Multiple sequence alignment - TraesCS2A01G358400

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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 TraesCS2A01G358400 chr2A 100.000 4079 0 0 1 4079 602654245 602650167 0.000000e+00 7533.0
1 TraesCS2A01G358400 chr2A 85.962 520 53 6 28 547 759785408 759785907 4.640000e-149 538.0
2 TraesCS2A01G358400 chr2D 92.581 3518 168 40 592 4079 459335776 459332322 0.000000e+00 4964.0
3 TraesCS2A01G358400 chr2B 91.216 3438 215 33 661 4072 540809021 540805645 0.000000e+00 4595.0
4 TraesCS2A01G358400 chr2B 89.234 548 37 8 1 547 641654644 641654118 0.000000e+00 665.0
5 TraesCS2A01G358400 chr2B 85.375 547 59 7 3 547 90198966 90199493 7.710000e-152 547.0
6 TraesCS2A01G358400 chr2B 84.940 498 53 8 3 497 254086281 254086759 6.130000e-133 484.0
7 TraesCS2A01G358400 chr4D 82.267 1438 225 16 1413 2829 497152534 497151106 0.000000e+00 1216.0
8 TraesCS2A01G358400 chr4D 80.246 1382 229 31 1467 2829 497160179 497158823 0.000000e+00 1000.0
9 TraesCS2A01G358400 chr4D 78.824 1327 233 28 1482 2799 497158412 497157125 0.000000e+00 850.0
10 TraesCS2A01G358400 chr4D 90.576 191 18 0 1138 1328 497152980 497152790 1.880000e-63 254.0
11 TraesCS2A01G358400 chr4B 82.091 1435 233 16 1413 2829 637724190 637722762 0.000000e+00 1205.0
12 TraesCS2A01G358400 chr4B 77.308 1560 300 41 1467 3002 637731676 637730147 0.000000e+00 870.0
13 TraesCS2A01G358400 chr4B 76.803 832 152 21 1482 2309 637729893 637729099 2.910000e-116 429.0
14 TraesCS2A01G358400 chr4B 90.576 191 18 0 1138 1328 637724594 637724404 1.880000e-63 254.0
15 TraesCS2A01G358400 chr5A 81.597 1440 231 19 1413 2829 676951099 676949671 0.000000e+00 1160.0
16 TraesCS2A01G358400 chr5A 77.386 1561 297 42 1467 3002 676962086 676960557 0.000000e+00 876.0
17 TraesCS2A01G358400 chr5A 82.286 875 126 23 1465 2328 676943958 676943102 0.000000e+00 730.0
18 TraesCS2A01G358400 chr5A 77.364 1290 250 25 1482 2765 676960320 676959067 0.000000e+00 726.0
19 TraesCS2A01G358400 chr5A 84.000 475 73 1 2358 2829 676943107 676942633 1.730000e-123 453.0
20 TraesCS2A01G358400 chr5A 88.384 198 23 0 1131 1328 676951561 676951364 5.270000e-59 239.0
21 TraesCS2A01G358400 chr6A 88.257 545 45 6 2 546 485882698 485883223 5.750000e-178 634.0
22 TraesCS2A01G358400 chr1A 85.897 546 55 8 1 546 63335367 63335890 2.750000e-156 562.0
23 TraesCS2A01G358400 chr1A 76.190 336 74 6 2073 2405 577705877 577705545 5.420000e-39 172.0
24 TraesCS2A01G358400 chr4A 84.560 557 62 13 1 553 674451033 674451569 7.760000e-147 531.0
25 TraesCS2A01G358400 chr3B 84.644 547 62 8 3 547 263335790 263335264 3.610000e-145 525.0
26 TraesCS2A01G358400 chr3B 75.701 214 45 5 2617 2829 345704081 345703874 2.590000e-17 100.0
27 TraesCS2A01G358400 chr5D 84.095 547 57 8 1 546 131177333 131176816 6.090000e-138 501.0
28 TraesCS2A01G358400 chr1B 73.754 1364 294 46 1486 2826 287841451 287842773 1.030000e-130 477.0
29 TraesCS2A01G358400 chr3D 87.234 188 21 2 1128 1312 554717218 554717031 1.150000e-50 211.0
30 TraesCS2A01G358400 chr3D 75.743 202 42 5 2629 2829 237823236 237823041 1.210000e-15 95.3
31 TraesCS2A01G358400 chr3D 81.395 86 16 0 3717 3802 19282873 19282958 2.030000e-08 71.3
32 TraesCS2A01G358400 chr3D 100.000 29 0 0 3718 3746 94246805 94246833 2.000000e-03 54.7


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 TraesCS2A01G358400 chr2A 602650167 602654245 4078 True 7533.0 7533 100.0000 1 4079 1 chr2A.!!$R1 4078
1 TraesCS2A01G358400 chr2D 459332322 459335776 3454 True 4964.0 4964 92.5810 592 4079 1 chr2D.!!$R1 3487
2 TraesCS2A01G358400 chr2B 540805645 540809021 3376 True 4595.0 4595 91.2160 661 4072 1 chr2B.!!$R1 3411
3 TraesCS2A01G358400 chr2B 641654118 641654644 526 True 665.0 665 89.2340 1 547 1 chr2B.!!$R2 546
4 TraesCS2A01G358400 chr2B 90198966 90199493 527 False 547.0 547 85.3750 3 547 1 chr2B.!!$F1 544
5 TraesCS2A01G358400 chr4D 497157125 497160179 3054 True 925.0 1000 79.5350 1467 2829 2 chr4D.!!$R2 1362
6 TraesCS2A01G358400 chr4D 497151106 497152980 1874 True 735.0 1216 86.4215 1138 2829 2 chr4D.!!$R1 1691
7 TraesCS2A01G358400 chr4B 637722762 637724594 1832 True 729.5 1205 86.3335 1138 2829 2 chr4B.!!$R1 1691
8 TraesCS2A01G358400 chr4B 637729099 637731676 2577 True 649.5 870 77.0555 1467 3002 2 chr4B.!!$R2 1535
9 TraesCS2A01G358400 chr5A 676959067 676962086 3019 True 801.0 876 77.3750 1467 3002 2 chr5A.!!$R3 1535
10 TraesCS2A01G358400 chr5A 676949671 676951561 1890 True 699.5 1160 84.9905 1131 2829 2 chr5A.!!$R2 1698
11 TraesCS2A01G358400 chr5A 676942633 676943958 1325 True 591.5 730 83.1430 1465 2829 2 chr5A.!!$R1 1364
12 TraesCS2A01G358400 chr6A 485882698 485883223 525 False 634.0 634 88.2570 2 546 1 chr6A.!!$F1 544
13 TraesCS2A01G358400 chr1A 63335367 63335890 523 False 562.0 562 85.8970 1 546 1 chr1A.!!$F1 545
14 TraesCS2A01G358400 chr4A 674451033 674451569 536 False 531.0 531 84.5600 1 553 1 chr4A.!!$F1 552
15 TraesCS2A01G358400 chr3B 263335264 263335790 526 True 525.0 525 84.6440 3 547 1 chr3B.!!$R1 544
16 TraesCS2A01G358400 chr5D 131176816 131177333 517 True 501.0 501 84.0950 1 546 1 chr5D.!!$R1 545
17 TraesCS2A01G358400 chr1B 287841451 287842773 1322 False 477.0 477 73.7540 1486 2826 1 chr1B.!!$F1 1340

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
553 558 0.468214 TCCTCCGCCTCTGAGTATGG 60.468 60.0 3.66 2.6 0.00 2.74 F
556 561 0.468214 TCCGCCTCTGAGTATGGGAG 60.468 60.0 3.66 0.0 0.00 4.30 F
1407 1580 0.804933 GAGTACGCACCCATTCCGTC 60.805 60.0 0.00 0.0 36.51 4.79 F
1442 1615 0.995731 GACGACGACGAACAGGTGAC 60.996 60.0 15.32 0.0 42.66 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1861 0.037232 GAGCCTTAAGGTGCACGAGT 60.037 55.000 22.55 0.42 37.57 4.18 R
2242 2558 2.758089 GCAAGCACTGGATGGCGAG 61.758 63.158 0.00 0.00 34.54 5.03 R
2874 4917 2.579787 GTCGTCACCGCTCCATCG 60.580 66.667 0.00 0.00 0.00 3.84 R
3085 5134 3.407424 TCTGTGGTGAACAATCTCAGG 57.593 47.619 0.00 0.00 38.67 3.86 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
50 51 3.264845 AACGGGCCAATGGGGAGT 61.265 61.111 4.39 0.00 40.01 3.85
97 98 8.958119 AGCATTTTTCGATACCTTGTAATCTA 57.042 30.769 0.00 0.00 0.00 1.98
106 107 6.088217 CGATACCTTGTAATCTACAGCAATCG 59.912 42.308 0.00 0.00 40.24 3.34
274 276 5.746307 AGCAATGCAATGTAGTGATACTG 57.254 39.130 8.35 0.00 0.00 2.74
310 312 2.225467 GTGAATTGCAGGAGGATAGGC 58.775 52.381 0.00 0.00 0.00 3.93
311 313 1.845791 TGAATTGCAGGAGGATAGGCA 59.154 47.619 0.00 0.00 0.00 4.75
314 316 2.353357 TTGCAGGAGGATAGGCAATG 57.647 50.000 0.00 0.00 40.94 2.82
315 317 1.216064 TGCAGGAGGATAGGCAATGT 58.784 50.000 0.00 0.00 32.54 2.71
316 318 1.565759 TGCAGGAGGATAGGCAATGTT 59.434 47.619 0.00 0.00 32.54 2.71
317 319 2.777114 TGCAGGAGGATAGGCAATGTTA 59.223 45.455 0.00 0.00 32.54 2.41
318 320 3.181451 TGCAGGAGGATAGGCAATGTTAG 60.181 47.826 0.00 0.00 32.54 2.34
320 322 4.384056 CAGGAGGATAGGCAATGTTAGTG 58.616 47.826 0.00 0.00 0.00 2.74
322 324 4.346418 AGGAGGATAGGCAATGTTAGTGAG 59.654 45.833 0.00 0.00 0.00 3.51
324 326 4.298626 AGGATAGGCAATGTTAGTGAGGA 58.701 43.478 0.00 0.00 0.00 3.71
325 327 4.910304 AGGATAGGCAATGTTAGTGAGGAT 59.090 41.667 0.00 0.00 0.00 3.24
326 328 6.084738 AGGATAGGCAATGTTAGTGAGGATA 58.915 40.000 0.00 0.00 0.00 2.59
327 329 6.212388 AGGATAGGCAATGTTAGTGAGGATAG 59.788 42.308 0.00 0.00 0.00 2.08
353 355 2.846206 TGCCATTGTCTGGGTCTTCTAT 59.154 45.455 0.00 0.00 46.06 1.98
375 377 9.109393 TCTATACACCATTGAAAGCTTCATTAC 57.891 33.333 0.00 0.00 39.84 1.89
468 472 7.824779 TGTGGTATGCAATGTTAGTGTGTATTA 59.175 33.333 0.00 0.00 0.00 0.98
548 553 0.826715 TTTCATCCTCCGCCTCTGAG 59.173 55.000 0.00 0.00 0.00 3.35
550 555 0.551396 TCATCCTCCGCCTCTGAGTA 59.449 55.000 3.66 0.00 0.00 2.59
553 558 0.468214 TCCTCCGCCTCTGAGTATGG 60.468 60.000 3.66 2.60 0.00 2.74
555 560 0.468214 CTCCGCCTCTGAGTATGGGA 60.468 60.000 3.66 3.91 0.00 4.37
556 561 0.468214 TCCGCCTCTGAGTATGGGAG 60.468 60.000 3.66 0.00 0.00 4.30
557 562 0.468214 CCGCCTCTGAGTATGGGAGA 60.468 60.000 3.66 0.00 0.00 3.71
558 563 1.626686 CGCCTCTGAGTATGGGAGAT 58.373 55.000 3.66 0.00 0.00 2.75
559 564 1.271934 CGCCTCTGAGTATGGGAGATG 59.728 57.143 3.66 0.00 0.00 2.90
560 565 2.603021 GCCTCTGAGTATGGGAGATGA 58.397 52.381 3.66 0.00 0.00 2.92
561 566 2.562298 GCCTCTGAGTATGGGAGATGAG 59.438 54.545 3.66 0.00 0.00 2.90
562 567 3.753519 GCCTCTGAGTATGGGAGATGAGA 60.754 52.174 3.66 0.00 0.00 3.27
563 568 4.676109 CCTCTGAGTATGGGAGATGAGAT 58.324 47.826 3.66 0.00 0.00 2.75
564 569 4.463539 CCTCTGAGTATGGGAGATGAGATG 59.536 50.000 3.66 0.00 0.00 2.90
565 570 5.323581 CTCTGAGTATGGGAGATGAGATGA 58.676 45.833 0.00 0.00 0.00 2.92
566 571 5.709594 TCTGAGTATGGGAGATGAGATGAA 58.290 41.667 0.00 0.00 0.00 2.57
567 572 5.538053 TCTGAGTATGGGAGATGAGATGAAC 59.462 44.000 0.00 0.00 0.00 3.18
568 573 4.279420 TGAGTATGGGAGATGAGATGAACG 59.721 45.833 0.00 0.00 0.00 3.95
569 574 4.474394 AGTATGGGAGATGAGATGAACGA 58.526 43.478 0.00 0.00 0.00 3.85
570 575 4.895889 AGTATGGGAGATGAGATGAACGAA 59.104 41.667 0.00 0.00 0.00 3.85
574 579 3.494048 GGGAGATGAGATGAACGAAGCAT 60.494 47.826 0.00 0.00 0.00 3.79
575 580 4.262207 GGGAGATGAGATGAACGAAGCATA 60.262 45.833 0.00 0.00 0.00 3.14
576 581 5.477510 GGAGATGAGATGAACGAAGCATAT 58.522 41.667 0.00 0.00 0.00 1.78
577 582 6.350528 GGGAGATGAGATGAACGAAGCATATA 60.351 42.308 0.00 0.00 0.00 0.86
579 584 6.986250 AGATGAGATGAACGAAGCATATACA 58.014 36.000 0.00 0.00 0.00 2.29
580 585 7.436933 AGATGAGATGAACGAAGCATATACAA 58.563 34.615 0.00 0.00 0.00 2.41
581 586 6.828502 TGAGATGAACGAAGCATATACAAC 57.171 37.500 0.00 0.00 0.00 3.32
582 587 6.573434 TGAGATGAACGAAGCATATACAACT 58.427 36.000 0.00 0.00 0.00 3.16
583 588 6.697455 TGAGATGAACGAAGCATATACAACTC 59.303 38.462 0.00 0.00 0.00 3.01
584 589 6.810911 AGATGAACGAAGCATATACAACTCT 58.189 36.000 0.00 0.00 0.00 3.24
586 591 5.720202 TGAACGAAGCATATACAACTCTGT 58.280 37.500 0.00 0.00 39.75 3.41
588 593 5.324784 ACGAAGCATATACAACTCTGTCA 57.675 39.130 0.00 0.00 36.96 3.58
595 600 5.734498 GCATATACAACTCTGTCAAAAAGCG 59.266 40.000 0.00 0.00 36.96 4.68
616 621 7.496529 AGCGTACATGCATCTACAATAAAAT 57.503 32.000 11.94 0.00 37.31 1.82
618 623 8.712363 AGCGTACATGCATCTACAATAAAATAG 58.288 33.333 11.94 0.00 37.31 1.73
704 709 1.203523 CTAGCCGTTGAGCTGTCTTCT 59.796 52.381 0.00 0.00 44.67 2.85
713 718 4.000331 TGAGCTGTCTTCTTCTTCCAAG 58.000 45.455 0.00 0.00 0.00 3.61
735 740 4.161189 AGCATCTCCACGCTGCTTATATAT 59.839 41.667 0.00 0.00 43.44 0.86
777 782 5.249852 ACCATTGTTTAGGCACTAGGACTAA 59.750 40.000 3.22 3.22 45.52 2.24
791 796 2.025226 AGGACTAAGATCGAGGTCACCA 60.025 50.000 0.00 0.00 0.00 4.17
908 917 2.673368 CCTGCTTCCTTGTTCGTATCAC 59.327 50.000 0.00 0.00 0.00 3.06
914 923 4.884668 TCCTTGTTCGTATCACTTTCCT 57.115 40.909 0.00 0.00 0.00 3.36
915 924 5.223449 TCCTTGTTCGTATCACTTTCCTT 57.777 39.130 0.00 0.00 0.00 3.36
931 940 3.031964 CTTGCAGCTTCTTCGCGGG 62.032 63.158 6.13 0.00 34.40 6.13
943 952 4.005472 CGCGGGCGAATCATCTGC 62.005 66.667 7.38 0.00 42.83 4.26
992 1001 3.302740 CGTATCATTTTCCGAGCAGCTTC 60.303 47.826 0.00 0.00 0.00 3.86
1025 1034 3.356529 AGGAACTAAGCAGGTGAATGG 57.643 47.619 0.00 0.00 36.02 3.16
1050 1060 4.230657 TGTCCGTCTTGTTTTGTTTTGTG 58.769 39.130 0.00 0.00 0.00 3.33
1055 1065 4.494484 GTCTTGTTTTGTTTTGTGGCTCT 58.506 39.130 0.00 0.00 0.00 4.09
1097 1111 8.992835 AGCATTTCATTATTTCTTCTGAAACC 57.007 30.769 0.00 0.00 43.90 3.27
1114 1128 5.250200 TGAAACCCTAATGCGTTCTGTATT 58.750 37.500 0.00 0.00 36.76 1.89
1115 1129 6.408035 TGAAACCCTAATGCGTTCTGTATTA 58.592 36.000 0.00 0.00 34.50 0.98
1116 1130 6.314400 TGAAACCCTAATGCGTTCTGTATTAC 59.686 38.462 0.00 0.00 34.50 1.89
1123 1137 8.082852 CCTAATGCGTTCTGTATTACTATCTGT 58.917 37.037 0.00 0.00 34.50 3.41
1335 1349 1.377987 GTCAATGCCGCCTACCCAA 60.378 57.895 0.00 0.00 0.00 4.12
1407 1580 0.804933 GAGTACGCACCCATTCCGTC 60.805 60.000 0.00 0.00 36.51 4.79
1441 1614 1.280746 GACGACGACGAACAGGTGA 59.719 57.895 15.32 0.00 42.66 4.02
1442 1615 0.995731 GACGACGACGAACAGGTGAC 60.996 60.000 15.32 0.00 42.66 3.67
2445 4485 6.848364 GTGATGTCACTGCTCTAATCAGAGTT 60.848 42.308 5.91 0.00 44.92 3.01
2874 4917 0.096976 CGTCGGTGATTGCATTCCAC 59.903 55.000 6.16 5.75 0.00 4.02
3182 5233 4.956085 TGAAGTTTCGATCTGGAGTTTGA 58.044 39.130 0.00 0.00 0.00 2.69
3306 5357 8.029642 ACAACTGTGTAAACTGTATTGCTATC 57.970 34.615 0.00 0.00 35.72 2.08
3398 5452 8.845227 TCTGTGATGCTACTTGTCAAAATTAAA 58.155 29.630 0.00 0.00 0.00 1.52
3448 5504 2.623878 TCTGTGCTTTACCGTTTCCA 57.376 45.000 0.00 0.00 0.00 3.53
3499 5576 1.683385 AGCCCTCAAACAAAGCAGAAC 59.317 47.619 0.00 0.00 0.00 3.01
3529 5608 5.607939 AATGAGATAACATACACCGGACA 57.392 39.130 9.46 0.00 0.00 4.02
3543 5622 0.385473 CGGACAAATGCCACGACAAC 60.385 55.000 0.00 0.00 0.00 3.32
3544 5623 0.385473 GGACAAATGCCACGACAACG 60.385 55.000 0.00 0.00 45.75 4.10
3545 5624 0.584396 GACAAATGCCACGACAACGA 59.416 50.000 0.00 0.00 42.66 3.85
3546 5625 1.196808 GACAAATGCCACGACAACGAT 59.803 47.619 0.00 0.00 42.66 3.73
3547 5626 2.413796 GACAAATGCCACGACAACGATA 59.586 45.455 0.00 0.00 42.66 2.92
3548 5627 2.158841 ACAAATGCCACGACAACGATAC 59.841 45.455 0.00 0.00 42.66 2.24
3549 5628 1.365699 AATGCCACGACAACGATACC 58.634 50.000 0.00 0.00 42.66 2.73
3550 5629 0.804544 ATGCCACGACAACGATACCG 60.805 55.000 0.00 0.00 42.66 4.02
3551 5630 1.153978 GCCACGACAACGATACCGA 60.154 57.895 0.00 0.00 42.66 4.69
3552 5631 1.138047 GCCACGACAACGATACCGAG 61.138 60.000 0.00 0.00 42.66 4.63
3563 5650 4.585955 ACGATACCGAGCAAGAATACAT 57.414 40.909 0.00 0.00 39.50 2.29
3622 5709 2.555757 ACCTTAGTTCTACGACAACGCT 59.444 45.455 0.00 0.00 43.96 5.07
3630 5717 2.551032 TCTACGACAACGCTCTCAAGAA 59.449 45.455 0.00 0.00 43.96 2.52
3649 5850 0.655733 AGGAAACACACAAAGCGTCG 59.344 50.000 0.00 0.00 0.00 5.12
3660 5861 2.449031 AAAGCGTCGCCATCCTCACA 62.449 55.000 14.86 0.00 0.00 3.58
3680 5881 4.151689 CACATTCGAAGGAACGTACAATGT 59.848 41.667 17.88 1.64 38.10 2.71
3694 5895 4.274950 CGTACAATGTTTTCACCTGGAACT 59.725 41.667 0.00 0.00 34.56 3.01
3841 6288 1.908619 TCAGCCATGGTGAGAAAGCTA 59.091 47.619 14.67 0.00 35.04 3.32
3846 6293 3.869912 GCCATGGTGAGAAAGCTAAGACA 60.870 47.826 14.67 0.00 0.00 3.41
3882 6330 2.123409 GCACCTCCTTTGCCAACAA 58.877 52.632 0.00 0.00 33.58 2.83
4072 6608 0.336737 CCACAGACTAGAGGGGAGGT 59.663 60.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.678048 GCTCTCCATCTTTTGCCGGT 60.678 55.000 1.90 0.00 0.00 5.28
14 15 1.673767 TCCCCTTGCTCTCCATCTTT 58.326 50.000 0.00 0.00 0.00 2.52
97 98 4.332819 GCAATTAGAACTACCGATTGCTGT 59.667 41.667 16.09 0.00 45.45 4.40
274 276 6.423302 TGCAATTCACAATTTCACACCATTAC 59.577 34.615 0.00 0.00 0.00 1.89
310 312 4.813161 CAGTGCCTATCCTCACTAACATTG 59.187 45.833 0.00 0.00 41.19 2.82
311 313 4.684485 GCAGTGCCTATCCTCACTAACATT 60.684 45.833 2.85 0.00 41.19 2.71
313 315 2.168521 GCAGTGCCTATCCTCACTAACA 59.831 50.000 2.85 0.00 41.19 2.41
314 316 2.483889 GGCAGTGCCTATCCTCACTAAC 60.484 54.545 27.48 0.00 46.69 2.34
315 317 1.762957 GGCAGTGCCTATCCTCACTAA 59.237 52.381 27.48 0.00 46.69 2.24
316 318 1.414158 GGCAGTGCCTATCCTCACTA 58.586 55.000 27.48 0.00 46.69 2.74
317 319 2.216148 GGCAGTGCCTATCCTCACT 58.784 57.895 27.48 0.00 46.69 3.41
318 320 4.865865 GGCAGTGCCTATCCTCAC 57.134 61.111 27.48 0.00 46.69 3.51
340 342 5.277250 TCAATGGTGTATAGAAGACCCAGA 58.723 41.667 0.00 0.00 40.94 3.86
353 355 5.123186 CGGTAATGAAGCTTTCAATGGTGTA 59.877 40.000 0.00 0.00 43.95 2.90
500 505 4.772886 AAGGTGTGGTGAAGTCTTAAGT 57.227 40.909 1.63 0.00 0.00 2.24
533 538 1.626686 CATACTCAGAGGCGGAGGAT 58.373 55.000 1.53 2.98 36.35 3.24
548 553 4.855715 TCGTTCATCTCATCTCCCATAC 57.144 45.455 0.00 0.00 0.00 2.39
550 555 3.494048 GCTTCGTTCATCTCATCTCCCAT 60.494 47.826 0.00 0.00 0.00 4.00
553 558 3.170791 TGCTTCGTTCATCTCATCTCC 57.829 47.619 0.00 0.00 0.00 3.71
555 560 6.986250 TGTATATGCTTCGTTCATCTCATCT 58.014 36.000 0.00 0.00 0.00 2.90
556 561 7.383572 AGTTGTATATGCTTCGTTCATCTCATC 59.616 37.037 0.00 0.00 0.00 2.92
557 562 7.212976 AGTTGTATATGCTTCGTTCATCTCAT 58.787 34.615 0.00 0.00 0.00 2.90
558 563 6.573434 AGTTGTATATGCTTCGTTCATCTCA 58.427 36.000 0.00 0.00 0.00 3.27
559 564 6.920758 AGAGTTGTATATGCTTCGTTCATCTC 59.079 38.462 0.00 0.00 0.00 2.75
560 565 6.699204 CAGAGTTGTATATGCTTCGTTCATCT 59.301 38.462 0.00 0.00 0.00 2.90
561 566 6.477033 ACAGAGTTGTATATGCTTCGTTCATC 59.523 38.462 0.00 0.00 35.25 2.92
562 567 6.341316 ACAGAGTTGTATATGCTTCGTTCAT 58.659 36.000 0.00 0.00 35.25 2.57
563 568 5.720202 ACAGAGTTGTATATGCTTCGTTCA 58.280 37.500 0.00 0.00 35.25 3.18
564 569 5.805486 TGACAGAGTTGTATATGCTTCGTTC 59.195 40.000 0.00 0.00 37.76 3.95
565 570 5.720202 TGACAGAGTTGTATATGCTTCGTT 58.280 37.500 0.00 0.00 37.76 3.85
566 571 5.324784 TGACAGAGTTGTATATGCTTCGT 57.675 39.130 0.00 0.00 37.76 3.85
567 572 6.647212 TTTGACAGAGTTGTATATGCTTCG 57.353 37.500 0.00 0.00 37.76 3.79
568 573 7.483059 GCTTTTTGACAGAGTTGTATATGCTTC 59.517 37.037 0.00 0.00 37.76 3.86
569 574 7.308435 GCTTTTTGACAGAGTTGTATATGCTT 58.692 34.615 0.00 0.00 37.76 3.91
570 575 6.402550 CGCTTTTTGACAGAGTTGTATATGCT 60.403 38.462 0.00 0.00 37.76 3.79
574 579 6.924612 TGTACGCTTTTTGACAGAGTTGTATA 59.075 34.615 0.00 0.00 37.76 1.47
575 580 5.756347 TGTACGCTTTTTGACAGAGTTGTAT 59.244 36.000 0.00 0.00 37.76 2.29
576 581 5.110598 TGTACGCTTTTTGACAGAGTTGTA 58.889 37.500 0.00 0.00 37.76 2.41
577 582 3.936453 TGTACGCTTTTTGACAGAGTTGT 59.064 39.130 0.00 0.00 41.18 3.32
579 584 4.554723 GCATGTACGCTTTTTGACAGAGTT 60.555 41.667 0.00 0.00 0.00 3.01
580 585 3.058914 GCATGTACGCTTTTTGACAGAGT 60.059 43.478 0.00 0.00 0.00 3.24
581 586 3.058983 TGCATGTACGCTTTTTGACAGAG 60.059 43.478 0.00 0.00 0.00 3.35
582 587 2.875317 TGCATGTACGCTTTTTGACAGA 59.125 40.909 0.00 0.00 0.00 3.41
583 588 3.266541 TGCATGTACGCTTTTTGACAG 57.733 42.857 0.00 0.00 0.00 3.51
584 589 3.501828 AGATGCATGTACGCTTTTTGACA 59.498 39.130 2.46 0.00 0.00 3.58
586 591 4.693095 TGTAGATGCATGTACGCTTTTTGA 59.307 37.500 24.20 6.02 29.86 2.69
588 593 5.621197 TTGTAGATGCATGTACGCTTTTT 57.379 34.783 24.20 0.00 29.86 1.94
616 621 7.540474 AAGGATTGTTACTGTGAGAACTCTA 57.460 36.000 3.51 0.00 0.00 2.43
618 623 6.706270 TCAAAGGATTGTTACTGTGAGAACTC 59.294 38.462 0.00 0.00 37.79 3.01
620 625 6.861065 TCAAAGGATTGTTACTGTGAGAAC 57.139 37.500 0.00 0.00 37.79 3.01
622 627 9.567776 TTATTTCAAAGGATTGTTACTGTGAGA 57.432 29.630 0.00 0.00 37.79 3.27
704 709 1.945819 GCGTGGAGATGCTTGGAAGAA 60.946 52.381 0.00 0.00 0.00 2.52
741 746 7.234577 TGCCTAAACAATGGTTTTCTCCTTAAT 59.765 33.333 2.92 0.00 44.63 1.40
743 748 6.015772 GTGCCTAAACAATGGTTTTCTCCTTA 60.016 38.462 2.92 0.00 44.63 2.69
748 753 5.476945 CCTAGTGCCTAAACAATGGTTTTCT 59.523 40.000 2.92 0.00 44.63 2.52
777 782 2.054232 ACGTATGGTGACCTCGATCT 57.946 50.000 17.38 0.00 0.00 2.75
814 819 0.684535 TGATGCGAACAAGGAGGACA 59.315 50.000 0.00 0.00 0.00 4.02
873 881 3.495806 GGAAGCAGGATAGTGATTGAGGG 60.496 52.174 0.00 0.00 0.00 4.30
874 882 3.390639 AGGAAGCAGGATAGTGATTGAGG 59.609 47.826 0.00 0.00 0.00 3.86
875 883 4.686191 AGGAAGCAGGATAGTGATTGAG 57.314 45.455 0.00 0.00 0.00 3.02
908 917 1.400759 GCGAAGAAGCTGCAAGGAAAG 60.401 52.381 1.02 0.00 0.00 2.62
914 923 3.049674 CCCGCGAAGAAGCTGCAA 61.050 61.111 8.23 0.00 34.40 4.08
931 940 2.032204 GTGATTGAGGCAGATGATTCGC 60.032 50.000 0.00 0.00 0.00 4.70
943 952 2.918712 AAGCGGGATAGTGATTGAGG 57.081 50.000 0.00 0.00 0.00 3.86
992 1001 1.490574 AGTTCCTTCCATCTCTCGGG 58.509 55.000 0.00 0.00 0.00 5.14
1025 1034 5.575218 ACAAAACAAAACAAGACGGACAATC 59.425 36.000 0.00 0.00 0.00 2.67
1050 1060 2.029560 TCATCGACATATGAGCAGAGCC 60.030 50.000 10.38 0.00 32.18 4.70
1055 1065 3.457610 TGCTTCATCGACATATGAGCA 57.542 42.857 10.38 9.24 37.20 4.26
1096 1110 7.542477 CAGATAGTAATACAGAACGCATTAGGG 59.458 40.741 0.00 0.00 0.00 3.53
1097 1111 8.082852 ACAGATAGTAATACAGAACGCATTAGG 58.917 37.037 0.00 0.00 0.00 2.69
1114 1128 3.920446 TCTGCGTGCAAAACAGATAGTA 58.080 40.909 9.78 0.00 35.58 1.82
1115 1129 2.766313 TCTGCGTGCAAAACAGATAGT 58.234 42.857 9.78 0.00 35.58 2.12
1116 1130 3.371898 TCATCTGCGTGCAAAACAGATAG 59.628 43.478 20.73 16.24 46.69 2.08
1123 1137 2.161855 AGGATTCATCTGCGTGCAAAA 58.838 42.857 0.00 0.00 0.00 2.44
1377 1550 2.353607 CGTACTCGCCGAGGATGC 60.354 66.667 19.61 0.69 33.35 3.91
1396 1569 2.812499 CGGATCGACGGAATGGGT 59.188 61.111 0.00 0.00 0.00 4.51
1508 1812 2.782222 GCGATGGCCGAGTAGTGGA 61.782 63.158 0.00 0.00 41.76 4.02
1557 1861 0.037232 GAGCCTTAAGGTGCACGAGT 60.037 55.000 22.55 0.42 37.57 4.18
1860 2170 3.958147 CTCGGCGATGTTGGTGCCT 62.958 63.158 11.27 0.00 46.67 4.75
2242 2558 2.758089 GCAAGCACTGGATGGCGAG 61.758 63.158 0.00 0.00 34.54 5.03
2550 4593 3.955101 CGCTCCCGCTCTACCTCG 61.955 72.222 0.00 0.00 0.00 4.63
2874 4917 2.579787 GTCGTCACCGCTCCATCG 60.580 66.667 0.00 0.00 0.00 3.84
3085 5134 3.407424 TCTGTGGTGAACAATCTCAGG 57.593 47.619 0.00 0.00 38.67 3.86
3219 5270 6.306356 CAGAAACAAAGCAAATTCCTACATCG 59.694 38.462 0.00 0.00 0.00 3.84
3351 5405 7.656542 CACAGATAGTGCAGAACATGAGATTAT 59.343 37.037 0.00 0.00 42.15 1.28
3373 5427 9.630098 ATTTAATTTTGACAAGTAGCATCACAG 57.370 29.630 0.00 0.00 0.00 3.66
3469 5525 6.573094 GCTTTGTTTGAGGGCTTCTTCAATAT 60.573 38.462 0.00 0.00 0.00 1.28
3523 5602 1.511318 TTGTCGTGGCATTTGTCCGG 61.511 55.000 0.00 0.00 0.00 5.14
3529 5608 1.735571 GGTATCGTTGTCGTGGCATTT 59.264 47.619 0.00 0.00 38.33 2.32
3543 5622 4.546570 TCATGTATTCTTGCTCGGTATCG 58.453 43.478 0.00 0.00 37.82 2.92
3544 5623 5.533482 ACTCATGTATTCTTGCTCGGTATC 58.467 41.667 0.00 0.00 0.00 2.24
3545 5624 5.537300 ACTCATGTATTCTTGCTCGGTAT 57.463 39.130 0.00 0.00 0.00 2.73
3546 5625 5.339008 AACTCATGTATTCTTGCTCGGTA 57.661 39.130 0.00 0.00 0.00 4.02
3547 5626 3.895232 ACTCATGTATTCTTGCTCGGT 57.105 42.857 0.00 0.00 0.00 4.69
3548 5627 3.557595 GGAACTCATGTATTCTTGCTCGG 59.442 47.826 10.25 0.00 0.00 4.63
3549 5628 4.437239 AGGAACTCATGTATTCTTGCTCG 58.563 43.478 10.25 0.00 0.00 5.03
3550 5629 6.810911 TCTAGGAACTCATGTATTCTTGCTC 58.189 40.000 10.25 0.00 41.75 4.26
3551 5630 6.609212 TCTCTAGGAACTCATGTATTCTTGCT 59.391 38.462 10.25 4.10 41.75 3.91
3552 5631 6.699642 GTCTCTAGGAACTCATGTATTCTTGC 59.300 42.308 10.25 0.00 41.75 4.01
3563 5650 5.105716 GCATTGTGTAGTCTCTAGGAACTCA 60.106 44.000 1.77 0.00 41.75 3.41
3622 5709 4.096382 GCTTTGTGTGTTTCCTTCTTGAGA 59.904 41.667 0.00 0.00 0.00 3.27
3630 5717 0.655733 CGACGCTTTGTGTGTTTCCT 59.344 50.000 0.00 0.00 39.84 3.36
3649 5850 1.134401 TCCTTCGAATGTGAGGATGGC 60.134 52.381 0.00 0.00 0.00 4.40
3660 5861 5.934935 AAACATTGTACGTTCCTTCGAAT 57.065 34.783 0.00 0.00 34.70 3.34
3680 5881 3.435026 CCCTCTCAAGTTCCAGGTGAAAA 60.435 47.826 0.00 0.00 33.94 2.29
3694 5895 0.687354 AGCTTCGCTTTCCCTCTCAA 59.313 50.000 0.00 0.00 33.89 3.02
3715 5918 1.613925 CTCCTCTTGAGGACGTTGTCA 59.386 52.381 14.79 0.00 37.45 3.58
3841 6288 3.834231 CCAAATTGGGTTCTGGATGTCTT 59.166 43.478 3.60 0.00 32.67 3.01


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

AutoCloner maintained by Alex Coulton.