Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022407.1 Corchorus olitorius cultivar O-4 contig22440, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4428
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:924 original size:286 final size:284
Alignment explanation
Indices: 389--949 Score: 763
Period size: 286 Copynumber: 2.0 Consensus size: 284
379 GTGTACTAAC
* * *
389 CATCACGGTTTTTGCCGAAAACGTATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGGCGCC
1 CATCACGGTTTTTGCCGAAAACGCATTTCGGAGCCTCAACTCAGTTTTGCTTGACTTTTCGCGCC
* * *
454 AAAGATTCTTGAAATATATATATTCATCTACCCAAATCCCAGCCAAAGTGGATCTAAGGATATGT
66 AAAGATCCTTGAAATATACATATTCATCTACCCAAATCCCAGCCAAAATGGATCTAAGGATATGT
* * *
519 TTTTACGAGCATCTGAATCTAGTTTCGATTTCAATAGAAATTACTTAGGAAAAAATTTGGAAAAA
131 TTTTACGAGCATCAGAATCTAGTTTCGATTTCAATAGAAATTAATTAGGAAAAAATTTGCAAAAA
* * *
584 TGATATTAGAAAGGTTAGAAGCCCTTCAATCTTTTTTGCGTTGAACCATATATTTTTTATCAGTA
196 TGATATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAACCATATATTTTTTATCAGTA
*
649 TTTTGGCCAAAAATTTTAGCCGAA
261 TTTTAGCCAAAAATTTTAGCCGAA
* * *
673 CATCACGGTTTTTGGCGAAAAACGCATTTCGGAGTCTCAACTCAGTTTTGCTTGATTTTTCGCGC
1 CATCACGGTTTTTGCCG-AAAACGCATTTCGGAGCCTCAACTCAGTTTTGCTTGACTTTTCGCGC
* * * * * *
738 CAGAA-CTCCTTGAAATATCCATATTCATTTAGCCAAATCTCAG-CAACAATGGATTTAAGGATA
65 CA-AAGATCCTTGAAATATACATATTCATCTACCCAAATCCCAGCCAA-AATGGATCTAAGGATA
* * *
801 TTTTTTTTACGAGTATCAGAATCTTG-TTCTGATTT-AATTAGAAATTAATTAGG-AAAAATTTG
128 -TGTTTTTACGAGCATCAGAATCTAGTTTC-GATTTCAA-TAGAAATTAATTAGGAAAAAATTTG
* **
863 CAAAAATTGATATTAGAAATGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATATATTTTTT
190 CAAAAA-TGATATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAACCATATATTTTTT
*
928 ATGAGTATTTTAGCCAAAAATT
254 ATCAGTATTTTAGCCAAAAATT
950 GAGTAAAAAT
Statistics
Matches: 241, Mismatches: 29, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
284 19 0.08
285 108 0.45
286 114 0.47
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (284 bp):
CATCACGGTTTTTGCCGAAAACGCATTTCGGAGCCTCAACTCAGTTTTGCTTGACTTTTCGCGCC
AAAGATCCTTGAAATATACATATTCATCTACCCAAATCCCAGCCAAAATGGATCTAAGGATATGT
TTTTACGAGCATCAGAATCTAGTTTCGATTTCAATAGAAATTAATTAGGAAAAAATTTGCAAAAA
TGATATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAACCATATATTTTTTATCAGTA
TTTTAGCCAAAAATTTTAGCCGAA
Found at i:1557 original size:561 final size:569
Alignment explanation
Indices: 673--1801 Score: 1559
Period size: 561 Copynumber: 2.0 Consensus size: 569
663 TTTAGCCGAA
*
673 CATCACGGTTTTTGGCGAAAAACGCATTTCGGAGTCTCAACTCAGTTTTGCTTGATTTTTCGCGC
1 CATCACGGTTTTTGGCGAAAAACGCATTTCGGAGTCTCAACTCAGTTTTGCTTGACTTTTCGCGC
* * * * *
738 CAGAACTCCTTGAAATATCCATATTCATTTAGCCAAATCTCAGCAACAATGGATTTAAGGATATT
66 CAGAAATCCTTGAAATATCCATATTAATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATT
* * * *
803 TTTTTTACGAGTATCAGAATCTTGTTCTGATTTAATTAGAAATTAATTAGGAAAAATTTGCAAAA
131 GTTTTTACGAGCATCAGAATCTAGTTCTGATTTAAATAGAAATTAATTAGGAAAAA-TTG----A
* *
868 ATTGATATTAGAAATGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATATATTTTTTATGAG
191 ATT-ATATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATAAATTTTTTATGAG
* * * * *
933 TATTTTAGCCAAAAATTGAGTAAAAATTTTTCGGATCACTTTTTGCAAAATTTTAGTCGAAATCG
255 TATTTTAGACAAAAATAGAGGAAAAATTTTTCGGATCACTTTTTGCAAAATTGTAGCCGAAATCG
*
998 TGTACTAACCATCACGGTTTTTGGCGAAAAACGTATTTCGGAGCCTCGACTCAGTTTTGCTTGAC
320 TGTACTAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGAC
* * * *
1063 TTTTGGCGCCA-AAGATCCTTGAAATATCTATATTCATCTATCCAAATCTCAGCAACAATGGATT
385 TTTTGGCGCCAGAA-ATCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATT
* *
1127 TAAGTATATGTTTTTACGAGCATCAGAAACTTGTTTCGATTTAATCAAAAATTAATTAGG-AAAA
449 TAAGGATATGTTTTTACGAGCAACAGAAACTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAA
* * * * *
1191 CTTG-GAAAAATGATATTAGAAGGGTTAGAAGCCCTTCAATCTTTTTTCAGGTAAC
514 CTTGCAAAAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTCAGGTAAC
*
1246 CATCACGGTTTTTGGCGAAAAACGCATTTCGGAG-C-CAAGACTCAGTTTTGCTTGACTTTTGGC
1 CATCACGGTTTTTGGCGAAAAACGCATTTCGGAGTCTC-A-ACTCAGTTTTGCTTGACTTTTCGC
* * *
1309 GCCA-AAGATCCTTGAAATATCTATATTAATCTACCCAACTCCCAGCCAA-AGTGGATTTAAGGA
64 GCCAGAA-ATCCTTGAAATATCCATATTAATCTACCCAAATCCCAG-CAACAATGGATTTAAGGA
*
1372 TA-TGTTTTTACGAGCATCTGAATCTAGTT-TCGATTTAAATAGAAATTAATTAGGAAAAA-TG-
127 TATTGTTTTTACGAGCATCAGAATCTAGTTCT-GATTTAAATAGAAATTAATTAGGAAAAATTGA
* * *
1433 A-T-T-TTAGAAAGGTTAAAAGCCCTTCAATCTTTTTTGTGTTGAATTATAAATTTTTTATGAGT
191 ATTATATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATAAATTTTTTATGAGT
* * * *
1495 ATTTTTGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTCTTCAAAATTGTAGCCGAAATCG
256 ATTTTAGACAAAAATAGAGGAAAAATTTTTCGGATCACTTTT-TGCAAAATTGTAGCCGAAATCG
* * * *
1559 TGTACTAACCATCATGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCGACTCAGTTTTGCTTGAT
320 TGTACTAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGAC
*
1624 TTTTGGCGCCAGAACTCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATTT
385 TTTTGGCGCCAGAAATCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATTT
* * * * *
1689 AAGGATATTTTTTTCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAA
450 AAGGATATGTTTTTACGAGCAACAGAAACTTGTTTCGATTTAATCAAAAATTAATTAGG-AAAAA
*
1754 TTTGCAAAAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTT
514 CTTGCAAAAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTT
1802 GCGTTGAATT
Statistics
Matches: 494, Mismatches: 52, Indels: 29
0.86 0.09 0.05
Matches are distributed among these distances:
560 14 0.03
561 263 0.53
562 3 0.01
563 7 0.01
564 39 0.08
565 1 0.00
570 2 0.00
571 2 0.00
572 54 0.11
573 106 0.21
574 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (569 bp):
CATCACGGTTTTTGGCGAAAAACGCATTTCGGAGTCTCAACTCAGTTTTGCTTGACTTTTCGCGC
CAGAAATCCTTGAAATATCCATATTAATCTACCCAAATCCCAGCAACAATGGATTTAAGGATATT
GTTTTTACGAGCATCAGAATCTAGTTCTGATTTAAATAGAAATTAATTAGGAAAAATTGAATTAT
ATTAGAAAGGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATAAATTTTTTATGAGTATTTT
AGACAAAAATAGAGGAAAAATTTTTCGGATCACTTTTTGCAAAATTGTAGCCGAAATCGTGTACT
AACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTGG
CGCCAGAAATCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATTTAAGGAT
ATGTTTTTACGAGCAACAGAAACTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACTTGCAA
AAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTCAGGTAAC
Found at i:1914 original size:334 final size:331
Alignment explanation
Indices: 1242--4418 Score: 3760
Period size: 334 Copynumber: 9.6 Consensus size: 331
1232 TTTTTTCAGG
* ** *
1242 TAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCAAGACTCAGTTTTGCTTGACTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * * *
1307 GCGCCAAAGATCCTTGAAATATCTATATTAATCTACCCAACTCCCAGCCAA-AGTGGATTTAAGG
66 GCGCCAAA-CTCCTTGAAATATCCATATTCATCTACCCAAATCTCAG-CAACAATGGATTTAAGG
* * *
1371 ATATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGG-AAAAA-T-G
129 ATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTGG
* *
1433 ----AT--T-TTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGTGTTGAATTATAAATTTTTTA
194 AAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTA
* * * * * *
1490 TGAGTATTTTTGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTCTTCAAAATTGTAGCCGA
258 TGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTCGA
1554 AATCGTGTAC
322 AATCGTGTAC
* *
1564 TAACCATCATGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCGACTCAGTTTTGCTTGATTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* *
1629 GCGCCAGAACTCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATGGATTTAAGGA
66 GCGCCA-AACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGA
* * *
1694 TATTTTTTTCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTTGC
130 TATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAA-TTG-
* * *
1759 AAAAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTATATATTTTTTA
193 GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTA
* * ** *
1824 TGATTATTTTAGCCAAAAATTGACTAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGAA
258 TGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAA
1889 ATCGTGTAC
323 ATCGTGTAC
* * * * * * *
1898 TAACCATCACGGTTTTTAGCTAAAACCGCTTTTCCGAGCCCCGGCTCAGTTTTGCAT-AGTTTTT
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGA-TTTTT
*
1962 GGCGCCAAGACTCCTTCAAATATCCCA-ATTCATCTACCCAAATCTCAGCAACAATGGATTTAAG
65 GGCGCCAA-ACTCCTTGAAATAT-CCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAG
* * * *
2026 TATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACTTG
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTG
* * **
2091 GAAAAATGATATTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTTTTTGCGTTAAATTATATAAA
193 GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC-----TTTTTTGCGTTGAATTATATATT
* *
2156 TTGTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAG
253 TTTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAG
2221 TCGAAATCGTGTAC
318 TCGAAATCGTGTAC
* * *
2235 TAACCATCACGGTTTTTGGCGAAAAACGTATTTCGGAGCCTCGACTCAGTTTTGCTTGACTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * *
2300 GCGCCAAAGATCCTTGAAATATCTATATTAATCTACCCAAATCCCAGCCAA-AGTGGATTTAAGG
66 GCGCCAAA-CTCCTTGAAATATCCATATTCATCTACCCAAATCTCAG-CAACAATGGATTTAAGG
* * *
2364 ATATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATT
129 ATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGG-AAAA-AATT
* *
2429 GGAAAAATGATTTTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATAAATTTTT
192 GGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTT
* * * * *
2493 TATGAGTATTTTGGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTCTTCAAATTTTTAGCC
256 TATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTC
2557 GAAATCGTGTAC
320 GAAATCGTGTAC
* * * * * * *
2569 TGACCATCACGGTTTTTAGCTAAAATCGC-TTTC-GAGCCCCGGCTCAGTTTTGCAT-AGTTTTT
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGA-TTTTT
* * *
2631 GGCGCCATGACTCCTTCAAATATCCCA-ATTCATCTACCCAAATCTCAGCAATAATGGATTTAAG
65 GGCGCCA-AACTCCTTGAAATAT-CCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAG
* * * *
2695 TATATGTTTTTACGAGCATCGGAATCTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACA-T
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAA-ATT
* * **
2759 GGAAAAATGATATTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTATGCGTTAAATTATATAAAT
192 GGAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC--TTTTT-TGCGTTGAATTATATATTT
*
2824 TTTATGAGTATTTTGGCCAAAAATTGAGGTAAAATTTTTC-GG---G----T-CAAAATTTTAGT
254 TTTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGT
2880 CGAAATCGTGTAC
319 CGAAATCGTGTAC
* * * *
2893 TAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTTACTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * * * *
2958 GCGCCAAAGATCCTTGAAATTTCTATATTAATCTACCCAAATCCCATCCAA-AGTGGATTTAAGG
66 GCGCCAAA-CTCCTTGAAATATCCATATTCATCTACCCAAATCTCA-GCAACAATGGATTTAAGG
* * * *
3022 ATACGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAATAATAATT
129 ATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAA-AA-AATT
* * * *
3087 GGAAAAATGATTTTAGAAAG-GTTAAAATCCCTTCAATCTTTTTTGTGTTGAATTATAAATTTTT
192 GGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTT
** * * * *
3151 TATGAGTATAATGGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTCTTCAAAATTTTAGCC
256 TATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTC
*
3215 AAAATCGTGTAC
320 GAAATCGTGTAC
* *
3227 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCTACTCAGTTTTGCTTGATTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * *
3292 GAGCCAGAACTCATTGAAATATCCATATTCCTCAACCCAAATCTCAGCAACAATGGATTTAAGAA
66 GCGCCA-AACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGA
* * *
3357 TAT-TTTTTCCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATCAGGAAAAAATTTG
130 TATGTTTTT-ACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAA-TTG
* * * * *
3421 CAAAAAATGATATTATAAGCGTTAAAAGCCATTCAATCTATTTTGCGTTGAAATATATATTTTTT
193 -GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTT
* ** *
3486 ATGAGTATTTTAGCCAAAAATTGACTAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTCGA
257 ATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGA
3551 AATCGTGTAC
322 AATCGTGTAC
* * ** * * * * *
3561 TAACTATCACGGTTTTTAGCTTAAACCGCTTTTCCGAGCCCCGTCTCAGTTTTGCAT-AGTTTTT
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGA-TTTTT
* * * *
3625 GGAGCCAAGACTCCTTCAAATATCC-TAACTCATCTACCCAAATCTCAGCAACAATGGATTTATG
65 GGCGCCAA-ACTCCTTGAAATATCCAT-ATTCATCTACCCAAATCTCAGCAACAATGGATTTAAG
* * * * *
3689 TATATGTTTTTACGAGCATCGGAATCTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACTTG
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTG
* * * **
3754 GAAAAATGATACTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTATGCGTTAAATTATATAAATT
193 GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC--TTTTT-TGCGTTGAATTATATATTTT
* * * * *
3819 TTATGAGTATTTTGTCCAAAAATTGATGTAAAATTTTTTGGGTCAATTTTTGCAAAATTTTAGTC
255 TTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTC
* *
3884 GAAATCATATAC
320 GAAATCGTGTAC
* * * *
3896 T--CCATCACGGTTTTTGACGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGACTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * * * *
3959 GCGCCAAAGATCCTTGAAATATCTATCTTAATCTACCTAAATCCCAGCCAA-AGTGGATTTAAGG
66 GCGCCAAA-CTCCTTGAAATATCCATATTCATCTACCCAAATCTCAG-CAACAATGGATTTAAGG
* * * *
4023 AAATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAATT
129 ATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGG-AAAA-AATT
* * *
4088 GGAAAAATGATTTTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGTGTTGAATTATAAATTTTT
192 GGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTT
* * * * * *
4152 TATGAGTATTTTTGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTCTTCAAAATTGTAGCC
256 TATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTT-TGCAAAATTTTAGTC
*
4216 AAAATCGTGTAC
320 GAAATCGTGTAC
* * *
4228 TAACCATCATGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCGACTCAG-TTTGGTTGATTTTTG
1 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
* * * * *
4292 GAGCCAGAACTCATTGAAATATCCATATTCTTCAACTCAAATCTCAGCAACAATGGATTTAAGGA
66 GCGCCA-AACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGA
* * * *
4357 TATTTTTTTCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATCAGGAAAAAATT
130 TATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATT
4419 TGCAAAAAAT
Statistics
Matches: 2421, Mismatches: 346, Indels: 167
0.83 0.12 0.06
Matches are distributed among these distances:
321 3 0.00
322 157 0.06
323 7 0.00
324 53 0.02
325 54 0.02
326 125 0.05
327 7 0.00
328 34 0.01
329 6 0.00
330 35 0.01
331 29 0.01
332 266 0.11
333 353 0.15
334 840 0.35
335 158 0.07
336 6 0.00
337 242 0.10
338 8 0.00
339 35 0.01
340 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (331 bp):
TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTG
GCGCCAAACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGAT
ATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGAAAAAATTGGAA
AAATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGA
GTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGTCGAAATC
GTGTAC
Found at i:3072 original size:658 final size:653
Alignment explanation
Indices: 1242--4426 Score: 3529
Period size: 658 Copynumber: 4.8 Consensus size: 653
1232 TTTTTTCAGG
* * *
1242 TAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCAAGACTCAGTTTTGCTTGACTTTTG
1 TAACCATCACGGTTTTTAGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGATTTTTG
* * * * *
1307 GCGCCAAAGA-TCCTTGAAATATCTATATTAATCTACCCAACTCCCAGCCAAAGTGGATTTAAGG
66 GCGCC-AAGACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAG-CAAAATGGATTTAAGG
* *
1371 ATATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGG-AAAAAT-G-
129 ATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTT-AATAGAAATTAATTAGGAAAAAATGGA
* *
1433 ---AT--T-TTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGTGTTGAATTATA-AATTTTTTA
193 AAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTAAATTATATAA-TTTTTA
* * * * * *
1490 TGAGTATTTTTGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTTCTTCAAAATTGTAGCCGAA
256 TGAGTATTTTGGCCAAAAATTGAGGAAAATTTTTC-GG--AG-----TTCAAAATTTTAGTCGAA
* *
1555 ATCGTGTACTAACCATCATGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCGACTCAGTTTTGCT
313 ATCGTGTACTAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCT
* * * *
1620 TGATTTTTGGCGCCAGAA-CTCATTGAAATATCCATATTCATCAACCCAAATCTCAGCAACAATG
378 TGATTTTTGGCGCCA-AAGATCCTTGAAATATCTATATTCATCTACCCAAATCTCAGCAACAATG
* * * *
1684 GATTTAAGGATATTTTTTTCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATTAGGA
442 GATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAATAGAAATTAATTAGGA
* * * *
1749 AAAAATTTGCAAAAAATGATATTAGAAGCGTTAAAAGCCATTCAATCTATTTTGCGTTGAATTAT
507 AAAAAATTG-GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTAT
* * * * * ** *
1814 ATATTTTTTATGATTATTTTAGCCAAAAATTGACTAAAAATTTTTCGGATCAGTTTTTGCAAAAT
571 AAATTTTTTATGAGTATTTTGGACAAAAATAGAGGAAAAA-TTTTCGGGTCAGTTTTTGCAAAAT
*
1879 TTTAGTCGAAATCGTGTAC
635 TTTAGCCGAAATCGTGTAC
* * * * * * *
1898 TAACCATCACGGTTTTTAGCTAAAACCGCTTTTCCGAGCCCCGGCTCAGTTTTGCAT-AGTTTTT
1 TAACCATCACGGTTTTTAGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGA-TTTTT
*
1962 GGCGCCAAGACTCCTTCAAATATCCCA-ATTCATCTACCCAAATCTCAGCAACAATGGATTTAAG
65 GGCGCCAAGACTCCTTGAAATAT-CCATATTCATCTACCCAAATCTCAGCAA-AATGGATTTAAG
* * *
2026 TATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACTTG
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAT-AGAAATTAATTAGGAAAAA-ATG
* *
2091 GAAAAATGATATTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTTTTTGCGTTAAATTATATAAA
191 GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC-----TTTTTTGCGTTAAATTATATAAT
* *
2156 TTGTATGAGTATTTTGGCCAAAAATTGAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATTTTAG
251 TTTTATGAGTATTTTGGCCAAAAATTGAGG-AAAATTTTTC-GG---A--GTT-CAAAATTTTAG
* *
2221 TCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAAACGTATTTCGGAGCCTCGACTCAGTT
308 TCGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTT
* * *
2286 TTGCTTGACTTTTGGCGCCAAAGATCCTTGAAATATCTATATTAATCTACCCAAATCCCAGCCAA
373 TTGCTTGATTTTTGGCGCCAAAGATCCTTGAAATATCTATATTCATCTACCCAAATCTCAG-CAA
* * *
2351 -AGTGGATTTAAGGATATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAAT
437 CAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAATAGAAATTAAT
*
2415 TAGGAAAAATAATTGGAAAAATGATTTTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGCGTTG
502 TAGGAAAAA-AATTGGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTG
*
2479 AATTATAAATTTTTTATGAGTATTTTGGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTTCTT
565 AATTATAAATTTTTTATGAGTATTTTGGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTT-TG
*
2544 CAAATTTTTAGCCGAAATCGTGTAC
629 CAAAATTTTAGCCGAAATCGTGTAC
* * * * * *
2569 TGACCATCACGGTTTTTAGCTAAAATCGC-TTTC-GAGCCCCGGCTCAGTTTTGCAT-AGTTTTT
1 TAACCATCACGGTTTTTAGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGA-TTTTT
* *
2631 GGCGCCATGACTCCTTCAAATATCCCA-ATTCATCTACCCAAATCTCAGCAATAATGGATTTAAG
65 GGCGCCAAGACTCCTTGAAATAT-CCATATTCATCTACCCAAATCTCAGCAA-AATGGATTTAAG
* * *
2695 TATATGTTTTTACGAGCATCGGAATCTTGTTTCGATTTAATCAAAAATTAATTAGGAAAAACATG
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAT-AGAAATTAATTAGGAAAAA-ATG
* *
2760 GAAAAATGATATTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTATGCGTTAAATTATATAAATT
191 GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC--TTTTT-TGCGTTAAATTATATAATTT
2825 TTATGAGTATTTTGGCCAAAAATTGAGGTAAAATTTTTCGG-G-TCAAAATTTTAGTCGAAATCG
253 TTATGAGTATTTTGGCCAAAAATTGAGG-AAAATTTTTCGGAGTTCAAAATTTTAGTCGAAATCG
* * * *
2888 TGTACTAACCATCACGGTTTTTGGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTTAC
317 TGTACTAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGAT
* * * * *
2953 TTTTGGCGCCAAAGATCCTTGAAATTTCTATATTAATCTACCCAAATCCCATCCAA-AGTGGATT
382 TTTTGGCGCCAAAGATCCTTGAAATATCTATATTCATCTACCCAAATCTCA-GCAACAATGGATT
* * *
3017 TAAGGATACGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAATAA
446 TAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAATAGAAATTAATTAGGAA-AA
* * * *
3082 TAATTGGAAAAATGATTTTAGAAAG-GTTAAAATCCCTTCAATCTTTTTTGTGTTGAATTATAAA
510 AAATTGGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATAAA
** *
3146 TTTTTTATGAGTATAATGGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTTCTTCAAAATTTT
574 TTTTTTATGAGTATTTTGGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTT-TGCAAAATTTT
*
3211 AGCCAAAATCGTGTAC
638 AGCCGAAATCGTGTAC
* * * * *
3227 TAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCTACTCAGTTTTGCTTGATTTTTG
1 TAACCATCACGGTTTTTAGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGATTTTTG
* * * * *
3292 GAGCC-AGAACTCATTGAAATATCCATATTCCTCAACCCAAATCTCAGCAACAATGGATTTAAGA
66 GCGCCAAG-ACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAA-AATGGATTTAAGG
* * *
3356 ATAT-TTTTTCCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATCAGGAAAAAATTT
129 ATATGTTTTT-ACGAGCATCAGAATCTTGTTTCGATTTAA-TAGAAATTAATTAGGAAAAAA--T
* * * * *
3420 GCAAAAAATGATATTATAAGCGTTAAAAGCCATTCAATCTATTTTGCGTTGAAA-TATATATTTT
190 G-GAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTT-AAATTATATAATTT
* **
3484 TTATGAGTATTTTAGCCAAAAATTGACTAAAAATTTTTCGGATCAGTTTTTGCAAAATTTTAGTC
253 TTATGAGTATTTTGGCCAAAAATTGA-GGAAAATTTTTCGG---AG---TT-CAAAATTTTAGTC
* * ** * * * *
3549 GAAATCGTGTACTAACTATCACGGTTTTTAGCTTAAACCGCTTTTCCGAGCCCCGTCTCAGTTTT
310 GAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTT
* * * *
3614 GCAT-AGTTTTTGGAGCC-AAGACTCCTTCAAATATCCTA-ACTCATCTACCCAAATCTCAGCAA
375 GCTTGA-TTTTTGGCGCCAAAGA-TCCTTGAAATAT-CTATATTCATCTACCCAAATCTCAGCAA
* * * *
3676 CAATGGATTTATGTATATGTTTTTACGAGCATCGGAATCTTGTTTCGATTT-AATCAAAAATTAA
437 CAATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAAT-AGAAATTAA
* * *
3740 TTAGG-AAAAACTTGGAAAAATGATACTAGAAGCGTTAGAAGCCCTTCAATCTTTTTTTATGCGT
501 TTAGGAAAAAAATTGGAAAAATGATATTAGAAGCGTTAAAAGCCCTTCAATC--TTTTT-TGCGT
* * ** * * * * *
3804 TAAATTATATAA-ATTTTATGAGTATTTTGTCCAAAAATTGATGTAAAATTTTTTGGGTCAATTT
563 TGAATTATA-AATTTTTTATGAGTATTTTGGACAAAAATAGA-GGAAAAATTTTCGGGTCAGTTT
* * *
3868 TTGCAAAATTTTAGTCGAAATCATATAC
626 TTGCAAAATTTTAGCCGAAATCGTGTAC
*
3896 T--CCATCACGGTTTTT-GACGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGACTTTT
1 TAACCATCACGGTTTTTAG-CGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGATTTTT
* * * * * *
3958 GGCGCCAAAGA-TCCTTGAAATATCTATCTTAATCTACCTAAATCCCAGCCAAAGTGGATTTAAG
65 GGCGCC-AAGACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAG-CAAAATGGATTTAAG
* * *
4022 GAAATGTTTTTACGAGCATCTGAATCTAGTTTCGATTTAAATAGAAATTAATTAGGAAAAATAAT
128 GATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTT-AATAGAAATTAATTAGG-AAAA-AA-
* * *
4087 TGGAAAAATGATTTTAGAAAG-GTTAAAAGCCCTTCAATCTTTTTTGTGTTGAATTATA-AATTT
189 TGGAAAAATGATATTAG-AAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTAAATTATATAA-TT
* * * * * *
4150 TTTATGAGTATTTTTGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTTCTTCAAAATTGTAGC
252 TTTATGAGTATTTTGGCCAAAAATTGAGGAAAATTTTTC-GG--AG-----TTCAAAATTTTAGT
* * *
4215 CAAAATCGTGTACTAACCATCATGGTTTTTGGCGAAAACCGCATTTCGGAGTCTCGACTCAG-TT
309 CGAAATCGTGTACTAACCATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTT
* * * * * * * *
4279 TGGTTGATTTTTGGAGCCAGAA-CTCATTGAAATATCCATATTCTTCAACTCAAATCTCAGCAAC
374 TGCTTGATTTTTGGCGCCA-AAGATCCTTGAAATATCTATATTCATCTACCCAAATCTCAGCAAC
* * * * *
4343 AATGGATTTAAGGATATTTTTTTCCGAGCAACAGAATCTTGTTTCGATTTAATTAGAAATTAATC
438 AATGGATTTAAGGATATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAAATAGAAATTAATT
* *
4408 AGGAAAAAATTTGCAAAAA
503 AGGAAAAAAATTGGAAAAA
4427 AT
Statistics
Matches: 2200, Mismatches: 242, Indels: 163
0.84 0.09 0.06
Matches are distributed among these distances:
655 11 0.00
656 146 0.07
657 6 0.00
658 368 0.17
659 69 0.03
660 127 0.06
661 4 0.00
662 33 0.01
663 3 0.00
665 9 0.00
666 185 0.08
667 356 0.16
668 197 0.09
669 256 0.12
670 44 0.02
671 361 0.16
672 24 0.01
673 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (653 bp):
TAACCATCACGGTTTTTAGCGAAAAACGCATTTCGGAGCCACGACTCAGTTTTGCTTGATTTTTG
GCGCCAAGACTCCTTGAAATATCCATATTCATCTACCCAAATCTCAGCAAAATGGATTTAAGGAT
ATGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATAGAAATTAATTAGGAAAAAATGGAAAA
ATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTAAATTATATAATTTTTATGAGT
ATTTTGGCCAAAAATTGAGGAAAATTTTTCGGAGTTCAAAATTTTAGTCGAAATCGTGTACTAAC
CATCACGGTTTTTGGCGAAAACCGCATTTCGGAGCCTCGACTCAGTTTTGCTTGATTTTTGGCGC
CAAAGATCCTTGAAATATCTATATTCATCTACCCAAATCTCAGCAACAATGGATTTAAGGATATG
TTTTTACGAGCATCAGAATCTTGTTTCGATTTAAATAGAAATTAATTAGGAAAAAAATTGGAAAA
ATGATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGCGTTGAATTATAAATTTTTTATGAGT
ATTTTGGACAAAAATAGAGGAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTG
TAC
Done.