Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020884.1 Corchorus olitorius cultivar O-4 contig20917, 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: 94972
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1284 original size:332 final size:332
Alignment explanation
Indices: 1--3173 Score: 4394
Period size: 332 Copynumber: 9.6 Consensus size: 332
* *
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATATAGTACACGATTTCAGCTAAAATTTTG
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGG--ATAGTACACGATTTCGGCTAAAATTTTG
** * * *
66 CAAAAATTGAGTAGAAAAATTTTTCCTAAATTTTTTCACACAATAGTCGTAAAAATTATATAATT
64 CAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATT
131 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTT-AATTA
129 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTA
* *
195 ATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATCGTGG
194 ATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGG
* * *
260 CTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
259 CTAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
**
325 GAGCCGGCC
324 GAGCCGGGG
* *
334 CCCCGGAACACCTTTTTGGCCAAAAATCGTGATGGATAGTACACGATTTCGGCTAAAAATTTTGC
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCT-AAAATTTTGC
* * *
399 AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAAGTATATAATTT
65 AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTC
* *
464 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTATTTT-AATTAA
130 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAA
* * *
528 TTTCTAA-AAAAATCGAAACAAGTTTCTGATGCTCGT-AAAA-ATGTCTTTAAATCAATTGTGGC
195 TTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGC
* * *
590 TAAGATTTGGAATGATGAATATAAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATTG
260 TAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
655 AGTCC-GGG
325 AG-CCGGGG
* * * * *
663 CCCCGAAATACCTTTTTAACCAAAAACCGTGAT--A-AATACATGATTTCGGCTAAAAATTTTG-
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCT-AAAATTTTGC
* * *
724 -AAAATTGAGCCG-AAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAAGTATATTATTC
65 AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTC
*
787 AATGCC-AAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTT-AATTAA
130 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAA
*
850 TTTCTAATA-AAATCGAAACAAGATTCTGATGCTCGTAAAAATA--TCTTTAAATCAATTGTGGC
195 TTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGC
* * * **
912 TGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAACTCATATAAAACTG
260 TAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
**
977 AGTTGGGG
325 AGCCGGGG
* * * * *
985 CCCCGTAAGACCTTTTTAGCCAAAAACAGTGATGGATAGTACACTATTTCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
* * * * *
1050 AAAACTAAGCCGAAAAATTTTTCCTTAATTTTTTAACACAATAGTCGTAAAAAATATATAATTTA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* * * *
1115 ATGACAAAAATATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATGAAT
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAAT
* * *
1180 TTCTAATAGAAATAGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTAGCT
196 TTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGCT
* * *
1245 AAGATTTGGAATGATGAATATAGATATTTTAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
261 AAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
*
1310 GTCGGGG
326 GCCGGGG
* * * *
1317 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATGGTATACGATTTCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
*
1382 AAAATTGAGTCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAAGTT-
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAA-TTC
* *
1446 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAAATGAA
130 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAA
* * *
1511 TTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGAAAAAACACGTCTTTAAATCAATTGTAGC
195 TTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGC
* *
1576 TAAGATTTGGAATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTG
260 TAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
*
1641 AGCCGAGG
325 AGCCGGGG
*
1649 TCCCGGAACACCTTTTT----------C-T-A--GATAGTACACGATTTCGGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
* *
1700 AAAATTAAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCATAAAAAATATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* * * *
1765 ATGCCAAAAAGATTAAAAGGATTCTCACACTTCTAATATCGTTTTTCCAATTTTTTTTGAATTAA
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTGAATTAA
* ** * *
1830 ATTCTAATAGAAATCGAAACAAGATTCCAATGCTCGTAAAGACACGTCTTTAAATCAATTGTGAC
195 TTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGC
* * * *
1895 TGAGATTTGGTATGATGAATATAGATATTTCAGGGAGTCTTGGCGCAAAAAATCATGCAAAATTG
260 TAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
*
1960 AGCCGGAG
325 AGCCGGGG
* * * * *
1968 CCCCGGAACACCTTTTTAACCAAAAACCGTAATGGATAGTACACAATATCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
* * * *
2033 AAAACTGAGCGGAAAAGTTTTTCCTCAATTTTTTGACACAATATTCGTAAAAAATATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
** * *
2098 AAACCAAAAAGATTTAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATATTTTTGAATTAAT
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAAT
* * * * * ** * * *
2163 TTATAATAAAAATCGAAATATGATTCTGATGCTCGTAAAATCAAATCATTAAATCCAA-TATGAC
196 TTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAAT-CAATTGTGGC
* * ** *
2227 TGAA-ATTTGGTTAT-ATGAATATATATGTTTCAACAAGTCTTGGCGCCAAAAAT-ATTCAAAAC
260 T-AAGATTTGG-TATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * * *
2289 TGTGGCTGTG
323 TGAGCCGGGG
*** * ** * * * *
2299 -CCCGGAACGTGTTTTTAGCAAAAAATTGTGATGGTTAGAACACGATTTCGGCTAAAGTATTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
* * * * * *
2363 AAAACTGAGCCGAAAACTTTTTCCTTAATTTTTTGACACAATAGTTGTAAAAATTATATAATTCG
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* * * * *
2428 ATTCCAAAAAGATTAAAAGGCTTTTCACACTTTTAATATCATTTTTCCTA-TTTTTTGAATTAAA
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAAT
*
2492 TTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGGCT
196 TTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGCT
*
2557 GAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
261 AAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
2622 GCC-GGG
326 GCCGGGG
* *
2628 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATAGATAGTACACGATTTCGGCTAAAATTTTGTA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
* * *
2693 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATGGTTGTAAAAAGTATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
*
2758 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTGAATTAA
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTGAATTAA
* * * * *
2823 TTTCTAATAAAAAAACGAAACAAGATTCTGATGCTCGTAAAATCAAGTCTTTAAATAAATTGTGG
195 TTTCTAAT-AGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGG
* *
2888 CGT-AGATTTGGTTTGATGAATATAGATATTTCAAGGATTCTTGGCGCCAAAAATCATGCAAAAC
259 C-TAAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
*
2952 TGAGTC-GGG
323 TGAGCCGGGG
2961 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
3026 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* * * * * *
3091 ATGCCAAAATGATTACAAGGCTTTGCACGTTTTTAATATCATTTTTCCTATTTTTTTGAATTAAT
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAAT
* *
3156 TTCTAACAAAAATCGAAA
196 TTCTAATAGAAATCGAAA
3174 GAACTTCAAT
Statistics
Matches: 2528, Mismatches: 266, Indels: 94
0.88 0.09 0.03
Matches are distributed among these distances:
317 2 0.00
318 133 0.05
319 152 0.06
320 1 0.00
321 1 0.00
322 200 0.08
323 60 0.02
324 23 0.01
325 13 0.01
326 35 0.01
327 51 0.02
328 55 0.02
329 232 0.09
330 357 0.14
331 68 0.03
332 685 0.27
333 459 0.18
334 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (332 bp):
CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAAT
TTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGGCT
AAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
GCCGGGG
Found at i:1948 original size:651 final size:652
Alignment explanation
Indices: 1--3173 Score: 4190
Period size: 651 Copynumber: 4.8 Consensus size: 652
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATATAGTACACGATTTCAGCTAAAATTTTG
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGG--ATAGTACACGATTTCAGCTAAAATTTTG
** * * *
66 CAAAAATTGAGTAGAAAAATTTTTCCTAAATTTTTTCACACAATAGTCGTAAAAATTATATAATT
64 CAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATT
131 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAATTAA
129 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAATTAA
* * * *
196 TTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATCGTGGC
194 TTTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGGC
* *
261 TGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTG
259 TAAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
* *
326 AGCCGGCCCCCCGGAACACCTTTTTGGCCAAAAATCGTGATGGATAGTACACGATTTCGGCTAAA
324 AGCCGG-GCCCCGGAACACCTTTTT--------A-CATGA-GGATAGTACACGATTTCGGCT-AA
* *
391 AATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAAGTA
377 AATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATA
* * *
456 TATAATTTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTATTT
442 TATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTT
* * * *
521 T-AATTAATTTCTAA-AAAAATCGAAACAAGTTTCTGATGCTCGT-AAAA-ATGTCTTTAAATCA
507 TGAATTAATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCA
* *
582 ATTGTGGCTAAGATTTGGAATGATGAATATAAATATTTCAAGGAGTCTTGGCGCCAAAAATCATG
572 ATTGTGACTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATG
*
647 CAAAATTGAGTCCGGG
637 CAAAACTGAGTCCGGG
* * * * *
663 CCCCGAAATACCTTTTTAACCAAAAACCGTGAT--A-AATACATGATTTCGGCTAAAAATTTTG-
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCT-AAAATTTTGC
* * *
724 -AAAATTGAGCCG-AAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAAGTATATTATTC
65 AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTC
*
787 AATGCC-AAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTAATTAAT
130 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAATTAAT
*
851 TTCTAAT-AAAATCGAAACAAGATTCTGATGCTCGTAAAAA-TA-TCTTTAAATCAATTGTGGCT
195 TTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGGCT
* * **
913 GAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAACTCATATAAAACTGA
260 AAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
** * * * *
978 GTTGGGGCCCCGTAAGACCTTTTTAGCCAAAAACAGTGATGGATAGTACACTATTTCAGCTAAAA
325 G-CCGGGCCCCGGAACACCTTTTT--------ACA-TGA-GGATAGTACACGATTTCGGCTAAAA
* * * *
1043 TTTTGCAAAAACTAAGCCGAAAAATTTTTCCTTAATTTTTTAACACAATAGTCGTAAAAAATATA
379 TTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATA
* * * *
1108 TAATTTAATGACAAAAATATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTG
444 TAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTG
* *
1173 AATGAATTTCTAATAGAAATAGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAAT
509 AATTAATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAAT
* *
1238 TGT-AGCTAAGATTTGGAATGATGAATATAGATATTTTAAAGAGTCTTGGCGCCAAAAATCATGC
574 TGTGA-CTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC
*
1302 AAAACTGAGTCGGGG
638 AAAACTGAGTCCGGG
* *
1317 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATGGTATACGATTTCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
*
1382 AAAATTGAGTCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAAGTT-
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAA-TTC
*
1446 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAAATGAA
130 AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTT-AATTAA
* * * * *
1511 TTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGAAAAAACACGTCTTTAAATCAATTGTAGC
194 TTTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGGC
** *
1576 TAAGATTTGGAATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTG
259 TAAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
*
1641 AGCCGAGGTCCCGGAACACCTTTTT-C-T-A-GATAGTACACGATTTCGGCTAAAATTTTGCAAA
324 AGCCG-GGCCCCGGAACACCTTTTTACATGAGGATAGTACACGATTTCGGCTAAAATTTTGCAAA
* *
1702 AATTAAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCATAAAAAATATATAATTCAAT
388 AATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCAAT
* * * * *
1767 GCCAAAAAGATTAAAAGGATTCTCACACTTCTAATATCGTTTTTCCAATTTTTTTTGAATTAAAT
453 GCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTGAATTAATT
* * *
1832 TCTAATAGAAATCGAAACAAGATTCCAATGCTCGTAAAGACACGTCTTTAAATCAATTGTGACTG
517 TCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGACTA
* * * *
1897 AGATTTGGTATGATGAATATAGATATTTCAGGGAGTCTTGGCGCAAAAAATCATGCAAAATTGAG
582 AGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
1962 -CCGGAG
647 TCCGG-G
* * *
1968 CCCCGGAACACCTTTTTAACCAAAAACCGTAATGGATAGTACACAATATCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
* * * *
2033 AAAACTGAGCGGAAAAGTTTTTCCTCAATTTTTTGACACAATATTCGTAAAAAATATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
** * *
2098 AAACCAAAAAGATTTAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATATTTTTGAATTAAT
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTAT-TTTTTTAATTAAT
* * * * * * * *
2163 TTATAATAAAAATCGAAATATGATTCTGATGCTCGTAAAATCAAATCATTAAATCCAA-TATGAC
195 TTCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAAT-CAATTGTGGC
* * ** *
2227 TGAA-ATTTGGTTAT-ATGAATATATATGTTTCAACAAGTCTTGGCGCCAAAAAT-ATTCAAAAC
259 T-AAGATTTGGTT-TGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * * *** * *
2289 TGTGGCTGTG-CCCGGAACGTGTTTTTAGCAAAAAATTGTGATGGTTAGAACACGATTTCGGCTA
322 TG-AGCCGGGCCCCGGAACACCTTTTTA-C-----A---TGA-GGATAGTACACGATTTCGGCTA
* * * * * * *
2353 AAGTATTGCAAAAACTGAGCCGAAAACTTTTTCCTTAATTTTTTGACACAATAGTTGTAAAAATT
376 AAATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAAT
* * * * *
2418 ATATAATTCGATTCCAAAAAGATTAAAAGGCTTTTCACACTTTTAATATCATTTTTCCTA-TTTT
441 ATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT
* * *
2482 TTGAATTAAATTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATC
506 TTGAATTAATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATC
* * *
2547 AATTGTGGCTGAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
571 AATTGTGACTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
2612 GCAAAACTGAG-CCGGG
636 GCAAAACTGAGTCCGGG
* * * *
2628 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATAGATAGTACACGATTTCGGCTAAAATTTTGTA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
* * *
2693 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATGGTTGTAAAAAGTATATAATTCA
66 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
*
2758 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTGAATTAA
131 ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTT-AATTAA
* * *
2823 TTTCTAATAAAAAAACGAAACAAGATTCTGATGCTCGTAAAATCAAGTCTTTAAATAAATTGTGG
194 TTTCTAAT-AAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGG
*
2888 CGT-AGATTTGGTTTGATGAATATAGATATTTCAAGGATTCTTGGCGCCAAAAATCATGCAAAAC
258 C-TAAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
*
2952 TGAGTCGGGCCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAA
322 TGAGCCGGGCCCCGGAACACCTTTTTA--C----A---TGA-GGATAGTACACGATTTCGGCTAA
3017 AATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATA
377 AATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATA
* * * * * *
3082 TATAATTCAATGCCAAAATGATTACAAGGCTTTGCACGTTTTTAATATCATTTTTCCTATTTTTT
442 TATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTT
* *
3147 TGAATTAATTTCTAACAAAAATCGAAA
507 TGAATTAATTTCTAATAGAAATCGAAA
3174 GAACTTCAAT
Statistics
Matches: 2216, Mismatches: 240, Indels: 108
0.86 0.09 0.04
Matches are distributed among these distances:
649 13 0.01
650 274 0.12
651 535 0.24
652 40 0.02
653 36 0.02
654 182 0.08
655 53 0.02
656 20 0.01
657 26 0.01
658 21 0.01
659 51 0.02
660 221 0.10
661 173 0.08
662 152 0.07
663 295 0.13
664 124 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (652 bp):
CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
ATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAATTAATT
TCTAATAAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAAATCAATTGTGGCTA
AGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
CCGGGCCCCGGAACACCTTTTTACATGAGGATAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
TGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCAATGCC
AAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTA
ATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTGACTAAGAT
TTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCCG
GG
Found at i:1983 original size:983 final size:977
Alignment explanation
Indices: 1--3173 Score: 4401
Period size: 983 Copynumber: 3.2 Consensus size: 977
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATATAGTACACGATTTCAGCTAAAATTTTG
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGG--ATAGTACACGATTTCAGCTAAAATTTTG
* ** * * *
66 CAAAAATTGAGTAGAAAAATTTTTCCTAAATTTTTTCACACAATAGTCGTAAAAATTATATAATT
64 CAAAAACTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATT
* *
131 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTTAATTA
129 CAATGACAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATTA
* *
195 ATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATCGTGG
194 ATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTAG
* * * *
260 CTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCAAAAAATCATGCAAAACT
259 CTAAGATTTGGTATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACT
* *
325 GAGCCGGCCCCCCGGAACACCTTTTTGGCCAAAAATCGTGATGGATAGTACACGATTTCGGCTAA
324 GAGCCGGCGCCCCGGAACACCTTTTTAGCCAAAAATCGTGATGGATAGTACACGATTTCGGCT-A
* *
390 AAATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAAGT
388 AAATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAAT
* *
455 ATATAATTTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTATT
453 ATATAA-TTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT
* * * *
520 TTAATTAATTTCTAA-AAAAATCGAAACAAGTTTCTGATGCTCGTAAAA-ATGTCTTTAAATCAA
517 TTAATTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGAAAAACAAGTCTTTAAATCAA
*
583 TTGTGGCTAAGATTTGGAATGATGAATATAAATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC
582 TTGTGGCTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGC
* * * * * *
648 AAAATTGAGTCCGGGCCCCGAAATACCTTTTTAACCAAAAACCGTGATAAATACATGATTTCGGC
647 AAAACTGAG-CCGGGCCCCGGAACACCTTTTT-A-C--ATA----GAT-AGTACACGATTTCGGC
*
713 TAAAAATTTTG-AAAATTGAGCCG-AAAATTTTTCCTCAATTTTTTGACACAATAGTCGGAAAAA
702 T-AAAATTTTGAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAA
*
776 GTATATTATTCAATGCC-AAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTA-TT
766 GTATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTT
839 TTTTT-AATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAA-ATA-TCTTTAAA
831 TTTTTGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAACA-AGTCTTTAAA
*
901 TCAATTGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAACTC
895 TCAATTGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATC
** *
966 ATATAAAACTGAGTTGGGG
960 ATGCAAAACTGAG-TCGGG
* * * * *
985 CCCCGTAAGACCTTTTTAGCCAAAAACAGTGATGGATAGTACACTATTTCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
* * * *
1050 AAAACTAAGCCGAAAAATTTTTCCTTAATTTTTTAACACAATAGTCGTAAAAAATATATAATTTA
66 AAAACTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* *
1115 ATGACAAAAATATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATGAAT
131 ATGACAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATTAAT
*
1180 TTCTAATAGAAATAGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTAGCT
196 TTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTAGCT
* *
1245 AAGATTTGGAATGATGAATATAGATATTTTAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
261 AAGATTTGGTATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
* * * * * * *
1310 GTCGGGGCCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATGGTATACGATTTCAGCTAAAA
326 GCCGGCGCCCCGGAACACCTTTTTAGCCAAAAATCGTGATGGATAGTACACGATTTCGGCTAAAA
*
1375 TTTTGCAAAAATTGAGTCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATA
391 TTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATA
1440 TAAGTTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTA
456 TAA-TTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTT-
* * *
1505 AATGAATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGAAAAAACACGTCTTTAAATCAAT
519 AATTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCG-AAAAACAAGTCTTTAAATCAAT
* *
1570 TGTAGCTAAGATTTGGAATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCA
583 TGTGGCTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
*
1635 AAACTGAGCCGAGGTCCCGGAACACCTTTTT-C-TAGATAGTACACGATTTCGGCTAAAATTTTG
648 AAACTGAGCCG-GGCCCCGGAACACCTTTTTACATAGATAGTACACGATTTCGGCTAAAATTTTG
* * *
1698 CAAAAATTAAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCATAAAAAATATATAATT
712 -AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAGTATATAATT
* * * * *
1763 CAATGCCAAAAAGATTAAAAGGATTCTCACACTTCTAATATCGTTTTTCCAATTTTTTTTGAATT
776 CAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTGAATT
* ** *
1828 AAATTCTAATAGAAATCGAAACAAGATTCCAATGCTCGTAAAGACACGTCTTTAAATCAATTGTG
841 AATTTCTAATA-AAATCGAAACAAGATTCTGATGCTCGTAAA-ACAAGTCTTTAAATCAATTGTG
* * * * *
1893 ACTGAGATTTGGTATGATGAATATAGATATTTCAGGGAGTCTTGGCGCAAAAAATCATGCAAAAT
904 GCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
*
1958 TGAGCCGGAG
969 TGAGTCGG-G
* * *
1968 CCCCGGAACACCTTTTTAACCAAAAACCGTAATGGATAGTACACAATATCAGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
* * *
2033 AAAACTGAGCGGAAAAGTTTTTCCTCAATTTTTTGACACAATATTCGTAAAAAATATATAATTCA
66 AAAACTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* *
2098 A-AACCAAAAAGATTTAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TATTTTTGAATTA
131 ATGA-CAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTA-TTTTGAATTA
* * * * * * ** *
2161 ATTTATAATAAAAATCGAAATATGATTCTGATGCTCGTAAAATCAAATCATTAAATCCAATATG-
194 ATTTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAAT-CAAT-TGT
* * *
2225 A-CTGAA-ATTTGGTTAT-ATGAATATATATGTTTCAACA-AGTCTTGGCGCCAAAAAT-ATTCA
257 AGCT-AAGATTTGG-TATGATGAATATAGATATTTCAA-AGAGTCTTGGCGCCAAAAATCATGCA
* * * * *** * * * *
2285 AAACTGTGGCTGTG-CCCGGAACGTGTTTTTAGCAAAAAATTGTGATGGTTAGAACACGATTTCG
319 AAACTGAGCCGGCGCCCCGGAACACCTTTTTAGCCAAAAATCGTGATGGATAGTACACGATTTCG
* * * * * *
2349 GCTAAAGTATTGCAAAAACTGAGCCGAAAACTTTTTCCTTAATTTTTTGACACAATAGTTGTAAA
384 GCTAAAATTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAA
* * * * * *
2414 AATTATATAATTCGATTCCAAAAAGATTAAAAGGCTTTTCACACTTTTAATATCATTTTTCCTAT
449 AAATATATAATT-AATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTAT
* *
2479 TTTTTGAATTAAATTCTAATAGAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAGTCTTTAA
513 TTTTTTAATTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCG-AAAAACAAGTCTTTAA
* *
2544 ATCAATTGTGGCTGAGATTTGGTATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAT
577 ATCAATTGTGGCTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAT
2609 CATGCAAAACTGAGCCGGGCCCCGGAACACCTTTTTAGCCAAAAACCGTGATAGATAGTACACGA
642 CATGCAAAACTGAGCCGGGCCCCGGAACACCTTTTT--------A-C---ATAGATAGTACACGA
* *
2674 TTTCGGCTAAAATTTTGTAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATGGTT
695 TTTCGGCTAAAATTTTG-AAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTC
2739 GTAAAAAGTATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTT
759 GTAAAAAGTATATAATTCAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTT
*
2804 CCTATTTTTTTTGAATTAATTTCTAATAAAAAAACGAAACAAGATTCTGATGCTCGTAAAATCAA
824 CCTATTTTTTTTGAATTAATTTCTAAT--AAAATCGAAACAAGATTCTGATGCTCGTAAAA-CAA
* *
2869 GTCTTTAAATAAATTGTGGC-GTAGATTTGGTTTGATGAATATAGATATTTCAAGGATTCTTGGC
886 GTCTTTAAATCAATTGTGGCTG-AGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGC
2933 GCCAAAAATCATGCAAAACTGAGTCGGG
950 GCCAAAAATCATGCAAAACTGAGTCGGG
* *
2961 CCCCGGAACACCTTTTTAGCCAAAAACCGTGATGGATAGTACACGATTTCGGCTAAAATTTTGCA
1 CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
*
3026 AAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
66 AAAACTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
* * * * * * * *
3091 ATGCCAAAATGATTACAAGGCTTTGCACGTTTTTAATATCATTTTTCCTATTTTTTTGAATTAAT
131 ATGACAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATTAAT
* *
3156 TTCTAACAAAAATCGAAA
196 TTCTAATAGAAATCGAAA
3174 GAACTTCAAT
Statistics
Matches: 1945, Mismatches: 199, Indels: 81
0.87 0.09 0.04
Matches are distributed among these distances:
974 9 0.00
975 15 0.01
976 14 0.01
977 53 0.03
978 39 0.02
979 25 0.01
980 149 0.08
981 185 0.10
982 283 0.15
983 534 0.27
984 66 0.03
985 9 0.00
986 100 0.05
989 1 0.00
993 351 0.18
994 111 0.06
995 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (977 bp):
CCCCGGAACACCTTTTTAACCAAAAACCGTGATGGATAGTACACGATTTCAGCTAAAATTTTGCA
AAAACTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATATAATTCA
ATGACAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTATTTTGAATTAAT
TTCTAATAGAAATCGAAACAAGATTCCGATGCTCGTAAAAACACGTCTTTAAATCAATTGTAGCT
AAGATTTGGTATGATGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
GCCGGCGCCCCGGAACACCTTTTTAGCCAAAAATCGTGATGGATAGTACACGATTTCGGCTAAAA
TTTTGCAAAAATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAATATA
TAATTAATGCCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTAA
TTAATTTCTAATAGAAATCGAAACAAGATTCTGATGCTCGAAAAACAAGTCTTTAAATCAATTGT
GGCTAAGATTTGGAATGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAA
CTGAGCCGGGCCCCGGAACACCTTTTTACATAGATAGTACACGATTTCGGCTAAAATTTTGAAAA
ATTGAGCCGAAAAATTTTTCCTCAATTTTTTGACACAATAGTCGTAAAAAGTATATAATTCAATG
CCAAAAAGATTAAAAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTGAATTAATTT
CTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAACAAGTCTTTAAATCAATTGTGGCTGAGA
TTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCG
GG
Found at i:26399 original size:18 final size:18
Alignment explanation
Indices: 26378--26473 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
26368 TGGTGGTGGG
* * *
26378 TCTTTGGGTTTTTCGGGT
1 TCTTTGGGTTTCTCAGGC
* *
26396 TCTTTTGGTTTCTCAGGT
1 TCTTTGGGTTTCTCAGGC
26414 TGC-TTGGGCTTT-TCAGGC
1 T-CTTTGGG-TTTCTCAGGC
* *
26432 TCTTTAGGCTTCTCAGGC
1 TCTTTGGGTTTCTCAGGC
*
26450 TCTTTGGGTTTGTCAGGC
1 TCTTTGGGTTTCTCAGGC
26468 TTCTTT
1 -TCTTT
26474 TCAGGCTCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
17 3 0.05
18 51 0.81
19 9 0.14
ACGTcount: A:0.05, C:0.19, G:0.27, T:0.49
Consensus pattern (18 bp):
TCTTTGGGTTTCTCAGGC
Found at i:26421 original size:36 final size:36
Alignment explanation
Indices: 26378--26474 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 36
26368 TGGTGGTGGG
* *
26378 TCTTTGGGTTTTTCGGGTTCTTTTGGTTTCTCAGGT
1 TCTTTGGGTTTTTCGGGTTCTTTTGGCTTCTCAGGC
* * * *
26414 TGC-TTGGGCTTTTCAGGCTCTTTAGGCTTCTCAGGC
1 T-CTTTGGGTTTTTCGGGTTCTTTTGGCTTCTCAGGC
* *
26450 TCTTTGGGTTTGTCAGGCTTCTTTT
1 TCTTTGGGTTTTTC-GGGTTCTTTT
26475 CAGGCTCTTT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
35 1 0.02
36 38 0.83
37 7 0.15
ACGTcount: A:0.05, C:0.19, G:0.27, T:0.49
Consensus pattern (36 bp):
TCTTTGGGTTTTTCGGGTTCTTTTGGCTTCTCAGGC
Found at i:26480 original size:30 final size:30
Alignment explanation
Indices: 26444--26520 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 30
26434 TTTAGGCTTC
26444 TCAGGCTCTTTGGGTTTGTCAGGCTTCTTT
1 TCAGGCTCTTTGGGTTTGTCAGGCTTCTTT
*
26474 TCAGGCTCTTTGGGTTTGTCAGGTTTCTTT
1 TCAGGCTCTTTGGGTTTGTCAGGCTTCTTT
*
26504 TCAGGCTCCTTGGGTTT
1 TCAGGCTCTTTGGGTTT
26521 CTTCTCAGGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.06, C:0.19, G:0.27, T:0.47
Consensus pattern (30 bp):
TCAGGCTCTTTGGGTTTGTCAGGCTTCTTT
Found at i:26540 original size:30 final size:30
Alignment explanation
Indices: 26506--26591 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
26496 GTTTCTTTTC
* *
26506 AGGCTCCTTGGGTTTCTTCTCAGGCTCTTT
1 AGGCTTCTCGGGTTTCTTCTCAGGCTCTTT
* *
26536 AGGCTTCTCGGGTTTCTTCTCGGGTTCTTT
1 AGGCTTCTCGGGTTTCTTCTCAGGCTCTTT
* * *
26566 AGGTTTATCGGGTTTTTTCTCAGGCT
1 AGGCTTCTCGGGTTTCTTCTCAGGCT
26592 GAGGCTGAGG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.07, C:0.22, G:0.26, T:0.45
Consensus pattern (30 bp):
AGGCTTCTCGGGTTTCTTCTCAGGCTCTTT
Found at i:26543 original size:21 final size:21
Alignment explanation
Indices: 26498--26543 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
26488 TTTGTCAGGT
* * *
26498 TTCTTTTCAGGCTCCTTGGGT
1 TTCTTCTCAGGCTCCTTAGGC
*
26519 TTCTTCTCAGGCTCTTTAGGC
1 TTCTTCTCAGGCTCCTTAGGC
26540 TTCT
1 TTCT
26544 CGGGTTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.26, G:0.20, T:0.48
Consensus pattern (21 bp):
TTCTTCTCAGGCTCCTTAGGC
Found at i:26565 original size:81 final size:81
Alignment explanation
Indices: 26440--26591 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 81
26430 GCTCTTTAGG
* * * * * *
26440 CTTCTCAGGCTCTTTGGGTTTGTCAGGCTTCTTTTCAGGCTCTTTGGGTTTGTCAGGTTTCTTT-
1 CTTCTCAGGCTCTTTAGGCTTCTCAGGCTTCTTCTCAGGCTCTTTAGGTTTATCAGGTTT-TTTC
26504 TCAGGCTCCTTGGGTTT
65 TCAGGCTCCTTGGGTTT
* * * * *
26521 CTTCTCAGGCTCTTTAGGCTTCTCGGGTTTCTTCTCGGGTTCTTTAGGTTTATCGGGTTTTTTCT
1 CTTCTCAGGCTCTTTAGGCTTCTCAGGCTTCTTCTCAGGCTCTTTAGGTTTATCAGGTTTTTTCT
26586 CAGGCT
66 CAGGCT
26592 GAGGCTGAGG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 3 0.05
81 56 0.95
ACGTcount: A:0.07, C:0.22, G:0.25, T:0.47
Consensus pattern (81 bp):
CTTCTCAGGCTCTTTAGGCTTCTCAGGCTTCTTCTCAGGCTCTTTAGGTTTATCAGGTTTTTTCT
CAGGCTCCTTGGGTTT
Found at i:26571 original size:51 final size:50
Alignment explanation
Indices: 26426--26571 Score: 136
Period size: 51 Copynumber: 2.9 Consensus size: 50
26416 CTTGGGCTTT
* * * *
26426 TCAGGCTCTTTAGGCTTCTCAGG-CTCTTT-GGGTT-TGTCAGGCTTCTTT
1 TCAGGCTCTTTAGGCTTCTCAGGTTTCTTTCGGGTTCT-TTAGGTTTCTTC
* * * * * * *
26474 TCAGGCTCTTTGGGTTTGTCAGGTTTCTTTTCAGGCTCCTTGGGTTTCTTC
1 TCAGGCTCTTTAGGCTTCTCAGGTTTC-TTTCGGGTTCTTTAGGTTTCTTC
*
26525 TCAGGCTCTTTAGGCTTCTCGGGTTTCTTCTCGGGTTCTTTAGGTTT
1 TCAGGCTCTTTAGGCTTCTCAGGTTTCTT-TCGGGTTCTTTAGGTTT
26572 ATCGGGTTTT
Statistics
Matches: 74, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
48 20 0.27
49 2 0.03
50 5 0.07
51 47 0.64
ACGTcount: A:0.07, C:0.22, G:0.25, T:0.46
Consensus pattern (50 bp):
TCAGGCTCTTTAGGCTTCTCAGGTTTCTTTCGGGTTCTTTAGGTTTCTTC
Found at i:27853 original size:5 final size:5
Alignment explanation
Indices: 27843--27878 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
27833 GACTCTACAA
27843 TATTG TATTG TATTG TATTG TATTG TATTG TATTG T
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG T
27879 TGGGTTGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (5 bp):
TATTG
Found at i:30589 original size:3 final size:3
Alignment explanation
Indices: 30581--30638 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
30571 CTCCATTCAA
* * *
30581 ATT ATT ATT ATT ATT ATT ATT -TT TTT ATC AGT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
30627 A-T ATT A-T ATT AT
1 ATT ATT ATT ATT AT
30639 ATAATATTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 8 0.17
3 38 0.83
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30628 original size:5 final size:5
Alignment explanation
Indices: 30612--30646 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
30602 TTTTTATCAG
*
30612 TATTA TTATTA TATTA TATTA TATTA TATAA TATT
1 TATTA -TATTA TATTA TATTA TATTA TATTA TATT
30647 GTTATATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:33926 original size:7 final size:8
Alignment explanation
Indices: 33911--33985 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 8
33901 TGTGAAAGAT
33911 GAAGAGAA
1 GAAGAGAA
33919 GAAG-GAA
1 GAAGAGAA
*
33926 GAAGACAA
1 GAAGAGAA
33934 GAA-AGAA
1 GAAGAGAA
*
33941 G-AGAACAAA
1 GAAG-A-GAA
33950 GAAGAGAAA
1 GAAGAG-AA
33959 GAAGCAG-A
1 GAAG-AGAA
33967 GAAGA-AA
1 GAAGAGAA
33974 GAAGAAGAA
1 GAAG-AGAA
33983 GAA
1 GAA
33986 CGCAAAGGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
6 1 0.02
7 17 0.32
8 16 0.30
9 15 0.28
10 4 0.08
ACGTcount: A:0.64, C:0.04, G:0.32, T:0.00
Consensus pattern (8 bp):
GAAGAGAA
Found at i:33935 original size:15 final size:15
Alignment explanation
Indices: 33911--33978 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
33901 TGTGAAAGAT
*
33911 GAAGAGAAGAAGGAA
1 GAAGACAAGAAGGAA
*
33926 GAAGACAAGAAAGAA
1 GAAGACAAGAAGGAA
33941 G-AGAACAAAGAAGAGAAA
1 GAAG-AC-AAGAAG-G-AA
*
33959 GAAG-CAGAGAAGAAA
1 GAAGACA-AGAAGGAA
33974 GAAGA
1 GAAGA
33979 AGAAGAACGC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
14 2 0.05
15 22 0.52
16 6 0.14
17 7 0.17
18 3 0.07
19 2 0.05
ACGTcount: A:0.63, C:0.04, G:0.32, T:0.00
Consensus pattern (15 bp):
GAAGACAAGAAGGAA
Found at i:33939 original size:12 final size:12
Alignment explanation
Indices: 33918--33985 Score: 75
Period size: 12 Copynumber: 5.6 Consensus size: 12
33908 GATGAAGAGA
*
33918 AGAAGGAAGAAG
1 AGAAGAAAGAAG
*
33930 ACAAGAAAGAAG
1 AGAAGAAAGAAG
*
33942 AGAACAAAGAAG
1 AGAAGAAAGAAG
*
33954 AGAA-AGAAGCAG
1 AGAAGA-AAGAAG
33966 AGAAGAAAGAAG
1 AGAAGAAAGAAG
33978 AAGAAGAA
1 -AGAAGAA
33986 CGCAAAGGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
11 1 0.02
12 38 0.81
13 8 0.17
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (12 bp):
AGAAGAAAGAAG
Found at i:38753 original size:21 final size:21
Alignment explanation
Indices: 38692--38755 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
38682 TTAACACTGT
38692 TTAGGTACTGTACATATGAGA
1 TTAGGTACTGTACATATGAGA
* *
38713 TTA--TAC-GTTACAGATTAGA
1 TTAGGTACTG-TACATATGAGA
38732 TTAGGTACTGTACATATGAGA
1 TTAGGTACTGTACATATGAGA
38753 TTA
1 TTA
38756 TTAGAGCAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 15 0.43
21 18 0.51
22 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (21 bp):
TTAGGTACTGTACATATGAGA
Found at i:52548 original size:7 final size:7
Alignment explanation
Indices: 52536--52590 Score: 110
Period size: 7 Copynumber: 7.9 Consensus size: 7
52526 CTGGCCTCAT
52536 CCCGCAG
1 CCCGCAG
52543 CCCGCAG
1 CCCGCAG
52550 CCCGCAG
1 CCCGCAG
52557 CCCGCAG
1 CCCGCAG
52564 CCCGCAG
1 CCCGCAG
52571 CCCGCAG
1 CCCGCAG
52578 CCCGCAG
1 CCCGCAG
52585 CCCGCA
1 CCCGCA
52591 TATATTTGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.15, C:0.58, G:0.27, T:0.00
Consensus pattern (7 bp):
CCCGCAG
Found at i:53970 original size:6 final size:6
Alignment explanation
Indices: 53961--53988 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53951 ATTTCTTCCG
53961 CCATAC CCATAC CCATAC CCATAC CCAT
1 CCATAC CCATAC CCATAC CCATAC CCAT
53989 TATCGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CCATAC
Found at i:83181 original size:6 final size:6
Alignment explanation
Indices: 83170--83197 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
83160 ATATGGTGTG
83170 TGTGCC TGTGCC TGTGCC TGTGCC TGTG
1 TGTGCC TGTGCC TGTGCC TGTGCC TGTG
83198 GGGGGCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.36, T:0.36
Consensus pattern (6 bp):
TGTGCC
Found at i:83242 original size:6 final size:6
Alignment explanation
Indices: 83231--83260 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
83221 ATGCTCTAGT
83231 TTGTAG TTGTAG TTGTAG TTGTAG TTGTAG
1 TTGTAG TTGTAG TTGTAG TTGTAG TTGTAG
83261 CTGAGCTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TTGTAG
Found at i:83357 original size:18 final size:19
Alignment explanation
Indices: 83321--83369 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
83311 TTGTGATTCA
*
83321 TTTCACTTTCACTTTTGAG
1 TTTCACTTTCACGTTTGAG
83340 TTTCACTTTCA-GTTTGAG
1 TTTCACTTTCACGTTTGAG
*
83358 TTTCATTTTCAC
1 TTTCACTTTCAC
83370 TCATTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (19 bp):
TTTCACTTTCACGTTTGAG
Found at i:86541 original size:6 final size:6
Alignment explanation
Indices: 86532--86557 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
86522 AATTGCCAAC
86532 ACTGCA ACTGCA ACTGCA ACTGCA AC
1 ACTGCA ACTGCA ACTGCA ACTGCA AC
86558 ATACCTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
ACTGCA
Done.