39 17.94 45.67 4.45
3257 3452 2.563013 ATCAGGTGCACCATCCAGGC 62.563 60.000 36.39 8.04 43.14 4.85
3258 3453 3.259314 AGGTGCACCATCCAGGCA 61.259 61.111 36.39 0.00 43.14 4.75
3259 3454 2.043652 GGTGCACCATCCAGGCAT 60.044 61.111 31.23 0.00 43.14 4.40
3260 3455 2.123428 GGTGCACCATCCAGGCATC 61.123 63.158 31.23 0.00 43.14 3.91
3261 3456 1.378911 GTGCACCATCCAGGCATCA 60.379 57.895 5.22 0.00 43.14 3.07
3262 3457 1.378911 TGCACCATCCAGGCATCAC 60.379 57.895 0.00 0.00 43.14 3.06
3263 3458 1.077212 GCACCATCCAGGCATCACT 60.077 57.895 0.00 0.00 43.14 3.41
3264 3459 0.682209 GCACCATCCAGGCATCACTT 60.682 55.000 0.00 0.00 43.14 3.16
3265 3460 1.408683 GCACCATCCAGGCATCACTTA 60.409 52.381 0.00 0.00 43.14 2.24
3266 3461 2.292267 CACCATCCAGGCATCACTTAC 58.708 52.381 0.00 0.00 43.14 2.34
3293 3488 8.329502 GTCCCCCTTAGTGCTTATATCAATATT 58.670 37.037 0.00 0.00 0.00 1.28
3374 3571 3.094572 CCGGTCTCCCTTAGTGTAAGAA 58.905 50.000 0.00 0.00 38.02 2.52
3377 3574 3.509184 GGTCTCCCTTAGTGTAAGAACGT 59.491 47.826 0.00 0.00 38.02 3.99
3388 3585 8.836268 TTAGTGTAAGAACGTTACAATTCCAT 57.164 30.769 7.81 0.00 36.74 3.41
3428 3625 6.015772 TCAGCCATTTTTAGGACAGTAAAACC 60.016 38.462 0.00 0.00 32.77 3.27
3436 3633 3.473625 AGGACAGTAAAACCGAAACCAG 58.526 45.455 0.00 0.00 0.00 4.00
3444 3641 1.053424 AACCGAAACCAGTCCTAGCA 58.947 50.000 0.00 0.00 0.00 3.49
3484 3681 5.595952 AGATTTGGGCCATTAGATCAAGAAC 59.404 40.000 7.26 0.00 0.00 3.01
3485 3682 3.297134 TGGGCCATTAGATCAAGAACC 57.703 47.619 0.00 0.00 0.00 3.62
3515 7512 1.227002 GACGGTCCGATCTTCAGCC 60.227 63.158 20.51 0.00 0.00 4.85
3517 7514 1.258445 ACGGTCCGATCTTCAGCCTT 61.258 55.000 20.51 0.00 0.00 4.35
3534 7531 3.538785 TTTCGCTAACTGGGCCGCA 62.539 57.895 0.00 0.00 0.00 5.69
3571 7568 4.157840 GCTACTCCGGTGGAAATTTTGAAT 59.842 41.667 8.63 0.00 0.00 2.57
3573 7570 3.895041 ACTCCGGTGGAAATTTTGAATGT 59.105 39.130 8.63 0.00 0.00 2.71
3683 7684 8.589701 AGAAAAGAAAAGAAAACTTCCTACCA 57.410 30.769 0.00 0.00 0.00 3.25
3751 10095 6.628175 GCTTTCCCTTTTAGTTGGATGGATTC 60.628 42.308 0.00 0.00 0.00 2.52
3805 10149 2.231716 TTCTGGTGCCTCTGCTACTA 57.768 50.000 0.00 0.00 38.71 1.82
4046 10390 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4103 10447 5.245526 TCTTATATTTAGGAACGGAGGGAGC 59.754 44.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.813896 CAACAAACTGACTGTGCGTG 58.186 50.000 0.00 0.00 0.00 5.34
35 36 2.420129 GGTGATTACCACGAGGCTGAAT 60.420 50.000 0.88 0.00 46.62 2.57
80 81 0.313987 TATAGAGGCCACATGTCGCG 59.686 55.000 9.41 0.00 0.00 5.87
97 98 3.334583 AACGTCAAGTGGCTCACATAT 57.665 42.857 7.86 0.00 36.74 1.78
117 118 5.869344 GTGATGCACATACAACTGTCTTCTA 59.131 40.000 0.00 0.00 34.08 2.10
129 130 2.684374 TGATGCCAAGTGATGCACATAC 59.316 45.455 0.00 0.00 40.88 2.39
177 178 2.424667 CCCATTCCCTGCAATACATGGA 60.425 50.000 13.71 0.00 40.91 3.41
179 180 1.965643 CCCCATTCCCTGCAATACATG 59.034 52.381 0.00 0.00 0.00 3.21
186 187 3.023116 CCCTCCCCATTCCCTGCA 61.023 66.667 0.00 0.00 0.00 4.41
188 189 3.010144 CACCCTCCCCATTCCCTG 58.990 66.667 0.00 0.00 0.00 4.45
262 263 7.315142 TCTTTGGATTGTGATTTCATAGCAAC 58.685 34.615 0.00 0.00 0.00 4.17
268 269 4.161001 GGCCTCTTTGGATTGTGATTTCAT 59.839 41.667 0.00 0.00 38.35 2.57
277 278 1.470285 CGCAATGGCCTCTTTGGATTG 60.470 52.381 3.32 4.72 38.35 2.67
289 297 1.268032 CGAATGTTCTACCGCAATGGC 60.268 52.381 0.00 0.00 43.94 4.40
358 366 3.325870 TCTCTACCATGAAAAGCACACG 58.674 45.455 0.00 0.00 0.00 4.49
547 577 7.336931 GGGATTGCTAAATCTGAGTGACTTAAA 59.663 37.037 0.00 0.00 41.74 1.52
558 588 4.277672 CCATGACTGGGATTGCTAAATCTG 59.722 45.833 0.00 0.00 41.74 2.90
585 615 3.321111 TCTCCATATTACCCTCTCGCAAC 59.679 47.826 0.00 0.00 0.00 4.17
617 651 9.692749 GGAAAAATTAGTTCCACTCCTTTAAAG 57.307 33.333 8.32 8.32 43.52 1.85
737 781 2.901051 ATCGTGCCCATCCGTTCGAC 62.901 60.000 0.00 0.00 0.00 4.20
870 914 0.902048 CTCTGAGGCAGTCCTGTCCA 60.902 60.000 0.00 1.75 44.46 4.02
1032 1078 1.229082 AGTAGGGCGGTTCAGTCCA 60.229 57.895 0.00 0.00 38.64 4.02
1056 1132 3.303938 ACCAGAGACGATGGAGATTCAT 58.696 45.455 6.04 0.00 40.51 2.57
1098 1175 0.796927 GGTTCAAAGTACGGCTCTGC 59.203 55.000 0.00 0.00 0.00 4.26
1106 1183 6.312487 GCGAGAAATTTAGGGTTCAAAGTAC 58.688 40.000 0.00 0.00 0.00 2.73
1170 1247 1.134580 CCATGACGCTCAAGGAGATGT 60.135 52.381 0.00 0.00 37.42 3.06
1176 1253 2.046023 TGGCCATGACGCTCAAGG 60.046 61.111 0.00 5.31 38.22 3.61
1473 1550 1.747709 TAGACGAGAACTCCTTCCCG 58.252 55.000 0.00 0.00 34.02 5.14
1574 1651 4.117661 ACGCGTCCTCCTCTTCGC 62.118 66.667 5.58 0.00 44.23 4.70
1869 1946 2.149578 GGCAGCATTATCGCTTGATCT 58.850 47.619 0.00 0.00 41.38 2.75
2790 2867 1.304381 AATGCCGACCTGCAACCAT 60.304 52.632 0.00 0.00 45.84 3.55
2829 2906 2.125912 CAGGCACTCTTCCCGTCG 60.126 66.667 0.00 0.00 34.60 5.12
3069 3262 4.024893 CGATCATACATACACACTTTGCCC 60.025 45.833 0.00 0.00 0.00 5.36
3160 3355 5.562298 TTGATATAAGCACTAAGGGGGAC 57.438 43.478 0.00 0.00 0.00 4.46
3161 3356 8.463055 AATATTGATATAAGCACTAAGGGGGA 57.537 34.615 0.00 0.00 0.00 4.81
3162 3357 9.838339 CTAATATTGATATAAGCACTAAGGGGG 57.162 37.037 0.00 0.00 0.00 5.40
3163 3358 9.838339 CCTAATATTGATATAAGCACTAAGGGG 57.162 37.037 0.00 0.00 0.00 4.79
3176 3371 9.692325 GCCTCAAAAGGATCCTAATATTGATAT 57.308 33.333 16.55 0.00 46.67 1.63
3177 3372 7.824289 CGCCTCAAAAGGATCCTAATATTGATA 59.176 37.037 16.55 3.31 46.67 2.15
3178 3373 6.656693 CGCCTCAAAAGGATCCTAATATTGAT 59.343 38.462 16.55 0.00 46.67 2.57
3179 3374 5.997746 CGCCTCAAAAGGATCCTAATATTGA 59.002 40.000 16.55 19.87 46.67 2.57
3180 3375 5.997746 TCGCCTCAAAAGGATCCTAATATTG 59.002 40.000 16.55 16.99 46.67 1.90
3181 3376 5.998363 GTCGCCTCAAAAGGATCCTAATATT 59.002 40.000 16.55 2.06 46.67 1.28
3182 3377 5.071788 TGTCGCCTCAAAAGGATCCTAATAT 59.928 40.000 16.55 0.00 46.67 1.28
3183 3378 4.407621 TGTCGCCTCAAAAGGATCCTAATA 59.592 41.667 16.55 0.03 46.67 0.98
3184 3379 3.199946 TGTCGCCTCAAAAGGATCCTAAT 59.800 43.478 16.55 4.18 46.67 1.73
3185 3380 2.569853 TGTCGCCTCAAAAGGATCCTAA 59.430 45.455 16.55 0.08 46.67 2.69
3186 3381 2.184533 TGTCGCCTCAAAAGGATCCTA 58.815 47.619 16.55 0.00 46.67 2.94
3187 3382 0.984230 TGTCGCCTCAAAAGGATCCT 59.016 50.000 9.02 9.02 46.67 3.24
3188 3383 1.821216 TTGTCGCCTCAAAAGGATCC 58.179 50.000 2.48 2.48 46.67 3.36
3189 3384 5.757850 AATATTGTCGCCTCAAAAGGATC 57.242 39.130 0.00 0.00 46.67 3.36
3190 3385 6.591935 TCTAATATTGTCGCCTCAAAAGGAT 58.408 36.000 0.00 0.00 46.67 3.24
3191 3386 5.984725 TCTAATATTGTCGCCTCAAAAGGA 58.015 37.500 0.00 0.00 46.67 3.36
3192 3387 6.677781 TTCTAATATTGTCGCCTCAAAAGG 57.322 37.500 0.00 0.00 46.44 3.11
3193 3388 9.013490 CAAATTCTAATATTGTCGCCTCAAAAG 57.987 33.333 0.00 0.00 0.00 2.27
3194 3389 8.735315 TCAAATTCTAATATTGTCGCCTCAAAA 58.265 29.630 0.00 0.00 0.00 2.44
3195 3390 8.275015 TCAAATTCTAATATTGTCGCCTCAAA 57.725 30.769 0.00 0.00 0.00 2.69
3196 3391 7.768582 TCTCAAATTCTAATATTGTCGCCTCAA 59.231 33.333 0.00 0.00 0.00 3.02
3197 3392 7.272244 TCTCAAATTCTAATATTGTCGCCTCA 58.728 34.615 0.00 0.00 0.00 3.86
3198 3393 7.715265 TCTCAAATTCTAATATTGTCGCCTC 57.285 36.000 0.00 0.00 0.00 4.70
3199 3394 8.562892 CAATCTCAAATTCTAATATTGTCGCCT 58.437 33.333 0.00 0.00 0.00 5.52
3200 3395 7.324616 GCAATCTCAAATTCTAATATTGTCGCC 59.675 37.037 0.00 0.00 0.00 5.54
3201 3396 8.072567 AGCAATCTCAAATTCTAATATTGTCGC 58.927 33.333 0.00 0.00 0.00 5.19
3217 3412 9.281371 CCTGATCTTATTGATTAGCAATCTCAA 57.719 33.333 0.00 2.97 43.64 3.02
3218 3413 8.435187 ACCTGATCTTATTGATTAGCAATCTCA 58.565 33.333 0.00 0.00 43.64 3.27
3219 3414 8.719648 CACCTGATCTTATTGATTAGCAATCTC 58.280 37.037 0.00 0.00 43.64 2.75
3220 3415 7.174599 GCACCTGATCTTATTGATTAGCAATCT 59.825 37.037 0.00 0.00 43.64 2.40
3221 3416 7.040892 TGCACCTGATCTTATTGATTAGCAATC 60.041 37.037 0.00 0.00 43.64 2.67
3223 3418 6.038603 GTGCACCTGATCTTATTGATTAGCAA 59.961 38.462 5.22 0.00 37.44 3.91
3224 3419 5.528690 GTGCACCTGATCTTATTGATTAGCA 59.471 40.000 5.22 0.00 37.44 3.49
3225 3420 5.049129 GGTGCACCTGATCTTATTGATTAGC 60.049 44.000 29.12 0.00 37.44 3.09
3226 3421 6.057533 TGGTGCACCTGATCTTATTGATTAG 58.942 40.000 34.75 0.00 38.19 1.73
3227 3422 6.000246 TGGTGCACCTGATCTTATTGATTA 58.000 37.500 34.75 7.38 34.41 1.75
3228 3423 4.858850 TGGTGCACCTGATCTTATTGATT 58.141 39.130 34.75 0.00 34.41 2.57
3229 3424 4.508551 TGGTGCACCTGATCTTATTGAT 57.491 40.909 34.75 0.00 35.97 2.57
3230 3425 3.998913 TGGTGCACCTGATCTTATTGA 57.001 42.857 34.75 8.78 36.82 2.57
3231 3426 3.567164 GGATGGTGCACCTGATCTTATTG 59.433 47.826 34.75 0.00 36.82 1.90
3232 3427 3.202818 TGGATGGTGCACCTGATCTTATT 59.797 43.478 34.75 9.55 36.82 1.40
3233 3428 2.779430 TGGATGGTGCACCTGATCTTAT 59.221 45.455 34.75 19.08 36.82 1.73
3234 3429 2.171237 CTGGATGGTGCACCTGATCTTA 59.829 50.000 34.75 20.36 36.82 2.10
3235 3430 0.994247 TGGATGGTGCACCTGATCTT 59.006 50.000 34.75 13.63 36.82 2.40
3236 3431 0.545171 CTGGATGGTGCACCTGATCT 59.455 55.000 34.75 15.21 36.82 2.75
3237 3432 0.465097 CCTGGATGGTGCACCTGATC 60.465 60.000 34.75 27.89 36.82 2.92
3238 3433 1.611419 CCTGGATGGTGCACCTGAT 59.389 57.895 34.75 22.10 36.82 2.90
3239 3434 3.080641 CCTGGATGGTGCACCTGA 58.919 61.111 34.75 18.02 36.82 3.86
3240 3435 2.753043 GCCTGGATGGTGCACCTG 60.753 66.667 34.75 18.88 38.35 4.00
3241 3436 2.563013 GATGCCTGGATGGTGCACCT 62.563 60.000 34.75 21.08 37.92 4.00
3242 3437 2.043652 ATGCCTGGATGGTGCACC 60.044 61.111 29.67 29.67 37.92 5.01
3243 3438 1.378911 TGATGCCTGGATGGTGCAC 60.379 57.895 8.80 8.80 37.92 4.57
3244 3439 1.378911 GTGATGCCTGGATGGTGCA 60.379 57.895 0.00 0.00 39.68 4.57
3245 3440 0.682209 AAGTGATGCCTGGATGGTGC 60.682 55.000 0.00 0.00 38.35 5.01
3246 3441 2.292267 GTAAGTGATGCCTGGATGGTG 58.708 52.381 0.00 0.00 38.35 4.17
3247 3442 1.134401 CGTAAGTGATGCCTGGATGGT 60.134 52.381 0.00 0.00 38.35 3.55
3248 3443 1.586422 CGTAAGTGATGCCTGGATGG 58.414 55.000 0.00 0.00 39.35 3.51
3263 3458 1.648116 AAGCACTAAGGGGGACGTAA 58.352 50.000 0.00 0.00 0.00 3.18
3264 3459 2.530460 TAAGCACTAAGGGGGACGTA 57.470 50.000 0.00 0.00 0.00 3.57
3265 3460 1.875488 ATAAGCACTAAGGGGGACGT 58.125 50.000 0.00 0.00 0.00 4.34
3266 3461 3.576982 TGATATAAGCACTAAGGGGGACG 59.423 47.826 0.00 0.00 0.00 4.79
3308 3503 3.496884 TCAAATCCTAATATTGTCGCCGC 59.503 43.478 0.00 0.00 0.00 6.53
3309 3504 4.988540 TCTCAAATCCTAATATTGTCGCCG 59.011 41.667 0.00 0.00 0.00 6.46
3374 3571 4.080582 TCCTCATCCATGGAATTGTAACGT 60.081 41.667 20.67 0.00 0.00 3.99
3377 3574 4.726317 TCCTCCTCATCCATGGAATTGTAA 59.274 41.667 20.67 2.24 31.23 2.41
3388 3585 1.492176 GGCTGATTTCCTCCTCATCCA 59.508 52.381 0.00 0.00 29.93 3.41
3428 3625 3.190874 GAGAATGCTAGGACTGGTTTCG 58.809 50.000 0.00 0.00 0.00 3.46
3444 3641 6.346096 CCCAAATCTTCAAATGCATGAGAAT 58.654 36.000 12.77 0.92 0.00 2.40
3515 7512 2.750888 GCGGCCCAGTTAGCGAAAG 61.751 63.158 0.00 0.00 0.00 2.62
3517 7514 3.950794 CTGCGGCCCAGTTAGCGAA 62.951 63.158 11.85 0.00 36.79 4.70
3534 7531 0.842467 AGTAGCAGCCCCTTTGGACT 60.842 55.000 0.00 0.00 35.39 3.85
3571 7568 1.317613 GTCCAAATGCACCACAGACA 58.682 50.000 0.00 0.00 0.00 3.41
3573 7570 0.478072 AGGTCCAAATGCACCACAGA 59.522 50.000 0.00 0.00 34.80 3.41
3655 7655 9.222916 GTAGGAAGTTTTCTTTTCTTTTCTTCG 57.777 33.333 0.00 0.00 40.61 3.79
3683 7684 3.368739 GCAAGGTTTGGCAATATTGAGCT 60.369 43.478 19.73 9.85 0.00 4.09
3751 10095 3.328050 AGGACAAGTTAGTGGAAGGAAGG 59.672 47.826 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.