Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019715.1 Corchorus olitorius cultivar O-4 contig19748, 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: 6540
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:988 original size:333 final size:333
Alignment explanation
Indices: 1--4555 Score: 2604
Period size: 334 Copynumber: 13.2 Consensus size: 333
* * *
1 CCCCGTAACGCATTTTTAGCCAAAAACCGTGA----TAACGTACACGATTTCGGCAAAAACATTG
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAA--TACACGATTTCGGCAAAAACTTTG
* * *
62 CAAAAATTTGACCCGAAAGATTTTT-TCCTAATTTTGAACCGCAATACTCGTAAAAATTATATAA
64 CAAAAA-TTGACCCGAAAGATTTTTCTTC-AATTTTTAACCGCAATACTCGTAAAAAATATATAA
* * * *
126 TTCAATGGCAGAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCATTCCCGA
127 TTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGA
* * *
191 ATTAATTTCTAATTAATTAGAAACAGGATTCTGAAGATCGTAAAAACAAATCCATAAATCCATTG
192 ATTAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTG
*
256 TGGCTGAGATTTGGGATGATGAATATAGATATTTGAATGTGTCTTGGCGCCAAAAATCATGCAAA
257 TGGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAA
321 ACTGAGCCGGGG
322 ACTGAGCCGGGG
** *
333 CCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAACTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* *
398 AAAATTGACCTGAAA-ATTTTTCCTT-AATTTTGAACCGCAATACTCGTAAAAAATATATAATTC
66 AAAATTGACCCGAAAGATTTTT-CTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTC
* * * * ** *
461 AACGACAAAAAGATTGAAGGGCTTTTCAGGCGTCTAATATCATTCTCTTTCAATTTTTTTTCGTA
130 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATT-T-TTTCAATTCTTTCCCGAA
** * * * * * * * *
526 TTAATTTCCGATTAAATCGAAACATGATTCAGATGCTCATAAAATCAAATCCTTAAATCCAATGT
193 TTAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGT
* ** * *
591 GGCTGAGATTTGGGATGATGAATATAGATATTTCG-ATCAGTCTTGAAGCAAAAAATTATGCAAA
258 GGCTGAGATTTGGGATGATGAATATAGATATTT-GAATGAGTCTTGGCGCCAAAAATCATGCAAA
* * *
655 ACTTACCCGGTG
322 ACTGAGCCGGGG
* ** * *
667 CCCCAGCTCGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAATAATTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* * *
732 AAAATTGACCCGAAATATTTTTCTTCAATTTTTAACCGCAATATTTGTAAAAAATATATAATTCA
66 AAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
* * *** * * *
797 ATGCCAAAAATATTGAAGATATTTTCACGCTTCTAATAACAGTTTTTCAATTCTTTCCCAAATTA
131 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
* * * * * *
862 ATTTCTAATTAATTAGAAATAAGATTCTGATGATCGTAAAAAAAAATCTATAAATCCATTATAGC
196 ATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
927 TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
261 TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
* *
992 AACCGGAG
326 AGCCGGGG
* *
1000 CCCCGGAACGTGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGACAAAAACTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* * *
1065 AAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGGAATAATCATAAAAAATATATAATTCA
66 AAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
** * * *
1130 ACGTGAAAAAGATTTAAGAGATTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
131 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
* * *
1195 ATTTCTAATTAACTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTATGGA
196 ATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
* * * *
1260 TGAGATTTGGGATGATTAATATTGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTT
261 TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
1325 AGCCGGGG
326 AGCCGGGG
* * *
1333 CCCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* *
1398 AATATTGACCCGAAAGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
66 AAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
* * *
1463 ACGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATCATTTTTTCAATTTTTTCCCGAATTA
131 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
*
1528 ATTTCTAATTAAATCGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
196 ATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
* * * * *
1593 TGATATTTGGGATGATTAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCTTGCAAAACTG
261 TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
1658 AGCCGGGG
326 AGCCGGGG
* **** * ****** * * * *
1666 CCCCGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAGCCAAAAACCG-TG
1 CCCCG----GAA-C--GC-GTTTTTAG-CCAAAAACCGTGATG-G---TTA---ATACA-CGAT-
* * * * * * *
1730 AT-GGTTAGTACACGATTTCGGCAAAAATTTTGCAAATATTGACCCAAAAGGTTTTTCATCAATT
48 TTCGG-CA-AAAAC--TTT--GC--AAA--------A-ATTGACCCGAAAGATTTTTCTTCAATT
* * * * *
1794 TTTAACCGCAATACTCGTAAAAAATATATAATTTAATGGCAGAAAGATTGAAGGGCTTTTCAGGC
96 TTTAACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGC
* * * * * ** *
1859 GTCTAATATCATTTTCTTTTTAATT-TTTTCAGTATTAATTTCCGATTAAATCGAAACATGCCCA
161 TTCTAATATCA--TT-TTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATAGAAACA-----A
* * ** ** * ** * * ** **
1923 AACGCTCGTTTTTTTCG-CACTACAATGGTTCCTTTTTAAA-AGATTGTGAGACCCAGGCATTT-
218 GA--TTC-TGATGATCGTAAAAACAA---ATCC---ATAAATCCATTGTG-G-CTGA-G-ATTTG
* * * *** ** * * **** *
1985 GCATGACCCTGGGAT-T-GTTCTAGGGGGGCCTCTAGTGCTTGGGCCTCCATTGCTCCATTGC-T
270 GGATGA---T-GAATATAG--ATA--TTTGAAT-GAGT-CTT-GG-CGCCAAAAAT-CA-TGCAA
** ** ***
2047 TGCTTTGCTTTGG
321 AACTGAGCCGGGG
** *** * * ** * *
2060 CCTCCCAAATCAAATTCTTAAATCCAATGTGACTGAGATTTGGGATAATGAATACA-GATATT--
1 CC-CCGGAA-CGCGTT-TT-TAGCCAA--AAACCGTGA--T-GG-T--T-AATACACGAT-TTCG
* ** * * ** * **
2122 TCAATGAGCCTTGGCGCCAAAAA-TCATGC-AAA-ACTTAGTCGGGTCCCCGGAACGCGTTTTT-
52 GCAA--AAACTT--TG-CAAAAATTGACCCGAAAGA-TT--T---TTCTTC--AA----TTTTTA
* * * * **** * * * ** *** **
2183 AGC-CAAAAATCGTGATGGTTAGTACACGATT--TCGACAAAAACTTTGCAA-AAATTGACCCGA
100 ACCGCAATACTCGTAAAAAATA-TATA--ATTCAACGCCAAAAAGATTG-AAGGGCTT--TTC--
* * * ** * ** * * * * ** * * *
2244 AAGATTTTTTTATCAATTTTT-AACCACAATACTCGTAA-AAAAATATAATTCAA-CGCCAAA-A
157 ACGCTTCTAATATCATTTTTTCAA-TTC-TTTCCCG-AATTAATTTCTAATTAAATAG--AAACA
* * ** *** * * ** ** * *
2305 AGA-T-TGACGGGCTTTTCACACTTCTAATAT-CATTTTTTCAATTCATTCCCGAATTA-ATTTC
217 AGATTCTGA--TGATCGT-A-AAAAC-AA-ATCCA-----TAAATCCATT-GTGGCTGAGATTTG
** * * * *** * *
2366 TAATTAATTAGAA-ACAGGAT-TCTG-ATGA-TCGTAAAAACAAAACCATAAATCCATTGTGGCT
270 GGA-TGA-T-GAATATA-GATATTTGAATGAGTC-T--TGGC---GCCAAAAAT-CA---T-GC-
* ** ** *
2427 GAGATTTGAGATGATGAATATAGT
319 -AAAACTGAGCCG--G------GG
***** * * *** * * * * *
2451 TATTTGAATGTGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCTTGGA-ACGCGTTTT
1 CCCCGGAACGCGT-TTTTAGCCAAAAA-C---C----GTGA----TGG--TT-AATACACG-ATT
* *
2515 TAGCCAAAAACCGTG-ATGGTTAATACACGATTTTTGGAAAAAATTTTGCAAAAATTGAACCGAA
49 T----------CG-GCA-----AA-A-AC----TTT-G-CAAAA----------ATTGACCCGAA
* * * *
2579 AGATTTTTCATCAATTTTTAACCGCAATACTCATAAGAAATATATAATTCAAAGCCAAAAAGATT
80 AGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATT
* * * *
2644 GAAGAGATTTTCACGCTTCTAATATCATTTTTTCAATTCTTTACCGAATTAATTTCTAATTAATT
145 GAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAAT
*
2709 AGAAACAAGATTTTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGCTGAGATTTGGGATG
210 AGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGCTGAGATTTGGGATG
* * * * * *
2774 ATTAATATAGATATTTCAATGAGTATTGGCGCCAAAAACCATACAAAACAT-AGCCGAGG
275 ATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAAC-TGAGCCGGGG
* * * * *
2833 CCCCGTAACGCATTTTTAGCCAAAAAGCCGTGATGATTAGTACACGATTTCGGCAAAAATTTTGC
1 CCCCGGAACGCGTTTTTAGCCAAAAA-CCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGC
* *
2898 AAATATTGACCC-AAAGGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATT
65 AAAAATTGACCCGAAA-GATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATT
* * * * * *
2962 CAATGCCAAAAAGATTGAAGGTCTTTTCACACTTCTATTATCATTTTTTCATTTCTTTCCCAAAT
129 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAAT
* *
3027 TAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCATAAATCCATTGTG
194 TAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTG
*
3092 GCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAAC
259 GCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAAC
* *
3157 TTAGTCGGGG
324 TGAGCCGGGG
* * * * * * *
3167 CACAGGAACGCGTTTTTAACCAAAAACAGTGCTGGTTAGTACACGATTTCGGTAAAAACTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* ** * *
3232 AAAATTGACCCGAAAGATTATTTCTT-GATTTAAAACCGCAAAACTCTTAAAAAATATATAATTC
66 AAAATTGACCCGAAAGATT-TTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTC
* * * * * *
3296 AACGACAGAAAGATTGAAGGGCTTTTCAGGCGTCTAATATCAGTTTCTTTCAATT-TTTTCCGTA
130 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA-TTT-TTTCAATTCTTTCCCGAA
** * * * * * * *
3360 TTAATTTCCGATTAAATCGAAACATGATTCAGATGCTCGTAAAATCAAATCCTTAAATCCAATGT
193 TTAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGT
* *
3425 GGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGAGTCAAAAATCATGCAAAA
258 GGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAA
3490 CTGAGCCGGGG
323 CTGAGCCGGGG
* * ** * *
3501 CCCCGGTACGCGTTTTTAGCCAAAAACCGTTATTCTTAGTACACAATTTCGGCAAAAACTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* * *
3566 AAAATTGATCCGAAA-ATTTTTTCCTT-AATTTTGAACCGCAATACTCGTAAATAATATATAATT
66 AAAATTGACCCGAAAGA-TTTTT-CTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATT
* * * * ** * ** *
3629 CAATGGCAGAAAGATTGAAGGGCTTTTCAGGGGTCTAATATCATTCTCTTTCAATTTTTTTTCGT
129 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATT-T-TTTCAATTCTTTCCCGA
** * * * * * * *
3694 ATTAATTTCCGATTAAATCGAAACATGATTCAGAT-ACTTGTAAAATCAAATCCTTAAATCCAAT
192 ATTAATTTCTAATTAAATAGAAACAAGATTCTGATGA-TCGTAAAAACAAATCCATAAATCCATT
* *
3758 GTGGCTAAGATTTGGGATGATGAATATAGATA-TTCAATGAGTCTTGGCGCCAAAAATCATGCAA
256 GTGGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAA
*
3822 AACTTAGCCGGGG
321 AACTGAGCCGGGG
* * *
3835 CCCCGGAACACGTTTTTAGCCAAAAACCGTGGTGGTTAGTACACGATTTCGGCAAAAACTTTGCA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
* * * ** *
3900 AAAATTGACTCGAATGATTTTTCCTT-AATTTTGAATAGCAATACTCGTAAAAAATATAAAATTC
66 AAAATTGACCCGAAAGATTTTT-CTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTC
** * * * *
3964 AACGGTAGAAAGATTGAAGGGCTTTTCAGGCATCTAATATCATTTTCTTTCAAATT-TTT-CCGT
130 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCA-TTT-TTTC-AATTCTTTCCCGA
** * * * * * *
4027 ATTAATTTCCGATTAAATCGAAACATGATTCAGATGCTCG-AAAAATCAAATCCTTAAATCCAAT
192 ATTAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAA-CAAATCCATAAATCCATT
* * * *
4091 GTGGATGAGATTTGGGATGATGAATATAGATATTTCAATCAGTCTTGGCGCCAAAAGTCATGCAA
256 GTGGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAA
* * *
4156 AACTTAGTCGGTG
321 AACTGAGCCGGGG
** * * * *
4169 CCCTAGATCGCGTTTTTTAGCCAAAAACCATGATGGTTAATACACGATTTTGGCAAAAATTTTGC
1 CCCCGGAACGCG-TTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGC
* * * * *
4234 AAAAATTGACCGGAAAGATTTTTCCTCAATTTTTAACCACAATAGTGGTAAAAAATATATAATTC
65 AAAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTC
* * * * * *
4299 AACGCCAAATAGATTGAAGGGCTTTGCATGCTTCTAATATTATTTTTT-TA-T-TTT-ACGAAAT
130 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCG-AAT
** * * * * ** * * * * * *
4360 TAATTTCCGATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCCA-GGT
194 TAATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAAT-CCATTGT
* * * * * * *
4424 GACTGAGATTTGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCTAAAATCATGCAAAA
258 GGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAA
*** ** *
4489 CACTGTTGAGG
323 CTGAGCCGGGG
* * * * *
4500 CCCCGGAACGCGTTTTCAGCTAAGAATCGTGATGGTTAGTACACGATTTCGGCAAA
1 CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAA
4556 TATTATGAAA
Statistics
Matches: 3286, Mismatches: 680, Indels: 516
0.73 0.15 0.12
Matches are distributed among these distances:
330 43 0.01
331 122 0.04
332 121 0.04
333 966 0.29
334 1049 0.32
335 321 0.10
336 2 0.00
337 2 0.00
338 1 0.00
340 2 0.00
341 3 0.00
342 7 0.00
343 1 0.00
344 3 0.00
345 1 0.00
346 6 0.00
349 5 0.00
350 5 0.00
351 3 0.00
352 2 0.00
353 3 0.00
355 2 0.00
356 1 0.00
357 6 0.00
366 94 0.03
367 3 0.00
368 36 0.01
369 8 0.00
370 1 0.00
373 3 0.00
374 6 0.00
375 13 0.00
376 9 0.00
377 11 0.00
378 6 0.00
379 1 0.00
380 21 0.01
381 18 0.01
382 13 0.00
383 18 0.01
384 20 0.01
385 20 0.01
386 17 0.01
387 15 0.00
388 18 0.01
389 21 0.01
390 13 0.00
391 17 0.01
392 3 0.00
393 10 0.00
394 19 0.01
395 8 0.00
396 3 0.00
397 6 0.00
400 6 0.00
401 5 0.00
402 10 0.00
403 14 0.00
406 1 0.00
407 2 0.00
408 4 0.00
409 3 0.00
410 6 0.00
411 21 0.01
412 18 0.01
413 5 0.00
414 9 0.00
415 9 0.00
416 19 0.01
417 10 0.00
419 2 0.00
421 3 0.00
424 2 0.00
425 3 0.00
426 5 0.00
427 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (333 bp):
CCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAAAAACTTTGCA
AAAATTGACCCGAAAGATTTTTCTTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
ATTTCTAATTAAATAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
AGCCGGGG
Found at i:1511 original size:666 final size:667
Alignment explanation
Indices: 1--1670 Score: 2413
Period size: 666 Copynumber: 2.5 Consensus size: 667
* * **
1 CCCCGTAACGCATTTTTAGCCAAAAACCGTGA---TAACGTACACGATTTCGGCAAAAACATTGC
1 CCCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCAAAAATTTTGC
* * *
63 AAAAATTTGACCCGAAAGATTTTTTCCT-AATTTTGAACCGCAATACTCGTAAAAATTATATAAT
65 AAAAA-TTGACCCGAAAGA-TTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAAT
* * *
127 TCAATGGCAGAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCATTCCCGAA
128 TCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAA
* *
192 TTAATTTCTAATTAATTAGAAACAGGATTCTGAAGATCGTAAAAACAAATCCATAAATCCATTGT
193 TTAATTTCTAATTAATTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGT
*
257 GGCTGAGATTTGGGATGATGAATATAGATATTTGAATGTGTCTTGGCGCCAAAAATCATGCAAAA
258 GGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAA
** * *
322 CTGAGCCGGGGCCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCA
323 CTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGACA
* * *
387 AAAACTTTGCAAAAATTGACCTGAAAATTTTTCCTTAATTTTGAACCGCAATACTCGTAAAAAAT
388 AAAACTTTGCAAAAATTGACCCGAAAATTTTTCCTTAATTTTGAACCGCAATAATCATAAAAAAT
* * * *
452 ATATAATTCAACGACAAAAAGATTGAAGGGCTTTTCAGGCGTCTAATATCATTCTCTTTCAATTT
453 ATATAATTCAACGACAAAAAGATTGAAGAGATTTTCACGCGTCTAATATCATTCTCTTTCAATTC
** * * * * * * *
517 TTTTTCGTATTAATTTCCGATTAAATCGAAACATGATTCAGATGCTCATAAAATCAAATCCTTAA
518 TTTCCCGAATTAATTTCCAATTAAATAGAAACAAGATTCAGATGATCATAAAAACAAATCCATAA
* * *
582 ATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCGATCAGTCTTGAAGCAAAAAAT
583 ATCCAATATGGATGAGATTTGGGATGATGAATATAGATATTTCAATCAGTCTTGAAGCAAAAAAT
* *
647 TATGCAAAACTTACCCGGTG
648 CATGCAAAACTTACCCGGGG
* *
667 CCCCAGCT--CGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCAATAATTTTG
1 CCCC-G-TAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTG
* * * *
730 CAAAAATTGACCCGAAATATTTTTCTTCAATTTTTAACCGCAATATTTGTAAAAAATATATAATT
64 CAAAAATTGACCCGAAAGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATT
* *** * * *
795 CAATGCCAAAAATATTGAAGATATTTTCACGCTTCTAATAACAGTTTTTCAATTCTTTCCCAAAT
129 CAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAAT
* * * * *
860 TAATTTCTAATTAATTAGAAATAAGATTCTGATGATCGTAAAAAAAAATCTATAAATCCATTATA
194 TAATTTCTAATTAATTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTG
925 GCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAAC
259 GCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * *
990 TGAACCGGAGCCCCGGAACGTGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGACAA
324 TGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGACAA
* *
1055 AAACTTTGCAAAAATTGACCCGAAAGATTTTT-CTTCAATTTTTAACCGGAATAATCATAAAAAA
389 AAACTTTGCAAAAATTGACCCGAAA-ATTTTTCCTT-AATTTTGAACCGCAATAATCATAAAAAA
** * *
1119 TATATAATTCAACGTGAAAAAGATTTAAGAGATTTTCACGCTTCTAATATCATT-T-TTTCAATT
452 TATATAATTCAACGACAAAAAGATTGAAGAGATTTTCACGCGTCTAATATCATTCTCTTTCAATT
* * * *
1182 CTTTCCCGAATTAATTTCTAATTAACTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATA
517 CTTTCCCGAATTAATTTCCAATTAAATAGAAACAAGATTCAGATGATCATAAAAACAAATCCATA
* * * * ** *
1247 AATCCATTATGGATGAGATTTGGGATGATTAATATTGATATTTCAATGAGTCTTGGCGCCAAAAA
582 AATCCAATATGGATGAGATTTGGGATGATGAATATAGATATTTCAATCAGTCTTGAAGCAAAAAA
*
1312 TCATGCAAAACTTAGCCGGGG
647 TCATGCAAAACTTACCCGGGG
1333 CCCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCA
1 CCCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCA
*
1398 AATATTGACCCGAAAGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
66 AAAATTGACCCGAAAGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
* * * *
1463 ACGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATCATTTTTTCAATTTTTTCCCGAATTA
131 ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
* *
1528 ATTTCTAATTAAATCGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
196 ATTTCTAATTAATTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
* * * * *
1593 TGATATTTGGGATGATTAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCTTGCAAAACTG
261 TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
1658 AGCCGGGGCCCCG
326 AGCCGGGGCCCCG
1671 CCAAAAATCA
Statistics
Matches: 886, Mismatches: 108, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
664 1 0.00
665 1 0.00
666 468 0.53
667 309 0.35
668 105 0.12
669 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (667 bp):
CCCCGTAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCA
AAAATTGACCCGAAAGATTTTTCATCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCA
ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
ATTTCTAATTAATTAGAAACAAGATTCTGATGATCGTAAAAACAAATCCATAAATCCATTGTGGC
TGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTGGCGCCAAAAATCATGCAAAACTG
AGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGACAAAA
ACTTTGCAAAAATTGACCCGAAAATTTTTCCTTAATTTTGAACCGCAATAATCATAAAAAATATA
TAATTCAACGACAAAAAGATTGAAGAGATTTTCACGCGTCTAATATCATTCTCTTTCAATTCTTT
CCCGAATTAATTTCCAATTAAATAGAAACAAGATTCAGATGATCATAAAAACAAATCCATAAATC
CAATATGGATGAGATTTGGGATGATGAATATAGATATTTCAATCAGTCTTGAAGCAAAAAATCAT
GCAAAACTTACCCGGGG
Found at i:1678 original size:33 final size:33
Alignment explanation
Indices: 1636--1703 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1626 TGAGACTTGG
*
1636 CGCCAAAAATCTTGCAAAACTGAGCCGGGGCCC
1 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
*
1669 CGCCAAAAATCATGCAAAACTGAGTCGGGGCCC
1 CGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
1702 CG
1 CG
1704 TAACGCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.32, G:0.25, T:0.12
Consensus pattern (33 bp):
CGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
Found at i:2851 original size:334 final size:332
Alignment explanation
Indices: 2070--4555 Score: 3020
Period size: 334 Copynumber: 7.5 Consensus size: 332
2060 CCTCCCAAAT
* * * * *
2070 CAAATTCTTAAATCCAATGTGACTGAGATTTGGGATAATGAATACAGATATTTCAATGAGCCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* * *
2135 GCGCCAAAAATCATGCAAAACTTAGTCGGGTCCCCGGAACGCGTTTTTAGCCAAAAATCGTGATG
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * *
2200 GTTAGTACACGATTTCGACAAAAACTTTGCAAAAATTGACCCGAAAGATTTTTTTATCAATTTTT
131 GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACCGAAAGA-TTTTTCATCAATTTTT
* * *
2265 AACCACAATACTCGTAAAAAA-ATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTC
195 AACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
* * ** * * * *
2329 TAATATCATTTTTTCAATTCATTCCCGAATTAATTTCTAATTAATTAGAAACAGGATTCTGATGA
260 TAATATCATTTTTTCAATT-TTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGATGA
2394 TCGTAAAAA
324 TCGTAAAAA
* * * * * * *
2403 CAAAACCATAAATCCATTGTGGCTGAGATTTGAGATGATGAATATAGTTATTTGAATGTGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* **
2468 GCGCCAAAAATCATGCAAAACTGAGCCGGGGCCTTGGAACGCGTTTTTAGCCAAAAACCGTGATG
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * *
2533 GTTAATACACGATTTTTGGAAAAAATTTTGCAAAAATTGAACCGAAAGATTTTTCATCAATTTTT
131 GTTAGTACACGA-TTTCGGCAAAAACTTTGCAAAAATTGAACCGAAAGATTTTTCATCAATTTTT
* * * * *
2598 AACCGCAATACTCATAAGAAATATATAATTCAAAGCCAAAAAGATTGAAGAGATTTTCACGCTTC
195 AACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
** * * * **
2663 TAATATCATTTTTTCAATTCTTTACCGAATTAATTTCTAATTAATTAGAAACAAGATTTTGATGA
260 TAATATCATTTTTTCAATT-TTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGATGA
2728 TCGTAAAAA
324 TCGTAAAAA
* * * *
2737 CAAATCCATAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTATTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* * * * * *
2802 GCGCCAAAAACCATACAAAACATAGCCGAGGCCCCGTAACGCATTTTTAGCCAAAAAGCCGTGAT
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAA-CCGTGAT
* * * *
2867 GATTAGTACACGATTTCGGCAAAAATTTTGCAAATATTG-ACCCAAAGGATTTTTCATCAATTTT
130 GGTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACCGAAA-GATTTTTCATCAATTTT
* * *
2931 TAACCGCAATACTCGTAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGTCTTTTCACACTT
194 TAACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT
* * * * ** *
2996 CTATTATCATTTTTTCATTTCTTTCCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
259 CTAATATCATTTTTTCAATT-TTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGATG
3061 ATCGTAAAAA
323 ATCGTAAAAA
* *
3071 CAAATCCATAAATCCATTGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* * * * * *
3136 GCGCCAAAAATCATGCAAAACTTAGTCGGGGCACAGGAACGCGTTTTTAACCAAAAACAGTGCTG
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * ** **
3201 GTTAGTACACGATTTCGGTAAAAACTTTGCAAAAATTGACCCGAAAGATTATTTC-TTGATTTAA
131 GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACCGAAAGATT-TTTCATCAATTTTT
* * * * * *
3265 AACCGCAAAACTCTTAAAAAATATATAATTCAACGACAGAAAGATTGAAGGGCTTTTCAGGCGTC
195 AACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
* *
3330 TAATATCAGTTTCTTTCAATTTTTTCCGTATTAATTTCCGATTAAATCGAAACATGATTCAGATG
260 TAATATCA-TTT-TTTCAATTTTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGATG
* *
3395 CTCGTAAAAT
323 ATCGTAAAAA
*
3405 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTGAATGAGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* * * * * *
3470 GAGTCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGTACGCGTTTTTAGCCAAAAACCGTTATT
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * * * *
3535 CTTAGTACACAATTTCGGCAAAAACTTTGCAAAAATTGATCCGAAA-ATTTTTTCCTTAATTTTG
131 GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACCGAAAGA-TTTTTCATCAATTTTT
* * * * * **
3599 AACCGCAATACTCGTAAATAATATATAATTCAATGGCAGAAAGATTGAAGGGCTTTTCAGGGGTC
195 AACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
** *
3664 TAATATCATTCTCTTTCAATTTTTTTTCGTATTAATTTCCGATTAAATCGAAACATGATTCAGAT
260 TAATATCATT-T-TTTCAA-TTTTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGAT
* *
3729 -ACTTGTAAAAT
322 GA-TCGTAAAAA
*
3740 CAAATCCTTAAATCCAATGTGGCTAAGATTTGGGATGATGAATATAGATA-TTCAATGAGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* *
3804 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACACGTTTTTAGCCAAAAACCGTGGTG
66 GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* * * *
3869 GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTG-ACTCGAATGATTTTTCCTTAATTTTG
131 GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAAC-CGAAAGATTTTTCATCAATTTTT
** * ** * * *
3933 AATAGCAATACTCGTAAAAAATATAAAATTCAACGGTAGAAAGATTGAAGGGCTTTTCAGGCATC
195 AACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTC
*
3998 TAATATCATTTTCTTTCAAATTTTT-CCGTATTAATTTCCGATTAAATCGAAACATGATTCAGAT
260 TAATATCA-TTT-TTTC-AATTTTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGAT
*
4062 GCTCG-AAAAA
322 GATCGTAAAAA
* *
4072 TCAAATCCTTAAATCCAATGTGGATGAGATTTGGGATGATGAATATAGATATTTCAATCAGTCTT
1 -CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTT
* * * ** * *
4137 GGCGCCAAAAGTCATGCAAAACTTAGTCGGTGCCCTAGATCGCGTTTTTTAGCCAAAAACCATGA
65 GGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCG-TTTTTAGCCAAAAACCGTGA
* * * *
4202 TGGTTAATACACGATTTTGGCAAAAATTTTGCAAAAATTG-ACCGGAAAGATTTTTCCTCAATTT
129 TGGTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACC-GAAAGATTTTTCATCAATTT
* * * * * *
4266 TTAACCACAATAGTGGTAAAAAATATATAATTCAACGCCAAATAGATTGAAGGGCTTTGCATGCT
193 TTAACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCT
* * * * *
4331 TCTAATATTATTTTTT-TA-TTTTA-CGAAATTAATTTCCGATGAAATCGTAACATGATTCAAAT
258 TCTAATATCATTTTTTCAATTTTTACCG-AATTAATTTCCGATTAAATCGAAACATGATTCAGAT
* * *
4393 GCTCGTGAAAT
322 GATCGTAAAAA
* * * * * * *
4404 CGAATCCTTAAATCCCAGGTGACTGAGATTTGGGACGACGAATATAGATAATTCAATGAGTCTTG
1 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
* * * ** * * * * *
4469 GGGCCTAAAATCATGCAAAACACT-GTTGAGGCCCCGGAACGCGTTTTCAGCTAAGAATCGTGAT
66 GCGCCAAAAATCATGCAAAAC-TTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
4533 GGTTAGTACACGATTTCGGCAAA
130 GGTTAGTACACGATTTCGGCAAA
4556 TATTATGAAA
Statistics
Matches: 1888, Mismatches: 239, Indels: 55
0.87 0.11 0.03
Matches are distributed among these distances:
330 43 0.02
331 125 0.07
332 8 0.00
333 373 0.20
334 1073 0.57
335 266 0.14
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (332 bp):
CAAATCCTTAAATCCAATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTG
GCGCCAAAAATCATGCAAAACTTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCAAAAACTTTGCAAAAATTGAACCGAAAGATTTTTCATCAATTTTTA
ACCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCT
AATATCATTTTTTCAATTTTTACCGAATTAATTTCCGATTAAATCGAAACATGATTCAGATGATC
GTAAAAA
Found at i:4703 original size:191 final size:191
Alignment explanation
Indices: 4369--4722 Score: 600
Period size: 191 Copynumber: 1.9 Consensus size: 191
4359 TTAATTTCCG
* *
4369 ATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCCAGGTGACTGAGATT
1 ATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGACTGAGATA
* *
4434 TGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCTAAAATCATGCAAAACACTGTTGAG
66 TGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACACAGTTGAG
* * *
4499 GCCCCGGAACGCGTTTTCAGCTAAGAATCGTGATGGTTAGTACACGATTTCGGCAAATATT
131 GCCCAGAAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAATATT
**
4560 ATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGGTTGAGATA
1 ATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGACTGAGATA
* * *
4625 TGGGATGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACCCAGTTGGG
66 TGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACACAGTTGAG
4690 GCCCAGAAACGCGTTTTCAGCCAAGAATCGTGA
131 GCCCAGAAACGCGTTTTCAGCCAAGAATCGTGA
4723 CACGATTTCG
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
191 151 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (191 bp):
ATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGACTGAGATA
TGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACACAGTTGAG
GCCCAGAAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTCGGCAAATATT
Found at i:5023 original size:514 final size:517
Alignment explanation
Indices: 4041--5069 Score: 1376
Period size: 514 Copynumber: 2.0 Consensus size: 517
4031 ATTTCCGATT
* * *
4041 AAATCGAAACATGATTCAGATGCTCGAAAAATCAAATCCTTAAATCCAATGTGGATGAGATTTGG
1 AAATCGAAACATGATTCAAATGCTCGAAAAATCAAATCCTTAAATCCAAGGTGGATGAGATATGG
* * * ** *
4106 GATGATGAATATAGATATTTCAATCAGTCTTGGCGCCAAAAGTCATGCAAAACTTAGTCGGTGCC
66 GATGACGAATATAGATAATTCAATCAGTCTTGGCGCCAAAAATCATGCAAAACCCAGTCGGGGCC
* * * *
4171 CTAGATCGCGTTTTTTAGCCAAAAACCATGATGGTTAATACACGATTTTGGCAAAAATTTTGCAA
131 CTAGAACGCGTTTTTCAGCCAAAAACCA-GATGG----TACACGATTTCGGCAAAAATTATGCAA
* * * **
4236 AAATTGACCGGAAAGATTTTTCCTCAATTTTTAACCACAATAGTGGTAAAAAATATATAATTCAA
191 AAATTGACCCGAAAGATTTTTCCCCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAA
* * *
4301 CGCCAAATAGATTGAAGGGCTTTGCATGCTTCTAATATTATTTTTTTATTTTACGAAATTAATTT
256 CGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTTTATTTTACGAAATTAATTT
* * * *
4366 CCGATGAAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCCAGGTGACTGAG
321 CCGATGAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGACTGAG
* ** * * *
4431 ATTTGGGACGACGAATATAGATAATTCAATGAGTCTTGGGGCCTAAAATCATGCAAAACACTGTT
386 ATTTGGGACAACGAATATAGATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACACAGCT
* *
4496 GAGGCCCCGGAACGCGTTTTCAG-CTAAGAATCGTGATGGTTA-GTACACGATTTCGGCAAATAT
451 GAGGCCCCGGAACGCGTTTTCAGTC-AAGAATCGTGATAG-AACGTACACGATTTCGGCAAATAT
4559 TATG
514 TATG
* ** * *
4563 AAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGGTTGAGATATGG
1 AAATCGAAACATGATTCAAATGCTCGAAAAATCAAATCCTTAAATCCAAGGTGGATGAGATATGG
* * *
4628 GATGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACCCAGTTGGGGCC
66 GATGACGAATATAGATAATTCAATCAGTCTTGGCGCCAAAAATCATGCAAAACCCAGTCGGGGCC
* * * *
4693 C-AGAAACGCG-TTTTCAGCCAAGAATC-G-T-G-ACACGATTTCGGCAAATATTATGTAAAAAT
131 CTAG-AACGCGTTTTTCAGCCAAAAACCAGATGGTACACGATTTCGGCAAAAATTATGCAAAAAT
* *
4752 TGACCCGAAATATTTTTCCCCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAATGCC
195 TGACCCGAAAGATTTTTCCCCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGCC
*
4817 AAAAAGATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTTTATACTTTTCCG-AATTAATTTC
260 AAAAAGATTGAAGGGCTTTGCACGCTTCTAATATAA-TTTTTT-TA-TTTTACGAAATTAATTTC
* *
4881 CGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGA
322 CGATGAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGACTGAGA
* * * *
4946 TTTGGGATAATGAATA-AGGATAATTCAATGAGTCTTGACGTCAAAAATCATGCAAAACTCAGCT
387 TTTGGGACAACGAATATA-GATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACACAGCT
* *
5010 GGGGCCCCGGAACGCGTTTTCAGTCAAGAATTGTGATAGAACGTACACGATTTCGGCAAA
451 GAGGCCCCGGAACGCGTTTTCAGTCAAGAATCGTGATAGAACGTACACGATTTCGGCAAA
5070 AATTTTGGAA
Statistics
Matches: 444, Mismatches: 56, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
512 117 0.26
513 8 0.02
514 175 0.39
515 7 0.02
517 1 0.00
518 1 0.00
519 1 0.00
521 15 0.03
522 119 0.27
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (517 bp):
AAATCGAAACATGATTCAAATGCTCGAAAAATCAAATCCTTAAATCCAAGGTGGATGAGATATGG
GATGACGAATATAGATAATTCAATCAGTCTTGGCGCCAAAAATCATGCAAAACCCAGTCGGGGCC
CTAGAACGCGTTTTTCAGCCAAAAACCAGATGGTACACGATTTCGGCAAAAATTATGCAAAAATT
GACCCGAAAGATTTTTCCCCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGCCA
AAAAGATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTTTATTTTACGAAATTAATTTCCGAT
GAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGACTGAGATTTG
GGACAACGAATATAGATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACACAGCTGAGGC
CCCGGAACGCGTTTTCAGTCAAGAATCGTGATAGAACGTACACGATTTCGGCAAATATTATG
Found at i:5247 original size:332 final size:323
Alignment explanation
Indices: 4563--5377 Score: 1028
Period size: 332 Copynumber: 2.5 Consensus size: 323
4553 AAATATTATG
* * * * *
4563 AAATCGTAACATGATTCAAATGCTCGTGAAATCGAATCCTTAAATCCAAGGTGGTTGAGATATGG
1 AAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATTTGG
* * ** * *
4628 GATGACGAATATAGATAATTCAATGAGTCTTGGGGCCAAAAATCATGCAAAACCCAGTTGGGGCC
66 GATAATGAATATAGATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTCAGCTGGGGCC
* * * *
4693 CAGAAACGCGTTTTCAGCCAAGAATCGTGACACGATTTCGGCAAATATTATGTAAAAATTGACCC
131 CCGGAACGCGTTTTCAGCCAAGAATCGTGACACGATTTCGGCAAAAATTATGGAAAAATTGACCC
* *
4758 GAAATATTTTTCCCCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAATGCCAAAAAG
196 GAAATATTTTTCACCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAG
** * *
4823 ATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTTTATACTTTTCCGAATTAATTTCCGATT
261 ATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTGAATACTTTCCCGAATTAATTTCCAATT
4886 AAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATTTGG
1 AAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATTTGG
*
4951 GATAATGAATA-AGGATAATTCAATGAGTCTTGACGTCAAAAATCATGCAAAACTCAGCTGGGGC
66 GATAATGAATATA-GATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTCAGCTGGGGC
* * *
5015 CCCGGAACGCGTTTTCAGTCAAGAATTGTGATAGAACGTACACGATTTCGGCAAAAATTTTGGAA
130 CCCGGAACGCGTTTTCAGCCAAGAA-T-CG-T-----G-ACACGATTTCGGCAAAAATTATGGAA
* * *
5080 AAATTGACCCGAAATATTTTTCACTAATTTTTAACCACAATACTCGT-AAAAATATATAATTCTA
186 AAATTGACCCGAAATATTTTTCACCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAA
* * * *
5144 CGCCAAAAAGATTGAAGGGCTTTTCACTCTTCTAATATCATTTTTAGAATTCTTTCCCGAATTAA
251 CGCCAAAAAGATTGAAGGGCTTTGCACGCTTCTAATATAATTTTT-GAATACTTTCCCGAATTAA
*
5209 TTTCTAATT
315 TTTCCAATT
* * * * ** *
5218 AAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTT-G
1 AAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATTTGG
** * * *
5282 TTTAGATTAATATAGATATTTCAATGAGTCTT-AGCGCCAAAAATCATGCAAAACTGAGAC-GGG
66 GATA-ATGAATATAGATAATTCAATGAGTCTTGA-CGCCAAAAATCATGCAAAACTCAG-CTGGG
* * * *
5345 GTCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
128 GCCCCGGAACGCGTTTTCAGCCAAGAATCGTGA
5378 TGGTTAGTAC
Statistics
Matches: 425, Mismatches: 52, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
322 1 0.00
323 138 0.32
324 2 0.00
325 1 0.00
326 1 0.00
329 1 0.00
330 1 0.00
331 62 0.15
332 216 0.51
333 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Consensus pattern (323 bp):
AAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAAGGTGGCTGAGATTTGG
GATAATGAATATAGATAATTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTCAGCTGGGGCC
CCGGAACGCGTTTTCAGCCAAGAATCGTGACACGATTTCGGCAAAAATTATGGAAAAATTGACCC
GAAATATTTTTCACCAATTTTTAACCACAATACTCATAAAAAATATATAATTCAACGCCAAAAAG
ATTGAAGGGCTTTGCACGCTTCTAATATAATTTTTGAATACTTTCCCGAATTAATTTCCAATT
Done.