Multiple sequence alignment - TraesCS7A01G202500

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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 TraesCS7A01G202500 chr7A 100.000 2531 0 0 1 2531 164395914 164398444 0.000000e+00 4674.0
1 TraesCS7A01G202500 chr7A 98.515 404 6 0 180 583 104653365 104653768 0.000000e+00 713.0
2 TraesCS7A01G202500 chr7A 78.947 133 26 2 737 868 5154363 5154494 3.470000e-14 89.8
3 TraesCS7A01G202500 chr7B 93.333 1680 81 10 578 2229 125501191 125502867 0.000000e+00 2453.0
4 TraesCS7A01G202500 chr7B 91.613 310 17 2 2230 2531 125502898 125503206 1.080000e-113 420.0
5 TraesCS7A01G202500 chr7B 89.051 137 14 1 44 179 125501060 125501196 4.330000e-38 169.0
6 TraesCS7A01G202500 chr7D 92.693 1697 75 11 578 2229 163253332 163255024 0.000000e+00 2401.0
7 TraesCS7A01G202500 chr7D 95.695 302 12 1 2230 2531 163255061 163255361 3.790000e-133 484.0
8 TraesCS7A01G202500 chr7D 91.758 182 14 1 1 181 163253156 163253337 4.180000e-63 252.0
9 TraesCS7A01G202500 chr4A 98.547 413 6 0 171 583 620356780 620356368 0.000000e+00 730.0
10 TraesCS7A01G202500 chr1B 98.547 413 5 1 171 583 670857926 670858337 0.000000e+00 728.0
11 TraesCS7A01G202500 chr1B 98.280 407 6 1 177 583 19078729 19078324 0.000000e+00 712.0
12 TraesCS7A01G202500 chr1B 97.821 413 8 1 171 583 39719018 39718607 0.000000e+00 712.0
13 TraesCS7A01G202500 chr1B 97.094 413 12 0 171 583 591222239 591222651 0.000000e+00 697.0
14 TraesCS7A01G202500 chr4B 98.540 411 5 1 171 581 266060865 266060456 0.000000e+00 725.0
15 TraesCS7A01G202500 chr4B 97.337 413 11 0 171 583 300036653 300037065 0.000000e+00 702.0
16 TraesCS7A01G202500 chr3B 97.337 413 11 0 171 583 677604666 677604254 0.000000e+00 702.0


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 TraesCS7A01G202500 chr7A 164395914 164398444 2530 False 4674.000000 4674 100.000000 1 2531 1 chr7A.!!$F3 2530
1 TraesCS7A01G202500 chr7B 125501060 125503206 2146 False 1014.000000 2453 91.332333 44 2531 3 chr7B.!!$F1 2487
2 TraesCS7A01G202500 chr7D 163253156 163255361 2205 False 1045.666667 2401 93.382000 1 2531 3 chr7D.!!$F1 2530

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
83 84 0.530211 CTCTTGCTCCTCCATCGCAG 60.530 60.0 0.0 0.0 34.82 5.18 F
572 574 0.843984 CCGGGTGGTAGGATGGATTT 59.156 55.0 0.0 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1135 0.468226 ACAAAGGCGAGAAGGTCACA 59.532 50.0 0.0 0.0 0.00 3.58 R
2115 2149 0.179062 GATGGATCTGGCTCGTTGCT 60.179 55.0 0.0 0.0 42.39 3.91 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
36 37 2.489073 CCTTCCCTACAGCCACAAAACT 60.489 50.000 0.00 0.00 0.00 2.66
39 40 1.609208 CCTACAGCCACAAAACTGCT 58.391 50.000 0.00 0.00 37.42 4.24
68 69 4.335647 CCCCACTGTGCGCCTCTT 62.336 66.667 4.18 0.00 0.00 2.85
83 84 0.530211 CTCTTGCTCCTCCATCGCAG 60.530 60.000 0.00 0.00 34.82 5.18
89 90 2.821366 CCTCCATCGCAGTGCACC 60.821 66.667 16.83 0.00 0.00 5.01
90 91 2.046988 CTCCATCGCAGTGCACCA 60.047 61.111 16.83 0.00 0.00 4.17
221 223 6.759497 ATAGGACAAATGTTTCCTACAAGC 57.241 37.500 0.00 0.00 45.37 4.01
222 224 4.469657 AGGACAAATGTTTCCTACAAGCA 58.530 39.130 0.00 0.00 40.70 3.91
223 225 4.520492 AGGACAAATGTTTCCTACAAGCAG 59.480 41.667 0.00 0.00 40.70 4.24
224 226 4.278419 GGACAAATGTTTCCTACAAGCAGT 59.722 41.667 0.00 0.00 40.89 4.40
225 227 5.186996 ACAAATGTTTCCTACAAGCAGTG 57.813 39.130 0.00 0.00 40.89 3.66
226 228 4.037923 ACAAATGTTTCCTACAAGCAGTGG 59.962 41.667 0.00 0.00 40.89 4.00
227 229 3.508845 ATGTTTCCTACAAGCAGTGGT 57.491 42.857 0.00 0.00 40.89 4.16
228 230 4.634012 ATGTTTCCTACAAGCAGTGGTA 57.366 40.909 0.00 0.00 40.89 3.25
229 231 4.002906 TGTTTCCTACAAGCAGTGGTAG 57.997 45.455 0.00 0.00 37.36 3.18
230 232 3.389983 TGTTTCCTACAAGCAGTGGTAGT 59.610 43.478 0.00 0.00 36.17 2.73
231 233 4.141574 TGTTTCCTACAAGCAGTGGTAGTT 60.142 41.667 0.00 0.00 36.17 2.24
232 234 5.070714 TGTTTCCTACAAGCAGTGGTAGTTA 59.929 40.000 0.00 0.00 36.17 2.24
233 235 4.796038 TCCTACAAGCAGTGGTAGTTAC 57.204 45.455 0.00 0.00 36.17 2.50
234 236 3.512724 TCCTACAAGCAGTGGTAGTTACC 59.487 47.826 0.00 1.25 46.62 2.85
245 247 3.480505 GGTAGTTACCACCACTTGTGT 57.519 47.619 3.45 0.00 45.73 3.72
246 248 3.812262 GGTAGTTACCACCACTTGTGTT 58.188 45.455 3.45 0.00 45.73 3.32
247 249 4.201657 GGTAGTTACCACCACTTGTGTTT 58.798 43.478 3.45 0.00 45.73 2.83
248 250 4.641541 GGTAGTTACCACCACTTGTGTTTT 59.358 41.667 3.45 0.00 45.73 2.43
249 251 4.712122 AGTTACCACCACTTGTGTTTTG 57.288 40.909 0.00 0.00 43.85 2.44
250 252 4.083565 AGTTACCACCACTTGTGTTTTGT 58.916 39.130 0.00 0.00 43.85 2.83
251 253 5.254901 AGTTACCACCACTTGTGTTTTGTA 58.745 37.500 0.00 0.00 43.85 2.41
252 254 5.889289 AGTTACCACCACTTGTGTTTTGTAT 59.111 36.000 0.00 0.00 43.85 2.29
253 255 4.647424 ACCACCACTTGTGTTTTGTATG 57.353 40.909 0.00 0.00 43.85 2.39
254 256 4.020543 ACCACCACTTGTGTTTTGTATGT 58.979 39.130 0.00 0.00 43.85 2.29
255 257 4.464597 ACCACCACTTGTGTTTTGTATGTT 59.535 37.500 0.00 0.00 43.85 2.71
256 258 4.803088 CCACCACTTGTGTTTTGTATGTTG 59.197 41.667 0.00 0.00 43.85 3.33
257 259 5.406649 CACCACTTGTGTTTTGTATGTTGT 58.593 37.500 0.00 0.00 40.26 3.32
258 260 6.404844 CCACCACTTGTGTTTTGTATGTTGTA 60.405 38.462 0.00 0.00 43.85 2.41
259 261 7.199766 CACCACTTGTGTTTTGTATGTTGTAT 58.800 34.615 0.00 0.00 40.26 2.29
260 262 7.167302 CACCACTTGTGTTTTGTATGTTGTATG 59.833 37.037 0.00 0.00 40.26 2.39
261 263 7.147983 ACCACTTGTGTTTTGTATGTTGTATGT 60.148 33.333 0.00 0.00 0.00 2.29
262 264 8.346300 CCACTTGTGTTTTGTATGTTGTATGTA 58.654 33.333 0.00 0.00 0.00 2.29
263 265 9.381027 CACTTGTGTTTTGTATGTTGTATGTAG 57.619 33.333 0.00 0.00 0.00 2.74
264 266 9.116067 ACTTGTGTTTTGTATGTTGTATGTAGT 57.884 29.630 0.00 0.00 0.00 2.73
272 274 9.511144 TTTGTATGTTGTATGTAGTATCTGTCG 57.489 33.333 0.00 0.00 0.00 4.35
273 275 8.441312 TGTATGTTGTATGTAGTATCTGTCGA 57.559 34.615 0.00 0.00 0.00 4.20
274 276 8.895737 TGTATGTTGTATGTAGTATCTGTCGAA 58.104 33.333 0.00 0.00 0.00 3.71
275 277 9.726232 GTATGTTGTATGTAGTATCTGTCGAAA 57.274 33.333 0.00 0.00 0.00 3.46
276 278 8.630278 ATGTTGTATGTAGTATCTGTCGAAAC 57.370 34.615 0.00 0.00 0.00 2.78
277 279 7.031372 TGTTGTATGTAGTATCTGTCGAAACC 58.969 38.462 0.00 0.00 0.00 3.27
278 280 5.813717 TGTATGTAGTATCTGTCGAAACCG 58.186 41.667 0.00 0.00 0.00 4.44
279 281 5.585844 TGTATGTAGTATCTGTCGAAACCGA 59.414 40.000 0.00 0.00 0.00 4.69
280 282 4.611310 TGTAGTATCTGTCGAAACCGAG 57.389 45.455 0.00 0.00 36.66 4.63
281 283 4.256110 TGTAGTATCTGTCGAAACCGAGA 58.744 43.478 0.00 0.00 36.66 4.04
282 284 4.331992 TGTAGTATCTGTCGAAACCGAGAG 59.668 45.833 5.76 5.76 45.37 3.20
283 285 3.345414 AGTATCTGTCGAAACCGAGAGT 58.655 45.455 10.88 3.24 44.63 3.24
284 286 4.511527 AGTATCTGTCGAAACCGAGAGTA 58.488 43.478 10.88 2.48 44.63 2.59
285 287 5.124645 AGTATCTGTCGAAACCGAGAGTAT 58.875 41.667 10.88 6.90 44.63 2.12
286 288 3.759527 TCTGTCGAAACCGAGAGTATG 57.240 47.619 10.88 0.00 44.63 2.39
287 289 3.079578 TCTGTCGAAACCGAGAGTATGT 58.920 45.455 10.88 0.00 44.63 2.29
288 290 4.256110 TCTGTCGAAACCGAGAGTATGTA 58.744 43.478 10.88 0.00 44.63 2.29
289 291 4.093998 TCTGTCGAAACCGAGAGTATGTAC 59.906 45.833 10.88 0.00 44.63 2.90
290 292 3.181517 TGTCGAAACCGAGAGTATGTACG 60.182 47.826 0.00 0.00 36.66 3.67
291 293 3.002791 TCGAAACCGAGAGTATGTACGT 58.997 45.455 0.00 0.00 0.00 3.57
292 294 3.096461 CGAAACCGAGAGTATGTACGTG 58.904 50.000 0.00 0.00 0.00 4.49
293 295 3.425359 CGAAACCGAGAGTATGTACGTGT 60.425 47.826 0.00 0.00 0.00 4.49
294 296 4.201714 CGAAACCGAGAGTATGTACGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
295 297 4.871993 AACCGAGAGTATGTACGTGTAG 57.128 45.455 0.00 0.00 0.00 2.74
296 298 3.866651 ACCGAGAGTATGTACGTGTAGT 58.133 45.455 0.00 0.00 0.00 2.73
297 299 5.011090 ACCGAGAGTATGTACGTGTAGTA 57.989 43.478 0.00 0.00 0.00 1.82
298 300 5.605534 ACCGAGAGTATGTACGTGTAGTAT 58.394 41.667 0.00 0.00 37.69 2.12
299 301 5.464722 ACCGAGAGTATGTACGTGTAGTATG 59.535 44.000 0.00 0.00 37.69 2.39
300 302 5.464722 CCGAGAGTATGTACGTGTAGTATGT 59.535 44.000 0.00 0.00 37.69 2.29
301 303 6.642540 CCGAGAGTATGTACGTGTAGTATGTA 59.357 42.308 0.00 0.00 37.69 2.29
302 304 7.148836 CCGAGAGTATGTACGTGTAGTATGTAG 60.149 44.444 0.00 0.00 37.69 2.74
303 305 7.380870 CGAGAGTATGTACGTGTAGTATGTAGT 59.619 40.741 0.00 0.00 37.69 2.73
304 306 9.684448 GAGAGTATGTACGTGTAGTATGTAGTA 57.316 37.037 0.00 0.00 37.69 1.82
424 426 9.646427 TTCACAAATATAACAAAAACTATGGGC 57.354 29.630 0.00 0.00 0.00 5.36
425 427 9.030452 TCACAAATATAACAAAAACTATGGGCT 57.970 29.630 0.00 0.00 0.00 5.19
426 428 9.301153 CACAAATATAACAAAAACTATGGGCTC 57.699 33.333 0.00 0.00 0.00 4.70
427 429 9.030452 ACAAATATAACAAAAACTATGGGCTCA 57.970 29.630 0.00 0.00 0.00 4.26
432 434 5.520376 ACAAAAACTATGGGCTCATATGC 57.480 39.130 6.77 0.00 35.53 3.14
433 435 4.955450 ACAAAAACTATGGGCTCATATGCA 59.045 37.500 6.77 0.00 35.53 3.96
434 436 5.421693 ACAAAAACTATGGGCTCATATGCAA 59.578 36.000 6.77 0.00 35.53 4.08
435 437 6.098695 ACAAAAACTATGGGCTCATATGCAAT 59.901 34.615 6.77 0.00 35.53 3.56
436 438 6.736110 AAAACTATGGGCTCATATGCAATT 57.264 33.333 6.77 0.00 35.53 2.32
437 439 6.736110 AAACTATGGGCTCATATGCAATTT 57.264 33.333 6.77 1.06 35.53 1.82
438 440 6.736110 AACTATGGGCTCATATGCAATTTT 57.264 33.333 6.77 0.00 35.53 1.82
439 441 6.736110 ACTATGGGCTCATATGCAATTTTT 57.264 33.333 6.77 0.00 35.53 1.94
542 544 8.200120 CACATGGTAGTATATGAGATATGTGGG 58.800 40.741 0.00 0.00 39.22 4.61
543 545 7.345653 ACATGGTAGTATATGAGATATGTGGGG 59.654 40.741 0.00 0.00 0.00 4.96
544 546 6.811574 TGGTAGTATATGAGATATGTGGGGT 58.188 40.000 0.00 0.00 0.00 4.95
545 547 7.946381 TGGTAGTATATGAGATATGTGGGGTA 58.054 38.462 0.00 0.00 0.00 3.69
546 548 8.403474 TGGTAGTATATGAGATATGTGGGGTAA 58.597 37.037 0.00 0.00 0.00 2.85
547 549 8.693625 GGTAGTATATGAGATATGTGGGGTAAC 58.306 40.741 0.00 0.00 0.00 2.50
548 550 9.476928 GTAGTATATGAGATATGTGGGGTAACT 57.523 37.037 0.00 0.00 0.00 2.24
550 552 9.476928 AGTATATGAGATATGTGGGGTAACTAC 57.523 37.037 0.00 0.00 0.00 2.73
551 553 7.735326 ATATGAGATATGTGGGGTAACTACC 57.265 40.000 0.00 0.00 45.71 3.18
570 572 4.313523 CCGGGTGGTAGGATGGAT 57.686 61.111 0.00 0.00 0.00 3.41
571 573 2.539983 CCGGGTGGTAGGATGGATT 58.460 57.895 0.00 0.00 0.00 3.01
572 574 0.843984 CCGGGTGGTAGGATGGATTT 59.156 55.000 0.00 0.00 0.00 2.17
573 575 1.214424 CCGGGTGGTAGGATGGATTTT 59.786 52.381 0.00 0.00 0.00 1.82
574 576 2.572290 CGGGTGGTAGGATGGATTTTC 58.428 52.381 0.00 0.00 0.00 2.29
575 577 2.748465 CGGGTGGTAGGATGGATTTTCC 60.748 54.545 0.00 0.00 36.96 3.13
576 578 2.424379 GGGTGGTAGGATGGATTTTCCC 60.424 54.545 0.00 0.00 35.03 3.97
586 588 9.268282 GTAGGATGGATTTTCCCTATATACTCA 57.732 37.037 0.00 0.00 35.03 3.41
613 615 9.791820 TTGTCAAAGATAACATTGCATTCATAG 57.208 29.630 0.00 0.00 0.00 2.23
618 620 7.912056 AGATAACATTGCATTCATAGCGTAT 57.088 32.000 0.00 0.00 33.85 3.06
635 637 6.616774 AGCGTATGTCTAGTTTCCTAGTAC 57.383 41.667 0.00 0.00 41.31 2.73
688 690 5.789643 CTCCAAAATTGAAGGAGTGGAAA 57.210 39.130 11.17 0.00 43.11 3.13
715 732 9.796180 TCTAGAGTAGATTTATCCACTAGGTTC 57.204 37.037 0.00 0.00 28.93 3.62
733 750 2.441164 TGTGGGGCACAAGCGTTT 60.441 55.556 0.00 0.00 41.69 3.60
837 854 6.525976 GCAAATAGAAAGAAGTGTCAAGCATC 59.474 38.462 0.00 0.00 0.00 3.91
930 948 9.023967 CATTCTAGTTGCTTATTTTATTGCCAC 57.976 33.333 0.00 0.00 0.00 5.01
935 953 7.092716 AGTTGCTTATTTTATTGCCACTTCTG 58.907 34.615 0.00 0.00 29.02 3.02
987 1005 8.034215 TGACTTGAATTTATTATGGTTTGCAGG 58.966 33.333 0.00 0.00 0.00 4.85
1103 1121 7.281774 GGATCTGCTACAATCAATTTTCTCTCA 59.718 37.037 0.00 0.00 0.00 3.27
1117 1135 6.365970 TTTTCTCTCACTTAGGCTCAATCT 57.634 37.500 0.00 0.00 0.00 2.40
1118 1136 4.998671 TCTCTCACTTAGGCTCAATCTG 57.001 45.455 0.00 0.00 0.00 2.90
1247 1265 3.002246 CCCAATATTCGTGTCCATGTTCG 59.998 47.826 0.00 0.00 0.00 3.95
1335 1353 4.643387 GCCACCGGCCTTCACTGT 62.643 66.667 0.00 0.00 44.06 3.55
1472 1506 4.219944 GGCCCATTACGTGATGACTATAGA 59.780 45.833 20.86 0.00 0.00 1.98
1578 1612 0.323178 AACAGCTCCCCTTGCATCAG 60.323 55.000 0.00 0.00 0.00 2.90
1649 1683 3.344515 GGTTGGAAGTGATACTTGGTCC 58.655 50.000 0.00 0.00 38.80 4.46
1699 1733 8.827832 ATAATTCAGATTGTGGAATTCAAGGA 57.172 30.769 7.93 0.00 41.45 3.36
1731 1765 2.283298 CCATGGATCTTCGTCAACAGG 58.717 52.381 5.56 0.00 0.00 4.00
1772 1806 1.003580 CCCAAGCTTAGACTGCAGGAA 59.996 52.381 19.93 8.18 32.20 3.36
1776 1810 5.128919 CCAAGCTTAGACTGCAGGAAATAT 58.871 41.667 19.93 0.00 32.20 1.28
1820 1854 0.178992 CCAAGAGTTGCCAAGACCCA 60.179 55.000 0.00 0.00 0.00 4.51
2021 2055 2.820787 GGGGAGTGATATCAGGAGTACG 59.179 54.545 5.42 0.00 0.00 3.67
2115 2149 5.789574 ACCTTGGAGTGAATATGGGTTAA 57.210 39.130 0.00 0.00 0.00 2.01
2120 2154 4.947388 TGGAGTGAATATGGGTTAAGCAAC 59.053 41.667 7.03 0.00 0.00 4.17
2205 2251 0.315251 CCCGAGCATGCTCTATTCGA 59.685 55.000 37.44 0.00 40.69 3.71
2251 2333 9.408648 TGTATTATTGGGAAATTTCCTCTTCTC 57.591 33.333 31.23 17.05 46.72 2.87
2332 2414 4.271807 TGCATTATATTTTGGTCCCCCA 57.728 40.909 0.00 0.00 39.65 4.96
2366 2448 7.145932 ACTTTGTAAGAGATGTTTATGGTGC 57.854 36.000 0.00 0.00 0.00 5.01
2396 2478 3.583086 ACTGCTTAAGCTGAACCTCCTAA 59.417 43.478 33.10 8.21 41.71 2.69
2445 2535 7.826744 TGTTTAATGTTGCACTGGATAGATGTA 59.173 33.333 0.00 0.00 0.00 2.29
2495 2585 7.152645 TCATTTTCTACTGTCGAGCTTTAAGT 58.847 34.615 0.00 0.00 0.00 2.24
2496 2586 8.301720 TCATTTTCTACTGTCGAGCTTTAAGTA 58.698 33.333 0.00 0.00 0.00 2.24
2499 2589 7.627298 TTCTACTGTCGAGCTTTAAGTATCT 57.373 36.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.787001 GGAAGGCCTGGGAGTCGG 61.787 72.222 5.69 0.00 0.00 4.79
5 6 1.003051 TAGGGAAGGCCTGGGAGTC 59.997 63.158 5.69 0.00 0.00 3.36
9 10 3.049080 GCTGTAGGGAAGGCCTGGG 62.049 68.421 5.69 0.00 0.00 4.45
18 19 1.817740 GCAGTTTTGTGGCTGTAGGGA 60.818 52.381 0.00 0.00 35.33 4.20
36 37 2.696893 GGGGGAGGGAGAGTAGCA 59.303 66.667 0.00 0.00 0.00 3.49
68 69 2.580815 CACTGCGATGGAGGAGCA 59.419 61.111 0.00 0.00 39.25 4.26
83 84 0.036858 GAAGGAGGAGAGTGGTGCAC 60.037 60.000 8.80 8.80 34.10 4.57
89 90 1.384525 ATCGACGAAGGAGGAGAGTG 58.615 55.000 0.00 0.00 0.00 3.51
90 91 2.018515 GAATCGACGAAGGAGGAGAGT 58.981 52.381 0.00 0.00 0.00 3.24
195 197 9.555727 GCTTGTAGGAAACATTTGTCCTATATA 57.444 33.333 1.00 0.00 45.89 0.86
196 198 8.052748 TGCTTGTAGGAAACATTTGTCCTATAT 58.947 33.333 1.00 0.00 45.89 0.86
197 199 7.398829 TGCTTGTAGGAAACATTTGTCCTATA 58.601 34.615 1.00 0.00 45.89 1.31
198 200 6.245408 TGCTTGTAGGAAACATTTGTCCTAT 58.755 36.000 1.00 0.00 45.89 2.57
199 201 5.626142 TGCTTGTAGGAAACATTTGTCCTA 58.374 37.500 0.00 0.00 42.68 2.94
200 202 4.469657 TGCTTGTAGGAAACATTTGTCCT 58.530 39.130 0.00 0.00 46.29 3.85
201 203 4.278419 ACTGCTTGTAGGAAACATTTGTCC 59.722 41.667 0.00 0.00 38.10 4.02
202 204 5.215160 CACTGCTTGTAGGAAACATTTGTC 58.785 41.667 0.00 0.00 38.10 3.18
203 205 4.037923 CCACTGCTTGTAGGAAACATTTGT 59.962 41.667 0.00 0.00 38.10 2.83
204 206 4.037923 ACCACTGCTTGTAGGAAACATTTG 59.962 41.667 0.00 0.00 38.10 2.32
205 207 4.215109 ACCACTGCTTGTAGGAAACATTT 58.785 39.130 0.00 0.00 38.10 2.32
206 208 3.832527 ACCACTGCTTGTAGGAAACATT 58.167 40.909 0.00 0.00 38.10 2.71
207 209 3.508845 ACCACTGCTTGTAGGAAACAT 57.491 42.857 0.00 0.00 38.10 2.71
208 210 3.389983 ACTACCACTGCTTGTAGGAAACA 59.610 43.478 0.00 0.00 38.98 2.83
209 211 4.004196 ACTACCACTGCTTGTAGGAAAC 57.996 45.455 0.00 0.00 38.98 2.78
210 212 4.699925 AACTACCACTGCTTGTAGGAAA 57.300 40.909 0.00 0.00 38.98 3.13
211 213 4.020839 GGTAACTACCACTGCTTGTAGGAA 60.021 45.833 0.80 0.00 45.73 3.36
212 214 3.512724 GGTAACTACCACTGCTTGTAGGA 59.487 47.826 0.80 0.00 45.73 2.94
213 215 3.858247 GGTAACTACCACTGCTTGTAGG 58.142 50.000 0.80 0.00 45.73 3.18
235 237 5.652994 ACAACATACAAAACACAAGTGGT 57.347 34.783 5.08 0.00 34.19 4.16
236 238 7.199766 ACATACAACATACAAAACACAAGTGG 58.800 34.615 5.08 0.00 34.19 4.00
237 239 9.381027 CTACATACAACATACAAAACACAAGTG 57.619 33.333 0.00 0.00 0.00 3.16
238 240 9.116067 ACTACATACAACATACAAAACACAAGT 57.884 29.630 0.00 0.00 0.00 3.16
246 248 9.511144 CGACAGATACTACATACAACATACAAA 57.489 33.333 0.00 0.00 0.00 2.83
247 249 8.895737 TCGACAGATACTACATACAACATACAA 58.104 33.333 0.00 0.00 0.00 2.41
248 250 8.441312 TCGACAGATACTACATACAACATACA 57.559 34.615 0.00 0.00 0.00 2.29
249 251 9.726232 TTTCGACAGATACTACATACAACATAC 57.274 33.333 0.00 0.00 0.00 2.39
250 252 9.726232 GTTTCGACAGATACTACATACAACATA 57.274 33.333 0.00 0.00 0.00 2.29
251 253 7.705325 GGTTTCGACAGATACTACATACAACAT 59.295 37.037 0.00 0.00 0.00 2.71
252 254 7.031372 GGTTTCGACAGATACTACATACAACA 58.969 38.462 0.00 0.00 0.00 3.33
253 255 6.195983 CGGTTTCGACAGATACTACATACAAC 59.804 42.308 0.00 0.00 39.00 3.32
254 256 6.093909 TCGGTTTCGACAGATACTACATACAA 59.906 38.462 0.00 0.00 40.88 2.41
255 257 5.585844 TCGGTTTCGACAGATACTACATACA 59.414 40.000 0.00 0.00 40.88 2.29
256 258 6.018425 TCTCGGTTTCGACAGATACTACATAC 60.018 42.308 0.00 0.00 40.88 2.39
257 259 6.051074 TCTCGGTTTCGACAGATACTACATA 58.949 40.000 0.00 0.00 40.88 2.29
258 260 4.880120 TCTCGGTTTCGACAGATACTACAT 59.120 41.667 0.00 0.00 40.88 2.29
259 261 4.256110 TCTCGGTTTCGACAGATACTACA 58.744 43.478 0.00 0.00 40.88 2.74
260 262 4.332268 ACTCTCGGTTTCGACAGATACTAC 59.668 45.833 0.00 0.00 40.88 2.73
261 263 4.511527 ACTCTCGGTTTCGACAGATACTA 58.488 43.478 0.00 0.00 40.88 1.82
262 264 3.345414 ACTCTCGGTTTCGACAGATACT 58.655 45.455 0.00 0.00 40.88 2.12
263 265 3.761311 ACTCTCGGTTTCGACAGATAC 57.239 47.619 0.00 0.00 40.88 2.24
264 266 4.880120 ACATACTCTCGGTTTCGACAGATA 59.120 41.667 0.00 0.00 40.88 1.98
265 267 3.695060 ACATACTCTCGGTTTCGACAGAT 59.305 43.478 0.00 0.00 40.88 2.90
266 268 3.079578 ACATACTCTCGGTTTCGACAGA 58.920 45.455 0.00 0.00 40.88 3.41
267 269 3.489180 ACATACTCTCGGTTTCGACAG 57.511 47.619 0.00 0.00 40.88 3.51
268 270 3.181517 CGTACATACTCTCGGTTTCGACA 60.182 47.826 0.00 0.00 40.88 4.35
269 271 3.181516 ACGTACATACTCTCGGTTTCGAC 60.182 47.826 0.00 0.00 40.88 4.20
270 272 3.002791 ACGTACATACTCTCGGTTTCGA 58.997 45.455 0.00 0.00 43.86 3.71
271 273 3.096461 CACGTACATACTCTCGGTTTCG 58.904 50.000 0.00 0.00 37.82 3.46
272 274 4.088823 ACACGTACATACTCTCGGTTTC 57.911 45.455 0.00 0.00 0.00 2.78
273 275 4.697352 ACTACACGTACATACTCTCGGTTT 59.303 41.667 0.00 0.00 0.00 3.27
274 276 4.256920 ACTACACGTACATACTCTCGGTT 58.743 43.478 0.00 0.00 0.00 4.44
275 277 3.866651 ACTACACGTACATACTCTCGGT 58.133 45.455 0.00 0.00 0.00 4.69
276 278 5.464722 ACATACTACACGTACATACTCTCGG 59.535 44.000 0.00 0.00 0.00 4.63
277 279 6.522233 ACATACTACACGTACATACTCTCG 57.478 41.667 0.00 0.00 0.00 4.04
278 280 8.586570 ACTACATACTACACGTACATACTCTC 57.413 38.462 0.00 0.00 0.00 3.20
398 400 9.646427 GCCCATAGTTTTTGTTATATTTGTGAA 57.354 29.630 0.00 0.00 0.00 3.18
399 401 9.030452 AGCCCATAGTTTTTGTTATATTTGTGA 57.970 29.630 0.00 0.00 0.00 3.58
400 402 9.301153 GAGCCCATAGTTTTTGTTATATTTGTG 57.699 33.333 0.00 0.00 0.00 3.33
401 403 9.030452 TGAGCCCATAGTTTTTGTTATATTTGT 57.970 29.630 0.00 0.00 0.00 2.83
406 408 8.792633 GCATATGAGCCCATAGTTTTTGTTATA 58.207 33.333 6.97 0.00 38.53 0.98
407 409 7.287466 TGCATATGAGCCCATAGTTTTTGTTAT 59.713 33.333 6.97 0.00 38.53 1.89
408 410 6.605194 TGCATATGAGCCCATAGTTTTTGTTA 59.395 34.615 6.97 0.00 38.53 2.41
409 411 5.421693 TGCATATGAGCCCATAGTTTTTGTT 59.578 36.000 6.97 0.00 38.53 2.83
410 412 4.955450 TGCATATGAGCCCATAGTTTTTGT 59.045 37.500 6.97 0.00 38.53 2.83
411 413 5.518848 TGCATATGAGCCCATAGTTTTTG 57.481 39.130 6.97 0.00 38.53 2.44
412 414 6.736110 ATTGCATATGAGCCCATAGTTTTT 57.264 33.333 6.97 0.00 38.53 1.94
413 415 6.736110 AATTGCATATGAGCCCATAGTTTT 57.264 33.333 6.97 0.00 38.53 2.43
414 416 6.736110 AAATTGCATATGAGCCCATAGTTT 57.264 33.333 6.97 0.00 38.53 2.66
415 417 6.736110 AAAATTGCATATGAGCCCATAGTT 57.264 33.333 6.97 0.00 38.53 2.24
416 418 6.736110 AAAAATTGCATATGAGCCCATAGT 57.264 33.333 6.97 0.00 38.53 2.12
516 518 8.200120 CCCACATATCTCATATACTACCATGTG 58.800 40.741 0.00 0.00 40.08 3.21
517 519 7.345653 CCCCACATATCTCATATACTACCATGT 59.654 40.741 0.00 0.00 0.00 3.21
518 520 7.345653 ACCCCACATATCTCATATACTACCATG 59.654 40.741 0.00 0.00 0.00 3.66
519 521 7.430844 ACCCCACATATCTCATATACTACCAT 58.569 38.462 0.00 0.00 0.00 3.55
520 522 6.811574 ACCCCACATATCTCATATACTACCA 58.188 40.000 0.00 0.00 0.00 3.25
521 523 8.693625 GTTACCCCACATATCTCATATACTACC 58.306 40.741 0.00 0.00 0.00 3.18
522 524 9.476928 AGTTACCCCACATATCTCATATACTAC 57.523 37.037 0.00 0.00 0.00 2.73
524 526 9.476928 GTAGTTACCCCACATATCTCATATACT 57.523 37.037 0.00 0.00 0.00 2.12
525 527 8.693625 GGTAGTTACCCCACATATCTCATATAC 58.306 40.741 0.00 0.00 40.53 1.47
526 528 8.403474 TGGTAGTTACCCCACATATCTCATATA 58.597 37.037 5.90 0.00 45.87 0.86
527 529 7.253421 TGGTAGTTACCCCACATATCTCATAT 58.747 38.462 5.90 0.00 45.87 1.78
528 530 6.626238 TGGTAGTTACCCCACATATCTCATA 58.374 40.000 5.90 0.00 45.87 2.15
529 531 5.473273 TGGTAGTTACCCCACATATCTCAT 58.527 41.667 5.90 0.00 45.87 2.90
530 532 4.886163 TGGTAGTTACCCCACATATCTCA 58.114 43.478 5.90 0.00 45.87 3.27
539 541 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
540 542 1.613332 ACCCGGTGGTAGTTACCCC 60.613 63.158 0.00 5.97 45.45 4.95
541 543 1.598517 CACCCGGTGGTAGTTACCC 59.401 63.158 9.99 0.00 45.57 3.69
553 555 0.843984 AAATCCATCCTACCACCCGG 59.156 55.000 0.00 0.00 38.77 5.73
554 556 2.572290 GAAAATCCATCCTACCACCCG 58.428 52.381 0.00 0.00 0.00 5.28
555 557 2.424379 GGGAAAATCCATCCTACCACCC 60.424 54.545 0.00 0.00 38.64 4.61
556 558 2.514160 AGGGAAAATCCATCCTACCACC 59.486 50.000 0.00 0.00 38.64 4.61
557 559 3.953542 AGGGAAAATCCATCCTACCAC 57.046 47.619 0.00 0.00 38.64 4.16
558 560 8.191110 AGTATATAGGGAAAATCCATCCTACCA 58.809 37.037 0.00 0.00 38.64 3.25
559 561 8.625467 AGTATATAGGGAAAATCCATCCTACC 57.375 38.462 0.00 0.00 38.64 3.18
560 562 9.268282 TGAGTATATAGGGAAAATCCATCCTAC 57.732 37.037 0.00 0.00 38.64 3.18
562 564 8.940012 ATGAGTATATAGGGAAAATCCATCCT 57.060 34.615 0.00 0.00 38.64 3.24
563 565 9.401058 CAATGAGTATATAGGGAAAATCCATCC 57.599 37.037 0.00 0.00 38.64 3.51
564 566 9.965902 ACAATGAGTATATAGGGAAAATCCATC 57.034 33.333 0.00 0.00 38.64 3.51
565 567 9.965902 GACAATGAGTATATAGGGAAAATCCAT 57.034 33.333 0.00 0.00 38.64 3.41
566 568 8.944138 TGACAATGAGTATATAGGGAAAATCCA 58.056 33.333 0.00 0.00 38.64 3.41
567 569 9.793259 TTGACAATGAGTATATAGGGAAAATCC 57.207 33.333 0.00 0.00 35.23 3.01
676 678 7.833285 ATCTACTCTAGATTTCCACTCCTTC 57.167 40.000 0.00 0.00 42.70 3.46
708 725 0.400213 TTGTGCCCCACAGAACCTAG 59.600 55.000 0.00 0.00 45.39 3.02
715 732 2.489275 AAACGCTTGTGCCCCACAG 61.489 57.895 0.00 0.00 45.39 3.66
744 761 4.336889 TGTTATCCTAGCCACACTATGC 57.663 45.455 0.00 0.00 0.00 3.14
807 824 7.750229 TGACACTTCTTTCTATTTGCAGATT 57.250 32.000 0.00 0.00 0.00 2.40
818 835 4.965814 TCTGATGCTTGACACTTCTTTCT 58.034 39.130 0.00 0.00 0.00 2.52
930 948 7.488187 TTGAAAGAATGAGTCACTTCAGAAG 57.512 36.000 8.77 8.77 33.98 2.85
935 953 9.741647 AAAGAAATTGAAAGAATGAGTCACTTC 57.258 29.630 0.00 1.19 0.00 3.01
987 1005 1.031571 TTTGCATGATGGCGACCTCC 61.032 55.000 0.00 0.00 36.28 4.30
1037 1055 1.831736 CTTGGAGTCCGAACATAGGGT 59.168 52.381 4.30 0.00 0.00 4.34
1071 1089 3.031013 TGATTGTAGCAGATCCTTCGGA 58.969 45.455 0.00 0.00 35.55 4.55
1084 1102 8.394121 GCCTAAGTGAGAGAAAATTGATTGTAG 58.606 37.037 0.00 0.00 0.00 2.74
1103 1121 3.618690 GGTCACAGATTGAGCCTAAGT 57.381 47.619 0.00 0.00 45.55 2.24
1117 1135 0.468226 ACAAAGGCGAGAAGGTCACA 59.532 50.000 0.00 0.00 0.00 3.58
1118 1136 1.264288 CAACAAAGGCGAGAAGGTCAC 59.736 52.381 0.00 0.00 0.00 3.67
1247 1265 2.936498 CCATTGTTACATGGAGGACGAC 59.064 50.000 0.00 0.00 40.30 4.34
1335 1353 9.577110 GTCTGCAAAATTTCTTCATCAATATGA 57.423 29.630 0.00 0.00 40.43 2.15
1472 1506 5.189180 GGAATATCAGACCAGTTGAGCTTT 58.811 41.667 0.00 0.00 0.00 3.51
1524 1558 7.361885 GCTGCAGTAAGACTCTGTAACTAGTTA 60.362 40.741 16.64 11.38 35.60 2.24
1578 1612 5.535157 GCTAACAAGCATATGCGAGTTTGC 61.535 45.833 33.62 33.62 44.92 3.68
1605 1639 3.117851 GGCCAACTAAATAAGGAGAGGCT 60.118 47.826 0.00 0.00 37.47 4.58
1697 1731 2.109774 TCCATGGCAATGAATTGGTCC 58.890 47.619 6.96 0.00 38.21 4.46
1699 1733 3.649843 AGATCCATGGCAATGAATTGGT 58.350 40.909 6.96 0.00 38.21 3.67
1731 1765 3.477530 GGGCCATCTCCAAAGTGTATAC 58.522 50.000 4.39 0.00 0.00 1.47
1772 1806 0.769247 GGGGGCGGTTAGTGGATATT 59.231 55.000 0.00 0.00 0.00 1.28
1820 1854 8.099537 CAGACCACTAGCCATGATATTTTAGAT 58.900 37.037 0.00 0.00 0.00 1.98
2021 2055 4.022068 TCTGGGTTCATGCAAGAAAATGAC 60.022 41.667 5.85 0.00 32.63 3.06
2115 2149 0.179062 GATGGATCTGGCTCGTTGCT 60.179 55.000 0.00 0.00 42.39 3.91
2205 2251 1.064463 ACGTGATGATCAAGGGCCATT 60.064 47.619 12.73 0.00 30.01 3.16
2291 2373 1.534729 AAGGTTGAATTCCGAGTGCC 58.465 50.000 2.27 0.00 0.00 5.01
2366 2448 6.595716 AGGTTCAGCTTAAGCAGTAATACAAG 59.404 38.462 28.39 5.85 45.16 3.16


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

AutoCloner maintained by Alex Coulton.