Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_pilon, 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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:233974 original size:17 final size:16
Alignment explanation
Indices: 233952--233994 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
233942 ATATTTATAT
*
233952 ATATATATATACGTCAC
1 ATATATATATACAT-AC
*
233969 ATATATAT-TACATAT
1 ATATATATATACATAC
233984 ATATATATATA
1 ATATATATATA
233995 AATTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
16 6 0.26
17 8 0.35
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (16 bp):
ATATATATATACATAC
Found at i:235228 original size:2 final size:2
Alignment explanation
Indices: 235221--235259 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
235211 TTTATTTACT
*
235221 TA TA TA TA TA T- TA TA TA T- TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
235260 TTTACTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:241588 original size:2 final size:2
Alignment explanation
Indices: 241581--241646 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
241571 TACTGTTGAC
241581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241623 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
241647 TATTAATCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244750 original size:21 final size:21
Alignment explanation
Indices: 244726--244778 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
244716 ATTCTGACTA
*
244726 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
244747 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
244768 TCGCAATGCGA
1 TCGCATTGCGA
244779 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:244810 original size:20 final size:20
Alignment explanation
Indices: 244787--244974 Score: 304
Period size: 20 Copynumber: 9.4 Consensus size: 20
244777 GAATATGTAA
* *
244787 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
244807 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
244827 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
244847 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
* *
244867 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
244887 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
244907 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
* *
244927 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
244947 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
244967 ATCGCAAC
1 ATCGCAAC
244975 ACTGAATTTC
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 154 1.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:245821 original size:24 final size:24
Alignment explanation
Indices: 245787--245840 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
245777 GTATTCGAAA
245787 TTTGATATTGGCCAATACCCGGAC
1 TTTGATATTGGCCAATACCCGGAC
* * * *
245811 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGCCAATACCCGGAC
245835 TTTGAT
1 TTTGAT
245841 GATGTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGCCAATACCCGGAC
Found at i:246058 original size:13 final size:14
Alignment explanation
Indices: 246026--246057 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
246016 AAGAAGAAAA
246026 AAAAATCCCCAAAG
1 AAAAATCCCCAAAG
*
246040 AAAAATCCCCGAAG
1 AAAAATCCCCAAAG
246054 AAAA
1 AAAA
246058 TGCCACGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.25, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAAATCCCCAAAG
Found at i:248116 original size:18 final size:18
Alignment explanation
Indices: 248093--248127 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
248083 AGAAAAAGGC
248093 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
248111 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
248128 CAACTGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:248364 original size:20 final size:20
Alignment explanation
Indices: 248339--248655 Score: 271
Period size: 20 Copynumber: 16.4 Consensus size: 20
248329 TAACTAAAAA
* *
248339 ATCGCAATGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
248359 ATCGCAATGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
248379 ATCGCAACGAGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
248399 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* * *
248419 ATCGCAACGGGTATTCGACT
1 ATCGCAACGCGAATTTGACT
*
248439 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* * *
248459 ATCGTAACTC-AA----A-A
1 ATCGCAACGCGAATTTGACT
*
248473 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
248493 ATCTCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
248513 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
** *
248533 ATCATAACGGGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* **
248553 ATCGCAA--C-AA---AAAA
1 ATCGCAACGCGAATTTGACT
* * *
248567 ATTGCAACACAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
248587 ATTGCAACGAGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
248607 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* * *
248627 ATCGCAACGGGTATTCGACT
1 ATCGCAACGCGAATTTGACT
248647 ATCGCAACG
1 ATCGCAACG
248656 AGAAAATCGC
Statistics
Matches: 241, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
14 14 0.06
15 3 0.01
16 1 0.00
17 4 0.02
19 3 0.01
20 216 0.90
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:248477 original size:94 final size:94
Alignment explanation
Indices: 248379--248704 Score: 341
Period size: 94 Copynumber: 3.5 Consensus size: 94
248369 AAATTTGACT
* * * *
248379 ATCGCAACGAGAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGGGTATTCGACTATCGC
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCGC
* * **
248444 AACGCGAATTTGATTATCGTAACTCAAAA
66 AACGCGAATTTGACTATCGCAACAAAAAA
* * * * **
248473 ATCGCAATGCGAATTTGACTATCTCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCAT
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCGC
*
248538 AACGGGAATTTGACTATCGCAACAAAAAA
66 AACGCGAATTTGACTATCGCAACAAAAAA
* * * * *
248567 ATTGCAAC-ACAAATTTGACTATTGCAACGAGAATTTGACTATCGCAACGTGAATTTGATTATCG
1 ATCGCAACGA-GAATTTGACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCG
* * * * *
248631 CAACGGGTATTCGACTATCGCAACGAGAAA
65 CAACGCGAATTTGACTATCGCAACAAAAAA
* * * * * * *
248661 ATCGCAAAGCGTATTAGACTATCGCAAAGCGAA-TTGACTTTCGC
1 ATCGCAACGAGAATTTGACTATCGCAACGAGAATTTGACTATCGC
248705 GTTGCGATTT
Statistics
Matches: 191, Mismatches: 39, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
93 10 0.05
94 181 0.95
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (94 bp):
ATCGCAACGAGAATTTGACTATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGACTATCGC
AACGCGAATTTGACTATCGCAACAAAAAA
Found at i:248513 original size:74 final size:74
Alignment explanation
Indices: 248399--248540 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
248389 GAATTTGACT
* * * * *
248399 ATCGCAACGTGAATTTGACTATCGCAACGGGTATTCGACTATCGCAACGCGAATTTGATTATCGT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTCGACTATCGCAACGCGAATTTGACTATCAT
248464 AACTCAAAA
66 AACTCAAAA
* * *
248473 ATCGCAATGCGAATTTGACTATCTCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCAT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTCGACTATCGCAACGCGAATTTGACTATCAT
248538 AAC
66 AAC
248541 GGGAATTTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTCGACTATCGCAACGCGAATTTGACTATCAT
AACTCAAAA
Found at i:248547 original size:134 final size:134
Alignment explanation
Indices: 248304--248560 Score: 433
Period size: 134 Copynumber: 1.9 Consensus size: 134
248294 ATCATTTGAA
*
248304 TATCGCAACGCGAATTTGATTATCGTAACTAAAAAATCGCAATGCAAATTTGACTATCGCAATGC
1 TATCGCAACGCGAATTTGATTATCGTAACTAAAAAATCGCAATGCAAATTTGACTATCGCAACGC
* *
248369 AAATTTGACTATCGCAACGAGAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGGGTATT
66 AAATTTGACTATCGCAACGAGAATTTGACTATCACAACGGGAATTTGACTATCGCAACGGGTATT
248434 CGAC
131 CGAC
* * *
248438 TATCGCAACGCGAATTTGATTATCGTAACTCAAAAATCGCAATGCGAATTTGACTATCTCAACGC
1 TATCGCAACGCGAATTTGATTATCGTAACTAAAAAATCGCAATGCAAATTTGACTATCGCAACGC
* * *
248503 GAATTTGACTATCGCAACGCGAATTTGACTATCATAACGGGAATTTGACTATCGCAAC
66 AAATTTGACTATCGCAACGAGAATTTGACTATCACAACGGGAATTTGACTATCGCAAC
248561 AAAAAAATTG
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
134 114 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (134 bp):
TATCGCAACGCGAATTTGATTATCGTAACTAAAAAATCGCAATGCAAATTTGACTATCGCAACGC
AAATTTGACTATCGCAACGAGAATTTGACTATCACAACGGGAATTTGACTATCGCAACGGGTATT
CGAC
Found at i:248704 original size:19 final size:20
Alignment explanation
Indices: 248661--248704 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
248651 CAACGAGAAA
*
248661 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
248681 ATCGCAAAGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
248700 TTCGC
1 ATCGC
248705 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:248723 original size:20 final size:20
Alignment explanation
Indices: 248694--248751 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
248684 GCAAAGCGAA
248694 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCGTTGCGATT
* * *
248714 TTGTCTTTCGCATTGCAATT
1 TTGACTTTCGCGTTGCGATT
* *
248734 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCGTTGCGA
248752 AAGTATACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCGATT
Found at i:248889 original size:29 final size:28
Alignment explanation
Indices: 248855--248909 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
248845 ATAAGAATTA
*
248855 TTTACACATCAATATTAAACAAATCAACT
1 TTTACAAATCAAT-TTAAACAAATCAACT
**
248884 TTTACAAATCAATTTTTACAAATCAA
1 TTTACAAATCAATTTAAACAAATCAA
248910 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (28 bp):
TTTACAAATCAATTTAAACAAATCAACT
Found at i:248910 original size:14 final size:14
Alignment explanation
Indices: 248850--248911 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
248840 CACAAATAAG
*
248850 AATTATTTACACATC
1 AATT-TTTACAAATC
**
248865 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
248880 AACTTTTACAAATC
1 AATTTTTACAAATC
248894 AATTTTTACAAATC
1 AATTTTTACAAATC
248908 AATT
1 AATT
248912 AAACAAGCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 12 0.31
16 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:250367 original size:21 final size:21
Alignment explanation
Indices: 250312--250418 Score: 108
Period size: 21 Copynumber: 5.1 Consensus size: 21
250302 TCTAGAATGT
* *
250312 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
* *
250333 TGGCAGTGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* **
250354 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
250375 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
*
250396 TAGGG-GAGGCCTCTTGAACGA
1 T-GGGAGGGGCCTCTTGAACGA
250417 TG
1 TG
250419 ACAGGTGAGT
Statistics
Matches: 68, Mismatches: 17, Indels: 3
0.77 0.19 0.03
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:250419 original size:42 final size:42
Alignment explanation
Indices: 250312--250423 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
250302 TCTAGAATGT
* * *
250312 TGGGAG-GGACCTCTTCAACGATGGCAGTGGCCTCTTGAACGA
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
250354 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
250396 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
250424 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
42 51 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:250947 original size:20 final size:18
Alignment explanation
Indices: 250909--250955 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 18
250899 GAAACTTAAA
*
250909 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
250927 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
250947 ATCGCAACG
1 ATCGCAACG
250956 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:252951 original size:20 final size:20
Alignment explanation
Indices: 252928--252968 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
252918 TCTGAAACTT
252928 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
*
252948 AAAATCGCAACACGAAAATG
1 AAAATCACAACACGAAAATG
252968 A
1 A
252969 CTATCGCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:252974 original size:20 final size:20
Alignment explanation
Indices: 252935--253004 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
252925 CTTAAAATCA
**
252935 CAACACGAAAATGAAAATCG
1 CAACACGAAAATGACTATCG
252955 CAACACGAAAATGACTATCG
1 CAACACGAAAATGACTATCG
* **
252975 CAACGCGAATTTGACTATCG
1 CAACACGAAAATGACTATCG
*
252995 CAACGCGAAA
1 CAACACGAAA
253005 CTAAAATCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.14
Consensus pattern (20 bp):
CAACACGAAAATGACTATCG
Found at i:253444 original size:21 final size:22
Alignment explanation
Indices: 253405--253446 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
253395 ATAGACGGAT
253405 TTCGCCGGAGATGGGGACTGAC
1 TTCGCCGGAGATGGGGACTGAC
*
253427 TTCGTCGGAGAT-GGGACTGA
1 TTCGCCGGAGATGGGGACTGA
253447 GTTGTGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
TTCGCCGGAGATGGGGACTGAC
Found at i:255163 original size:22 final size:22
Alignment explanation
Indices: 255133--255174 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
255123 TGTGATTCGA
255133 TTAACAAAAATATATTATCATT
1 TTAACAAAAATATATTATCATT
* *
255155 TTAATAAAAATTTATTATCA
1 TTAACAAAAATATATTATCA
255175 AATAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAACAAAAATATATTATCATT
Found at i:255610 original size:110 final size:110
Alignment explanation
Indices: 255417--255636 Score: 404
Period size: 110 Copynumber: 2.0 Consensus size: 110
255407 TTGTATTTTC
* *
255417 TATTCACTTATATTTCAAAAAGGATGTTCTTTTATTAAAAATAATTAACAGTCACTCTCCAAACA
1 TATTCACTTATATTTCAAAAAGGATGTTCTTTTATTAAAAATAATTAAAAATCACTCTCCAAACA
255482 ATTTGGAGAATACTTCATTAATCTTCTTAATAAATGAACATTGTT
66 ATTTGGAGAATACTTCATTAATCTTCTTAATAAATGAACATTGTT
* *
255527 TATTCACTTATATTTTAAAAAGGATGTTCTTTTATTAAAAATAATTAAAAATCACTCTTCAAACA
1 TATTCACTTATATTTCAAAAAGGATGTTCTTTTATTAAAAATAATTAAAAATCACTCTCCAAACA
255592 ATTTGGAGAATACTTCATTAATCTTCTTAATAAATGAACATTGTT
66 ATTTGGAGAATACTTCATTAATCTTCTTAATAAATGAACATTGTT
255637 GTAATCCCTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 106 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (110 bp):
TATTCACTTATATTTCAAAAAGGATGTTCTTTTATTAAAAATAATTAAAAATCACTCTCCAAACA
ATTTGGAGAATACTTCATTAATCTTCTTAATAAATGAACATTGTT
Found at i:255997 original size:95 final size:95
Alignment explanation
Indices: 255817--255998 Score: 231
Period size: 95 Copynumber: 1.9 Consensus size: 95
255807 GACGAAACAT
* * * **
255817 CAAATATTTCATATAACTCTAATCTTCCACAATCATCATGGCACACGTTACATTAAATGAACTCT
1 CAAACATTTCACATAACTCTAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTCT
** *
255882 CCATCTACATAATTATAGAGATGAGAATAA
66 CCATCTACATAACCAAAGAGATGAGAATAA
* ** *
255912 CAAACATTTCACATAA-TCTTAATATTCTACAATCATCATACCACGTGTTACATTAAATGAATTC
1 CAAACATTTCACATAACTC-TAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTC
*
255976 TCCATCTACATACCCAAAGAGAT
65 TCCATCTACATAACCAAAGAGAT
255999 TAAAACAACA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 2 0.03
95 71 0.97
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.31
Consensus pattern (95 bp):
CAAACATTTCACATAACTCTAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTCT
CCATCTACATAACCAAAGAGATGAGAATAA
Found at i:256023 original size:95 final size:96
Alignment explanation
Indices: 255827--256024 Score: 211
Period size: 95 Copynumber: 2.1 Consensus size: 96
255817 CAAATATTTC
* **
255827 ATATAA-CTCTAATCTTCCACAATCATCATGGCACACGTTACATTAAATGAACTCTCCATCTACA
1 ATATAATCTCTAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTCTCCATCTACA
** * * * **
255891 TAATTATAGAGATGAGAATAACAAACATTTC
66 TAACCAAAGAGATGAAAACAACAAACATTAA
* * ** *
255922 ACATAATCT-TAATATTCTACAATCATCATACCACGTGTTACATTAAATGAATTCTCCATCTACA
1 ATATAATCTCTAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTCTCCATCTACA
* * * *
255986 TACCCAAAGAGATTAAAACAACATATATTAA
66 TAACCAAAGAGATGAAAACAACAAACATTAA
256017 ATATAATC
1 ATATAATC
256025 ATAGACATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
95 80 0.98
96 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (96 bp):
ATATAATCTCTAATATTCCACAATCATCATACCACACGTTACATTAAATGAACTCTCCATCTACA
TAACCAAAGAGATGAAAACAACAAACATTAA
Found at i:258732 original size:18 final size:18
Alignment explanation
Indices: 258709--258762 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
258699 CTCAACCGTT
258709 AAATAGTTAACGACATTA
1 AAATAGTTAACGACATTA
258727 AAATAGGTT---G---TT-
1 AAATA-GTTAACGACATTA
258739 AAATAGTTAACGACATTA
1 AAATAGTTAACGACATTA
258757 AAATAG
1 AAATAG
258763 GTTGTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 3 0.11
12 5 0.18
13 2 0.07
14 1 0.04
16 1 0.04
17 2 0.07
18 11 0.39
19 3 0.11
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (18 bp):
AAATAGTTAACGACATTA
Found at i:258742 original size:30 final size:30
Alignment explanation
Indices: 258706--258774 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
258696 TCACTCAACC
258706 GTTAAATAGTTAACGACATTAAAATAGGTT
1 GTTAAATAGTTAACGACATTAAAATAGGTT
258736 GTTAAATAGTTAACGACATTAAAATAGGTT
1 GTTAAATAGTTAACGACATTAAAATAGGTT
*
258766 GTTATATAG
1 GTTAAATAG
258775 ATACAAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (30 bp):
GTTAAATAGTTAACGACATTAAAATAGGTT
Found at i:264731 original size:2 final size:2
Alignment explanation
Indices: 264724--264760 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
264714 ATAATACTCC
*
264724 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
264761 GTTATGATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:268609 original size:15 final size:15
Alignment explanation
Indices: 268589--268619 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
268579 GCGTAATCTA
268589 AAATTTGTAATTCTG
1 AAATTTGTAATTCTG
268604 AAATTTGTAATTCTG
1 AAATTTGTAATTCTG
268619 A
1 A
268620 CAACATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
AAATTTGTAATTCTG
Found at i:269832 original size:64 final size:65
Alignment explanation
Indices: 269764--269927 Score: 215
Period size: 64 Copynumber: 2.5 Consensus size: 65
269754 AAATAGTCTG
* *
269764 GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTGAATCA-GA
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTGAATCATGA
** ** * *
269828 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTG
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTGAATCA-TG
269893 A
65 A
269894 -TGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 GTGCATCGATGCATGG-ATTG-TGCATCGGTGCAT
269928 GCCTTTGAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 54 0.63
65 15 0.17
66 4 0.05
67 13 0.15
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCGATGTTTCAATTGAATCATGA
Found at i:269849 original size:19 final size:19
Alignment explanation
Indices: 269825--269875 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
269815 TAATTGAATC
269825 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
269844 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
269863 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
269876 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:269913 original size:21 final size:21
Alignment explanation
Indices: 269889--269928 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
269879 CAATTTATTC
269889 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
269910 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
269929 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:272040 original size:18 final size:19
Alignment explanation
Indices: 272013--272050 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
272003 TCTTACTATA
* *
272013 TATTTTTTTTTGAA-AAAT
1 TATTTGTTTTGGAAGAAAT
272031 TATTTGTTTTGGAAGAAAT
1 TATTTGTTTTGGAAGAAAT
272050 T
1 T
272051 GGCAGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTGTTTTGGAAGAAAT
Found at i:278355 original size:45 final size:46
Alignment explanation
Indices: 278305--278409 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 46
278295 TGCATGGATT
* *
278305 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTGAATCA-GA
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCAATTGAATCATGA
** * *
278350 GTGCATCGATGCATGGAATGCATTCAATGTTTCAATTTATTCATTGA
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCAATTGAATCA-TGA
278397 -TGCATCGATGCAT
1 GTGCATCGATGCAT
278410 GGGATGCATC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 37 0.71
46 13 0.25
47 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTCAATTGAATCATGA
Found at i:278417 original size:17 final size:17
Alignment explanation
Indices: 278395--278427 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
278385 TTTATTCATT
278395 GATGCATCGATGCATGG
1 GATGCATCGATGCATGG
*
278412 GATGCATCGGTGCATG
1 GATGCATCGATGCATG
278428 CCTTTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (17 bp):
GATGCATCGATGCATGG
Found at i:280607 original size:17 final size:17
Alignment explanation
Indices: 280585--280680 Score: 67
Period size: 17 Copynumber: 5.4 Consensus size: 17
280575 AATTTATATG
280585 ATATAA-ATTAAAATTA
1 ATATAATATTAAAATTA
280601 TATATAATATTAAAATTA
1 -ATATAATATTAAAATTA
280619 ATATTTAATTATTTAAAAAATTA
1 ATA--TAA-TA-TT--AAAATTA
280642 ATATTAA-ATTTAAAA--A
1 ATA-TAATA-TTAAAATTA
280658 ATATAATA-TAAAATTAA
1 ATATAATATTAAAATT-A
280675 ATATAA
1 ATATAA
280681 AACCTCTTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 22
0.76 0.00 0.24
Matches are distributed among these distances:
14 5 0.07
15 3 0.04
16 5 0.07
17 16 0.24
18 14 0.21
19 3 0.04
20 6 0.09
21 2 0.03
22 4 0.06
23 10 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATATTAAAATTA
Found at i:280616 original size:24 final size:23
Alignment explanation
Indices: 280546--280625 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 23
280536 TAATTAAGAT
280546 AAATATAAAATTT-TAATAATATATA
1 AAAT-TAAAATTTAT-ATAATAT-TA
*
280571 AAA-T--AATTTATATGATA-T-
1 AAATTAAAATTTATATAATATTA
280589 AAATTAAAATTATATATAATATTA
1 AAATTAAAATT-TATATAATATTA
*
280613 AAATTAATATTTA
1 AAATTAAAATTTA
280626 ATTATTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
18 3 0.07
19 2 0.04
21 14 0.31
22 9 0.20
23 4 0.09
24 10 0.22
25 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
AAATTAAAATTTATATAATATTA
Found at i:280629 original size:29 final size:28
Alignment explanation
Indices: 280596--280676 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
280586 TATAAATTAA
280596 AATTATATATAATATTAAAATTAATATTT
1 AATTATATATAATATTAAAATTAA-ATTT
* * * *
280625 AATTATTTAAAAAATTAATATTAAATTT
1 AATTATATATAATATTAAAATTAAATTT
* *
280653 AA-AAAATATAATA-TAAAATTAAAT
1 AATTATATATAATATTAAAATTAAAT
280677 ATAAAACCTC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
26 10 0.24
27 6 0.14
28 6 0.14
29 20 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTATATATAATATTAAAATTAAATTT
Found at i:280664 original size:21 final size:20
Alignment explanation
Indices: 280612--280672 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
280602 ATATAATATT
280612 AAAATTAATATTTAATTATTTAA
1 AAAATTAATA-TTAA--ATTTAA
280635 AAAATTAATATTAAATTTAA
1 AAAATTAATATTAAATTTAA
*
280655 AAAATATAATATAAAATT
1 AAAAT-TAATATTAAATT
280673 AAATATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 11 0.31
21 11 0.31
22 4 0.11
23 10 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTAATATTAAATTTAA
Found at i:287971 original size:18 final size:18
Alignment explanation
Indices: 287935--287973 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
287925 CCGGTAAAAA
* **
287935 TTACCTAAAATATTTATT
1 TTACCTAAAACATCAATT
287953 TTACCTAAAACATCAATT
1 TTACCTAAAACATCAATT
287971 TTA
1 TTA
287974 ACATTTCGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (18 bp):
TTACCTAAAACATCAATT
Found at i:290789 original size:22 final size:21
Alignment explanation
Indices: 290761--290802 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
290751 AATTTATTTT
*
290761 ATTTAAGGTTTATGATTTTATA
1 ATTTAAGGTTTA-GAATTTATA
290783 ATTTAAGGTTTAGAATTTAT
1 ATTTAAGGTTTAGAATTTAT
290803 GGTTGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (21 bp):
ATTTAAGGTTTAGAATTTATA
Found at i:295954 original size:17 final size:17
Alignment explanation
Indices: 295934--295976 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
295924 TTAAAATTTT
295934 TTATTATAA-ATTTAAAA
1 TTATTA-AATATTTAAAA
295951 TTATTAAATATTT-AAA
1 TTATTAAATATTTAAAA
295967 TATATTAAAT
1 T-TATTAAAT
295977 TATACTCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTATTAAATATTTAAAA
Found at i:297137 original size:2 final size:2
Alignment explanation
Indices: 297076--297118 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
297066 CAACTATTAA
297076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
297118 A
1 A
297119 AAAATTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:297914 original size:21 final size:21
Alignment explanation
Indices: 297890--297929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
297880 TAACAAAGGT
297890 AGTACCGATACTCCT-TGTAGG
1 AGTACCGATAC-CCTCTGTAGG
*
297911 AGTACTGATACCCTCTGTA
1 AGTACCGATACCCTCTGTA
297930 CTGGGAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (21 bp):
AGTACCGATACCCTCTGTAGG
Found at i:299496 original size:24 final size:24
Alignment explanation
Indices: 299469--299557 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 24
299459 GATATCAGAA
*
299469 ATCAAAACAGAATTCAGAACATAT
1 ATCAAAACAAAATTCAGAACATAT
* * * *
299493 ATCAGAACAAAAATCCA-AATCAGAA
1 ATCAAAAC-AAAATTCAGAA-CATAT
* ** *
299518 ATCAGAACAAAATTCAGGTCATGT
1 ATCAAAACAAAATTCAGAACATAT
*
299542 ATCAAAACAGAATTCA
1 ATCAAAACAAAATTCA
299558 AGTCGGAAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
24 32 0.65
25 17 0.35
ACGTcount: A:0.53, C:0.18, G:0.10, T:0.19
Consensus pattern (24 bp):
ATCAAAACAAAATTCAGAACATAT
Found at i:300536 original size:27 final size:27
Alignment explanation
Indices: 300498--300551 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
300488 ATTTACTTGG
*
300498 ATTCCTTAATTAATTTAAAACAACTAC
1 ATTCCTTAATTAATTTAAAAAAACTAC
300525 ATTCCTTAATTAATTTAAAAAAACTAC
1 ATTCCTTAATTAATTTAAAAAAACTAC
300552 TTAGTCTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTCCTTAATTAATTTAAAAAAACTAC
Found at i:301452 original size:18 final size:18
Alignment explanation
Indices: 301429--301468 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
301419 ACTAAGCACA
301429 TAACTTGTAATTTAATCC
1 TAACTTGTAATTTAATCC
301447 TAACTTGTAATTTAATCC
1 TAACTTGTAATTTAATCC
301465 TAAC
1 TAAC
301469 AATTCCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (18 bp):
TAACTTGTAATTTAATCC
Found at i:307905 original size:6 final size:6
Alignment explanation
Indices: 307898--307995 Score: 178
Period size: 6 Copynumber: 16.3 Consensus size: 6
307888 CCGTCCCGTC
* *
307898 GTCGTC GTCGTC GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
307946 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
307994 GT
1 GT
307996 AATACGTGTC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:309803 original size:23 final size:22
Alignment explanation
Indices: 309750--309805 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
309740 TTTATTATTG
* * *
309750 TAAAAAATAATTTAATTAATTT
1 TAAATAATATTTTAAATAATTT
309772 T-AATGAATATTTTAAATAATTTT
1 TAAAT-AATATTTTAAATAA-TTT
309795 TAAATAATATT
1 TAAATAATATT
309806 ACAAGGAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 10 0.36
24 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATAATATTTTAAATAATTT
Found at i:312396 original size:26 final size:28
Alignment explanation
Indices: 312362--312426 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 28
312352 CGTTTAAATT
*
312362 TTTAATATT-ATA-TTCGTATTCGTTTA
1 TTTATTATTGATAGTTCGTATTCGTTTA
312388 TTTATTATTGATAGTGTTCGTATTCGTTTA
1 TTTATTATTGATA--GTTCGTATTCGTTTA
312418 TTTATTATT
1 TTTATTATT
312427 CACGAACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.24
27 3 0.09
30 23 0.68
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (28 bp):
TTTATTATTGATAGTTCGTATTCGTTTA
Found at i:312467 original size:23 final size:23
Alignment explanation
Indices: 312417--312491 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
312407 GTATTCGTTT
*
312417 ATTTATTATTCACGAACATATTC
1 ATTTAATATTCACGAACATATTC
* ** *
312440 GTTTAATATTCACGAATGTGTTC
1 ATTTAATATTCACGAACATATTC
* ** *
312463 ATTTATATGTTCGTGAACTTATTC
1 ATTTA-ATATTCACGAACATATTC
312487 ATTTA
1 ATTTA
312492 GTGTTCGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (23 bp):
ATTTAATATTCACGAACATATTC
Found at i:318338 original size:37 final size:37
Alignment explanation
Indices: 318295--318369 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
318285 ATATATAGAC
318295 AAACAAATGGTTTCCCACCTCAATTATTCCTACTTGT
1 AAACAAATGGTTTCCCACCTCAATTATTCCTACTTGT
318332 AAACAAATGGTTTCCCACCTCAATTATTCCTACTTGT
1 AAACAAATGGTTTCCCACCTCAATTATTCCTACTTGT
318369 A
1 A
318370 GAGTGACTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (37 bp):
AAACAAATGGTTTCCCACCTCAATTATTCCTACTTGT
Found at i:320660 original size:4 final size:4
Alignment explanation
Indices: 320645--320688 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
320635 TTTATTAACT
* * *
320645 CATA CGTA CATA CATA TATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
320689 TCAGTTTGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (4 bp):
CATA
Found at i:325315 original size:53 final size:53
Alignment explanation
Indices: 325200--325315 Score: 121
Period size: 53 Copynumber: 2.2 Consensus size: 53
325190 TAATTATAAC
* * *
325200 ATTAATGTTAACCAAATTTAGACTATAAATGGTATATTATCCCAATCATTTGT
1 ATTAATGTTAACCAAACTTAGACTACAAATGGTATATTAACCCAATCATTTGT
** * *
325253 ATTTGTGTTAACCAAACTTAG-GTAACAAAT-GTCATATTAACCCAATTATTT-T
1 ATTAATGTTAACCAAACTTAGACT-ACAAATGGT-ATATTAACCCAATCATTTGT
325305 AATTAATGTTA
1 -ATTAATGTTA
325316 TAATTAATAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
52 4 0.08
53 47 0.92
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (53 bp):
ATTAATGTTAACCAAACTTAGACTACAAATGGTATATTAACCCAATCATTTGT
Found at i:326892 original size:30 final size:30
Alignment explanation
Indices: 326852--326912 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
326842 CTAGTTGAAC
*
326852 AGTATTGATACCATAAGCCTGAATTTGATA
1 AGTATCGATACCATAAGCCTGAATTTGATA
326882 AGTATCGATACCATAAGCCTGAATTTGATA
1 AGTATCGATACCATAAGCCTGAATTTGATA
326912 A
1 A
326913 AGTTATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (30 bp):
AGTATCGATACCATAAGCCTGAATTTGATA
Found at i:327407 original size:2 final size:2
Alignment explanation
Indices: 327400--327439 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
327390 ATGAACATGC
*
327400 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
327440 TATGATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327706 original size:22 final size:21
Alignment explanation
Indices: 327678--327740 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
327668 CAAGGGTTAC
327678 ATAGGTCTTTCGGGACATATA
1 ATAGGTCTTTCGGGACATATA
*
327699 TATAGGTCCTTT-GGGACATACA
1 -ATAGGT-CTTTCGGGACATATA
**
327721 CGAGGTCTTTCGGGACATAT
1 ATAGGTCTTTCGGGACATAT
327741 TTCACATGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 15 0.43
23 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (21 bp):
ATAGGTCTTTCGGGACATATA
Found at i:331998 original size:18 final size:19
Alignment explanation
Indices: 331963--331999 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
331953 CACGGAATGT
331963 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
331983 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
332000 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:343265 original size:31 final size:31
Alignment explanation
Indices: 343229--343287 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
343219 AACTTAAAAG
*
343229 AGTTTTACAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
343260 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
343288 ACATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:343359 original size:32 final size:32
Alignment explanation
Indices: 343320--344049 Score: 437
Period size: 32 Copynumber: 25.7 Consensus size: 32
343310 CAATCCATAT
* *
343320 TTTAAAATAAACCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343352 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343384 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343406 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343438 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
343460 TTTAAAATAAATCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343492 TTTAAAATAAATCAAT-C-TA-T-A-AAACTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* * * *
343519 --CAATAATAAAGCAATCTATAC-AACTACA--A
1 TTTAA-AATAAATCAATCCATACTAA-TAAATTA
**
343548 --T--AATAAATCAATCCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343573 --T-AAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343602 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343634 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343656 TTTAAATTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
343688 TTTAAAATAAATTAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
343718 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343736 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
343768 TTTAAAATAAATCAATTTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343800 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
**
343822 TTTAAAATAAATCAATTTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343854 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* ** *
343884 --T--AATAAATCAATTCATA-TTTTAAAATA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
** * * *
343911 AAT-CAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
343942 TTTAAAATAAATCAATTCATACTAATAAATTT
1 TTTAAAATAAATCAATCCATACTAATAAATTA
343974 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
343996 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
344028 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
344050 AACTACAATA
Statistics
Matches: 554, Mismatches: 54, Indels: 180
0.70 0.07 0.23
Matches are distributed among these distances:
20 1 0.00
22 90 0.16
23 8 0.01
24 7 0.01
25 10 0.02
26 85 0.15
27 14 0.03
28 20 0.04
29 5 0.01
30 23 0.04
31 23 0.04
32 268 0.48
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:343399 original size:86 final size:86
Alignment explanation
Indices: 343303--343460 Score: 289
Period size: 86 Copynumber: 1.8 Consensus size: 86
343293 CAACTACAAT
343303 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
343368 CCATATTAATAAATTATTTAA
66 CCATATTAATAAATTATTTAA
* * *
343389 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
343454 CCATATT
66 CCATATT
343461 TTAAAATAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (86 bp):
AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
CCATATTAATAAATTATTTAA
Found at i:343410 original size:54 final size:54
Alignment explanation
Indices: 343352--343783 Score: 327
Period size: 54 Copynumber: 7.9 Consensus size: 54
343342 AAATAAATTA
*
343352 TTTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
343406 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
** * *
343460 TTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCTATAAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT-AT
** * * * * * *
343515 ACTACAAT-AATAAAGCAAT-CT-ATACAACTA--CAATAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATA-AATTATTTAA-AATAAATCAATCCATAT
*
343566 TTTAAAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAA
1 TTT---A-AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C---C--AT--A
343631 TT
54 -T
** ** * ** **
343633 ATTTAAAATAAATCAATCCATA-TTTTAAATTAAAT-CAATCCATACTAATAAAT-T
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
* *
343687 ATTTAAAATAAATTAATCCATAC-AACTACA--A--T--AATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
*
343736 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
343784 TTATACTAAT
Statistics
Matches: 299, Mismatches: 45, Indels: 68
0.73 0.11 0.17
Matches are distributed among these distances:
48 29 0.10
49 4 0.01
50 6 0.02
51 5 0.02
52 18 0.06
53 7 0.02
54 143 0.48
55 12 0.04
56 8 0.03
57 5 0.02
58 16 0.05
59 3 0.01
62 6 0.02
63 9 0.03
64 22 0.07
65 1 0.00
66 1 0.00
67 1 0.00
68 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:343435 original size:22 final size:22
Alignment explanation
Indices: 343386--343434 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
343376 ATAAATTATT
**
343386 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
343408 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
343431 TAAA
1 TAAA
343435 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:343526 original size:26 final size:26
Alignment explanation
Indices: 343497--343560 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
343487 AATTATTTAA
343497 AATAAATCAATCTATAAAACTACAAT
1 AATAAATCAATCTATAAAACTACAAT
* *
343523 AATAAAGCAATCTATACAACTACAAT
1 AATAAATCAATCTATAAAACTACAAT
343549 AATAAATCAATC
1 AATAAATCAATC
343561 CATATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (26 bp):
AATAAATCAATCTATAAAACTACAAT
Found at i:343612 original size:196 final size:196
Alignment explanation
Indices: 343406--343820 Score: 586
Period size: 196 Copynumber: 2.1 Consensus size: 196
343396 CAATCCATAT
343406 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * *
343471 TCAATATATACTAATAAATTATTTAAAATAAATCAATCTATAAAACTACAATAATAAAGCAATCT
66 TCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAATAATAAAGCAATCC
***
343536 ATACAACTACAATAATAAATCAATCCATA-TTTTAAA-A-T-AAATAAATCAATCCATACAAATA
131 AT---ACTACAA-AATAAATCAATCCATACAAATAAATATTAAAATAAATCAATCCATACAAATA
343597 AATTA
192 AATTA
* *
343602 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAATTAAA
1 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
* * * *
343667 TCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATACAACTACAATAATAAATCAATCC
66 TCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAATAATAAAGCAATCC
* ** ** *
343732 ATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATTTATACTAATAAA
131 ATACTACAAAATAAATCAATCCATACAAATAAA-TA-TTAAAATAAATCAATCCATACAAATAAA
343797 TTA
194 TTA
343800 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
343821 TTTTAAAATA
Statistics
Matches: 194, Mismatches: 19, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
192 16 0.08
193 8 0.04
195 1 0.01
196 123 0.63
197 1 0.01
198 45 0.23
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (196 bp):
TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
TCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAAAACTACAATAATAAAGCAATCC
ATACTACAAAATAAATCAATCCATACAAATAAATATTAAAATAAATCAATCCATACAAATAAATT
A
Found at i:343660 original size:22 final size:22
Alignment explanation
Indices: 343634--343676 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
343624 TAATAAATTA
343634 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
343656 TTTAAATTAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
343677 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:343775 original size:14 final size:14
Alignment explanation
Indices: 343758--343811 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
343748 CAATCCATAC
343758 AAATAAATTATTTA
1 AAATAAATTATTTA
*
343772 AAATAAATCAATTTA
1 AAATAAAT-TATTTA
343787 TACTAATAAATTATTTA
1 -A--AATAAATTATTTA
343804 AAATAAAT
1 AAATAAAT
343812 CAATCTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 15 0.44
15 5 0.15
16 2 0.06
17 5 0.15
18 7 0.21
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:343826 original size:22 final size:22
Alignment explanation
Indices: 343800--343842 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
343790 TAATAAATTA
343800 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
*
343822 TTTAAAATAAATCAATTTATA
1 TTTAAAATAAATCAATCTATA
343843 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:343851 original size:22 final size:22
Alignment explanation
Indices: 343802--343850 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
343792 ATAAATTATT
**
343802 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCTATATAA
*
343824 TAAAATAAATCAATTTATACTAA
1 TAAAATAAATCAATCTATA-TAA
343847 TAAA
1 TAAA
343851 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:343862 original size:14 final size:15
Alignment explanation
Indices: 343736--343869 Score: 67
Period size: 18 Copynumber: 8.1 Consensus size: 15
343726 CAATCCATAT
343736 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
* *
343751 TCCATACAAATAAAT-TA
1 T--TTA-AAATAAATCAA
343768 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
*
343783 TTTATACTAATAAAT-TA
1 TTTA-A--AATAAATCAA
343800 TTTAAAATAAATCAATCTATA
1 TTTAAAAT--A--AATC-A-A
343821 TTTTAAAATAAATCAA
1 -TTTAAAATAAATCAA
*
343837 TTTATACTAATAAAT-TA
1 TTTA-A--AATAAATCAA
343854 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
343869 T
1 T
343870 CCATACAACT
Statistics
Matches: 92, Mismatches: 8, Indels: 38
0.67 0.06 0.28
Matches are distributed among these distances:
14 18 0.20
15 14 0.15
16 6 0.07
17 15 0.16
18 29 0.32
20 1 0.01
21 1 0.01
22 8 0.09
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAATCAA
Found at i:343997 original size:340 final size:331
Alignment explanation
Indices: 343303--344149 Score: 1154
Period size: 340 Copynumber: 2.5 Consensus size: 331
343293 CAACTACAAT
* *
343303 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACAAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * *
343368 CCATATTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAAT
66 CCATA-CAACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
** ** * ** * *
343432 AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT-CAATATATACTAATAAATTATTTA
124 AAATTATTTAAAATAAATCAATTTATATAATAAATTATTTAAAATAAATACTAATAAATTATTTA
* *
343496 AAATAAATCAATCTATAAAACTACAATAATAAAGCAATCTATACAACTACAATAATAAATCAATC
189 AAATAAATCAATATATAAAACTACAATAATAAAGCAATCCATACAACTACAATAATAAATCAATC
343561 CATATTTTAAAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTA
254 CATATTTTAAAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTA
343626 ATAAATTATTTAA
319 ATAAATTATTTAA
* *
343639 AATAAATCAATCCATATTTTAAATTAAATCAATCCATACTAATAAATTATTTAAAATAAATTAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
343704 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTAT
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
**
343769 TTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAAT-C-AATCTA-TATTTTAAAATA
131 TTAAAATAAATCAATTTATA-TAATAAATTATTTAAAATAAATACTAATAAATTA-TTTAAAATA
* * *
343831 AATCAATTTATACTAATAAATTATTTAA-AATAAATCAATCCATACAACTACAATAATAAATCAA
194 AATCAA--TATA-T-A-AAACTA--CAATAATAAAGCAATCCATACAACTACAATAATAAATCAA
* *
343895 TTCATATTTTAAAATAAATCAATCAATCAATCCATACAAATAAATTATTTAAAATAAATCAATTC
252 TCCATATTTTAAAATAAAT--A--AATCAATCCATACAAATAAATTATTTAAAATAAATCAATCC
*
343960 ATACTAATAAATTTTTTAA
313 ATACTAATAAATTATTTAA
*
343979 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
344044 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAAT-CATACTAATAAATTA
66 CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATC-AATCCATACTAATAAATTA
* * *
344108 TTTAAAATAAAT-TATTT-TATAATAATTTATTTTATAATAAAT
130 TTTAAAATAAATCAATTTATATAATAAATTA-TTTAAAATAAAT
344150 TATTTTATAA
Statistics
Matches: 460, Mismatches: 34, Indels: 32
0.87 0.06 0.06
Matches are distributed among these distances:
329 2 0.00
330 85 0.18
331 9 0.02
332 10 0.02
333 1 0.00
334 2 0.00
335 7 0.02
336 121 0.26
337 11 0.02
338 14 0.03
339 4 0.01
340 191 0.42
341 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (331 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATTTATATAATAAATTATTTAAAATAAATACTAATAAATTATTTAAAATAAA
TCAATATATAAAACTACAATAATAAAGCAATCCATACAACTACAATAATAAATCAATCCATATTT
TAAAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATT
ATTTAA
Found at i:344021 original size:54 final size:54
Alignment explanation
Indices: 343602--344048 Score: 310
Period size: 54 Copynumber: 8.0 Consensus size: 54
343592 AAATAAATTA
343602 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
343656 TTTAAATTAAATCAATCCATACTAATAAATTATTTAAAATAAATTAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** ** * ** * ** **
343713 TACAATAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACAAATAAAT-T
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C-AATCCATAT
** *
343767 ATTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATCAATCTATAT
1 -TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
** *
343822 TTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * ** * ** * * *
343879 TACAATAATAAATCAATTCATA-TTTTAAAATAAAT-CAATCAATCAATCCATACA
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-T
** * * * * *
343933 AATAAATTATTTAAAATAAATCAATTCATACTAATAAATTTTTTAAAATAAATCAATCCATAT
1 TTTAAA--A--T-AAATCAATCCATAC-TAAT---AAATTATTTAAAATAAATCAATCCATAT
*
343996 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
344049 CAACTACAAT
Statistics
Matches: 300, Mismatches: 67, Indels: 52
0.72 0.16 0.12
Matches are distributed among these distances:
53 2 0.01
54 149 0.50
55 14 0.05
56 24 0.08
57 28 0.09
58 55 0.18
59 1 0.00
60 2 0.01
61 1 0.00
63 9 0.03
64 15 0.05
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:344025 original size:22 final size:22
Alignment explanation
Indices: 343976--344024 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
343966 ATAAATTTTT
**
343976 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
343998 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
344021 TAAA
1 TAAA
344025 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:344131 original size:15 final size:15
Alignment explanation
Indices: 344098--344179 Score: 130
Period size: 15 Copynumber: 5.5 Consensus size: 15
344088 CAAATCATAC
344098 TAATAAATTA-TTTA
1 TAATAAATTATTTTA
*
344112 AAATAAATTATTTTA
1 TAATAAATTATTTTA
*
344127 TAATAATTTATTTTA
1 TAATAAATTATTTTA
344142 TAATAAATTATTTTA
1 TAATAAATTATTTTA
344157 TAATAAATTATTTTA
1 TAATAAATTATTTTA
*
344172 AAATAAAT
1 TAATAAAT
344180 AACCTTAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
14 9 0.15
15 53 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAAATTATTTTA
Found at i:344894 original size:2 final size:2
Alignment explanation
Indices: 344889--344914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
344879 TAAAAAAATA
344889 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
344915 TGACCAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345353 original size:21 final size:21
Alignment explanation
Indices: 345337--345413 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
345327 GCGTTGCATT
*
345337 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGCAAA
* * **
345358 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGCAAA
*
345378 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGCAAA
345399 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
345414 CTACAATGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGCAAA
Found at i:345378 original size:41 final size:41
Alignment explanation
Indices: 345333--345410 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
345323 ATTCGCGTTG
*
345333 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
345374 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
345411 AGTCTACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:345541 original size:6 final size:6
Alignment explanation
Indices: 345530--345566 Score: 53
Period size: 5 Copynumber: 6.7 Consensus size: 6
345520 AGACACGTAT
345530 GACCAC GACCAC GACCAC GA-CAC GACC-C GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
345567 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.50
6 15 0.50
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:346221 original size:22 final size:21
Alignment explanation
Indices: 346193--346264 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
346183 AATTTGGAAA
346193 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* * **
346215 ATCGCAAC-AAA-TTTGGAAA
1 ATCGCAACGAAACTGTAGACT
*
346234 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGA-AACTGTAGACT
*
346256 GTCGCAACG
1 ATCGCAACG
346265 CAATTTTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 3 0.08
21 3 0.08
22 19 0.51
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:346232 original size:41 final size:41
Alignment explanation
Indices: 346175--346263 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
346165 CAACGACTTT
* * *
346175 TCGCAACGAATTTGGAAAATCGCAACGATAACTGTAGACTA
1 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTA
*
346216 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTG
1 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTA
346257 TCGCAAC
1 TCGCAAC
346264 GCAATTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTA
Found at i:346281 original size:21 final size:21
Alignment explanation
Indices: 346234--346367 Score: 82
Period size: 20 Copynumber: 6.5 Consensus size: 21
346224 AATTTGGAAA
346234 ATCGCAACGACAACTGTAAACT
1 ATCGCAACG-CAACTGTAAACT
* * * *
346256 GTCGCAACGCAATTTTCAACT
1 ATCGCAACGCAACTGTAAACT
*
346277 ATCGCAACGCGAACTGGAAA--
1 ATCGCAACGC-AACTGTAAACT
* *
346297 ATCGCAACGCGAAATGGAAA--
1 ATCGCAACGC-AACTGTAAACT
* * * *
346317 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCAACTGTAAACT
*
346338 ATCGCAACGCGAACTGGAAA--
1 ATCGCAACGC-AACTGTAAACT
346358 ATCGCAACGC
1 ATCGCAACGC
346368 GAAATGGAAA
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.05
20 39 0.44
21 28 0.32
22 17 0.19
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCAACTGTAAACT
Found at i:346302 original size:20 final size:20
Alignment explanation
Indices: 346277--346586 Score: 219
Period size: 20 Copynumber: 15.6 Consensus size: 20
346267 ATTTTCAACT
346277 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
346297 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
346317 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
346338 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
346358 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
*
346378 ATCGCAACGCG-A-T----T
1 ATCGCAACGCGAACTGGAAA
* *
346392 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
346411 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
346433 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
* ** **
346452 ATCACAACGATAACTGTAGACT
1 ATCGCAACGCGAACTG--GAAA
*
346474 ATCGCAACTCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
346494 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
** ** *
346514 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAACTGGAA-A
*
346535 ATCGCAACGTGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
346555 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
346575 ATCGCAACGCGA
1 ATCGCAACGCGA
346587 TTTTCAACTA
Statistics
Matches: 221, Mismatches: 49, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.01
13 1 0.00
14 6 0.03
15 1 0.00
18 1 0.00
19 16 0.07
20 135 0.61
21 35 0.16
22 24 0.11
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:346333 original size:61 final size:61
Alignment explanation
Indices: 346257--346394 Score: 267
Period size: 61 Copynumber: 2.3 Consensus size: 61
346247 CTGTAAACTG
*
346257 TCGCAACGCAATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAA
1 TCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAA
346318 TCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAA
1 TCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAA
346379 TCGCAACGCGATTTTC
1 TCGCAACGCGATTTTC
346395 GCAACGAATT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (61 bp):
TCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAA
Found at i:346436 original size:22 final size:21
Alignment explanation
Indices: 346411--346481 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
346401 AATTTGGAAA
346411 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* * **
346433 ATCGCAACG-AA-TTTGGAAA
1 ATCGCAACGAAACTGTAGACT
*
346452 ATCACAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
346474 ATCGCAAC
1 ATCGCAAC
346482 TCGAACTGGA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 12 0.33
20 2 0.06
21 2 0.06
22 20 0.56
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:346450 original size:41 final size:41
Alignment explanation
Indices: 346393--346502 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
346383 AACGCGATTT
346393 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
* *
346434 TCGCAACGAATTTGGAAAATCACAACGATAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
346475 TCGCAACTCGAA-CTGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
346503 CGAAATGGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 45 0.71
42 14 0.22
43 4 0.06
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:346536 original size:61 final size:61
Alignment explanation
Indices: 346471--346604 Score: 252
Period size: 61 Copynumber: 2.2 Consensus size: 61
346461 ATAACTGTAG
346471 ACTATCGCAAC-TCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGT-GAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
346532 ACTATCGCAACGTGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGTGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
346593 ACTATCGCAACG
1 ACTATCGCAACG
346605 CGATTTTCAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 71 0.99
62 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (61 bp):
ACTATCGCAACGTGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:346540 original size:21 final size:20
Alignment explanation
Indices: 346514--346628 Score: 104
Period size: 21 Copynumber: 5.6 Consensus size: 20
346504 GAAATGGAAA
346514 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAA-T
* ** ** *
346535 ATCGCAACGTGAACTGGAAA
1 ATCGCAACGCGATTTTCAAT
** ** *
346555 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAAT
346575 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAA-T
346596 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAA-T
346617 ATCGCAACGCGA
1 ATCGCAACGCGA
346629 AATGCAACGC
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 33 0.42
21 46 0.58
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTTTCAAT
Found at i:346541 original size:177 final size:177
Alignment explanation
Indices: 346216--346566 Score: 429
Period size: 177 Copynumber: 2.0 Consensus size: 177
346206 CTGTAGACTA
* * * *
346216 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTGTCGCAACGCAATTTTCAACTATCG
1 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCAATTTGCAACAATCA
* ** * *
346281 CAACGCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAAC
66 CAACGAGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGCAACAATCGCAAC
*
346346 GCGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
131 GCGAACTGCAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
* * *
346393 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG-AATTTGGAA-AATCA
1 TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCAATTTGCAACAATCA
* ** * * *
346456 CAACGATAACTGTAGACTATCGCAACTCGAACTGGAAAATCGCAACGCGAAATGGAA-AATCGCA
66 CAACGAGAACTG--GAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGCAACAATCGCA
** * * * *
346520 ACGCGATTTTCAACTATCGCAACGTGAACTGGAAAATCGCAACGCGA
129 ACGCGAACTGCAA-AATCGCAACGCGAAATGGAAAATCGCAACGCGA
346567 AATGGAAAAT
Statistics
Matches: 146, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
175 13 0.09
176 22 0.15
177 111 0.76
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (177 bp):
TCGCAACAAATTTGGAAAATCGCAACGACAACTGTAAACTATCGCAACGCAATTTGCAACAATCA
CAACGAGAACTGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCGAAATGCAACAATCGCAAC
GCGAACTGCAAAATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
Found at i:346849 original size:22 final size:22
Alignment explanation
Indices: 346797--346862 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
346787 TAGTTTCATG
*
346797 ATAA-TTTATAAATTTTAATTTC
1 ATAACTTT-TAAATTTTATTTTC
*
346819 ATAACTTTTAAATTTTATTTTT
1 ATAACTTTTAAATTTTATTTTC
**
346841 ATAGGTTTTATAATATTTATTT
1 ATAACTTTTA-AAT-TTTATTT
346863 AATTTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 24 0.65
23 6 0.16
24 7 0.19
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (22 bp):
ATAACTTTTAAATTTTATTTTC
Found at i:348876 original size:17 final size:17
Alignment explanation
Indices: 348854--348909 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
348844 TATTTTTTAT
348854 TATTATATTTATATAAA
1 TATTATATTTATATAAA
*
348871 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
348888 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
348904 TATTAT
1 TATTAT
348910 TTATTTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:348878 original size:30 final size:31
Alignment explanation
Indices: 348844--348916 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 31
348834 ATAGTTTTTA
*
348844 TATTTTTTATT-ATTATATTTATATAAATAT
1 TATTTTTTATTAATAATATTTATATAAATAT
*
348874 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTTTATT--AATAATATTTATATAAATAT
348907 TATTTATTTA
1 TATTT-TTTA
348917 AACTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 11 0.30
33 22 0.59
34 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTTTTATTAATAATATTTATATAAATAT
Found at i:348949 original size:20 final size:21
Alignment explanation
Indices: 348924--348962 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
348914 TTAAACTTAT
348924 TAATTA-AT-TATTATTTGTGC
1 TAATTATATATATT-TTTGTGC
348944 TAATTATATATATTTTTGT
1 TAATTATATATATTTTTGT
348963 CTACAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (21 bp):
TAATTATATATATTTTTGTGC
Found at i:350690 original size:41 final size:42
Alignment explanation
Indices: 350645--350729 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
350635 GATGCCACAG
* * *
350645 GGGTACATGCC-ATCCCTCCAGTTTAGATGCCATCTCTGCAA
1 GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCTGCAA
* * *
350686 GGGTATATGCCAAGCCCACCAGTTCATATGTCATCTCTGCAA
1 GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCTGCAA
350728 GG
1 GG
350730 TTATATTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 10 0.27
42 27 0.73
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (42 bp):
GGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCTGCAA
Found at i:350773 original size:21 final size:20
Alignment explanation
Indices: 350727--350791 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
350717 CATCTCTGCA
* *
350727 AGGTTATATTTCTAGCCCAC
1 AGGTTACATTCCTAGCCCAC
*
350747 AGGGTTACATTCCTAGCCTACC
1 A-GGTTACATTCCTAGCCCA-C
* *
350769 AGGTTACATGCCTAGCCCGC
1 AGGTTACATTCCTAGCCCAC
350789 AGG
1 AGG
350792 GTTTTATGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 5 0.14
21 30 0.81
22 2 0.05
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (20 bp):
AGGTTACATTCCTAGCCCAC
Found at i:351367 original size:19 final size:19
Alignment explanation
Indices: 351331--351368 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
351321 TATTCCAATT
*
351331 GAAATTTAAAATTGTATTC
1 GAAATTTAAAATTATATTC
*
351350 GAAATTTAAAGTTATATTC
1 GAAATTTAAAATTATATTC
351369 CAATTAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
GAAATTTAAAATTATATTC
Found at i:352194 original size:117 final size:117
Alignment explanation
Indices: 351896--352350 Score: 662
Period size: 117 Copynumber: 3.9 Consensus size: 117
351886 TCAAACATAA
* * * * * *
351896 TAGGTACTGGCATGAATAGTACCTCGGGGGGACATGAGTGATATAATAGGGCAATGATAACATAT
1 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT
* * * * * *
351961 TCTCTGATAAAATAATAGAAGGTGCCCCCCCGAAAATGCACTTTCACCACTT
66 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGAAAACGCGCTTTCACCACTT
* *
352013 TAGGCACTGACATGAATAGTG-CCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATAT
1 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT
* * *
352077 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGAAAACGCGTTTTTATCACTT
66 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGAAAACGCGCTTTCACCACTT
*
352129 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATAT
1 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT
* * * *
352194 TCTCTAACAAAATAATGGAAGGCGCGCCCTCGGAAACGCGCTTTCACCATTT
66 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGAAAACGCGCTTTCACCACTT
*
352246 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATAT
1 TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT
* *
352311 TTTCTGACAAAATAATGGAAGGTGCGCCCCC-AGAAACGCG
66 TCTCTGACAAAATAATGGAAGGCGCGCCCCCGA-AAACGCG
352351 TCTTCACATG
Statistics
Matches: 302, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
116 101 0.33
117 201 0.67
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (117 bp):
TAGGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATAT
TCTCTGACAAAATAATGGAAGGCGCGCCCCCGAAAACGCGCTTTCACCACTT
Found at i:355864 original size:23 final size:23
Alignment explanation
Indices: 355831--355882 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
355821 AACCTTATAT
* * * *
355831 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTACAATTATACGC
*
355854 GGCACTACGGTACAATTATACGT
1 GGCACTACGGTACAATTATACGC
355877 GGCACT
1 GGCACT
355883 TTGGTGTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:360995 original size:23 final size:23
Alignment explanation
Indices: 360927--360995 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
360917 CAACCTTATA
*
360927 TGGCACTTCGGTGCATTTCTAAG
1 TGGCACTTCGGTGCATTTCTACG
* * *
360950 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
360973 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
360996 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:362095 original size:21 final size:21
Alignment explanation
Indices: 362053--362095 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
362043 TTTCTGGGCT
* *
362053 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
362074 AGGGGTATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
362095 A
1 A
362096 TCGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:362203 original size:13 final size:13
Alignment explanation
Indices: 362185--362216 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
362175 GTGAATATGA
362185 GTTTAATAAGTTC
1 GTTTAATAAGTTC
362198 GTTTAATAAGTTC
1 GTTTAATAAGTTC
362211 GTTTAA
1 GTTTAA
362217 GTTTCTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (13 bp):
GTTTAATAAGTTC
Found at i:362787 original size:23 final size:23
Alignment explanation
Indices: 362754--362821 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
362744 ATTATTATAT
*
362754 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
362777 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
362800 GGCACTTCGGTGCAATTATACG
1 GGCACTTCGGTGCAATTCTACG
362822 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:366328 original size:20 final size:20
Alignment explanation
Indices: 366303--366345 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
366293 TAATAATTAA
*
366303 TATTATTTATTATAAAAAAT
1 TATTATTAATTATAAAAAAT
* *
366323 TATTATTAATTTTAAAATAT
1 TATTATTAATTATAAAAAAT
366343 TAT
1 TAT
366346 AATAATTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATTAATTATAAAAAAT
Found at i:366351 original size:19 final size:20
Alignment explanation
Indices: 366315--366352 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
366305 TTATTTATTA
*
366315 TAAAAAATTATTATTAATTT
1 TAAAAAATTATTAATAATTT
*
366335 TAAAATATTA-TAATAATT
1 TAAAAAATTATTAATAATT
366353 CTACCTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAAAATTATTAATAATTT
Found at i:368040 original size:247 final size:250
Alignment explanation
Indices: 367397--368043 Score: 645
Period size: 246 Copynumber: 2.6 Consensus size: 250
367387 ATTGAGCTAC
* * *
367397 TTCTTCAATCCAAGAATCTTATTTGT-CTGAAAAAACTAAAACAAAATCTATTGGTGCAGAATGC
1 TTCTTCAATCCAAGAATCTTATTT-TCCTG-AAAAAC-AAAGCAAAATCTATTGGTGCAAAATGT
* * * * *
367461 ATTCCCTATACACACTCAAGAAGACCCAACCACCATATGATATGATATCACCATCCCAACTATTA
63 ATTCCCTATACATA-TCTAGAAGACCAAACAAACATATG---T-ATATCACCATCCCAACTATTA
* * *
367526 GACTTCA-TTGCCTTAAAAAATTAGGATTTGTTTGTTTTCTCATTTTGGGTTTATATCGTTCTTT
123 GACTTCACTT-CCTTAAAAAATTA-GA-TCGTTTGTTGTCTCATTTTGGGTTTATATCGTTCTCT
* * * * *
367590 ATAAATCAGATTAACTTTTTTCTTGAAATTTATTTAACTGACGACGACACTAATTTTAGTGTTGA
185 ATAAATCAGATCAACTTTTTTCTTCAAATTTATTTAACTGACGACGACACCAATTTTAATGTTAA
367655 G
250 G
** * * * *
367656 TTCTTGGATCCAAGAATCTTATTTGCCTGAAAAATCTATAGTAAAATCTAGTGGTGCAAAATGTA
1 TTCTTCAATCCAAGAATCTTATTTTCCTGAAAAA-C-AAAGCAAAATCTATTGGTGCAAAATGTA
* * * *
367721 TTCCTTATACAT-TCTAGAAGACCAAACAAACATAT-TATATCACCAT-CCAATTGTTAGACTTT
64 TTCCCTATACATATCTAGAAGACCAAACAAACATATGTATATCACCATCCCAACTATTAGACTTC
* * * *
367783 ACTGCCTTAAAAAATGT-G-TCG-TT-TTGTC-CTTTTTAAGGGTTTATGTTGTTCTCTATAAAT
129 ACTTCCTTAAAAAAT-TAGATCGTTTGTTGTCTCATTTT--GGGTTTATATCGTTCTCTATAAAT
* * * ** * * *
367843 CAGGTCAACTTTTTT-TTCAATTTTATTTAGCTGGTGACTACTCCAGTTTTAATGTTAAG
191 CAGATCAACTTTTTTCTTCAAATTTATTTAACTGACGACGACACCAATTTTAATGTTAAG
*
367902 TTCTT-AATCCAAGAATCTTATTTTCCTGAAAAACAACAGCAAAATGTATTGGTGCAAAATGTAT
1 TTCTTCAATCCAAGAATCTTATTTTCCTGAAAAACAA-AGCAAAATCTATTGGTGCAAAATGTAT
* * ** *
367966 TCCCTGTACATAGTCTAGAAGACCGAATGAGCATATGT-TATCACCATCCCAACTATTAGACTTC
65 TCCCTATACATA-TCTAGAAGACCAAACAAACATATGTATATCACCATCCCAACTATTAGACTTC
368030 ACTTCCTTAAAAAA
129 ACTTCCTTAAAAAA
368044 AACTAGGATT
Statistics
Matches: 323, Mismatches: 54, Indels: 34
0.79 0.13 0.08
Matches are distributed among these distances:
243 1 0.00
244 34 0.11
245 31 0.10
246 70 0.22
247 63 0.20
248 2 0.01
250 1 0.00
251 25 0.08
252 12 0.04
253 1 0.00
257 19 0.06
258 5 0.02
259 59 0.18
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (250 bp):
TTCTTCAATCCAAGAATCTTATTTTCCTGAAAAACAAAGCAAAATCTATTGGTGCAAAATGTATT
CCCTATACATATCTAGAAGACCAAACAAACATATGTATATCACCATCCCAACTATTAGACTTCAC
TTCCTTAAAAAATTAGATCGTTTGTTGTCTCATTTTGGGTTTATATCGTTCTCTATAAATCAGAT
CAACTTTTTTCTTCAAATTTATTTAACTGACGACGACACCAATTTTAATGTTAAG
Found at i:375223 original size:21 final size:21
Alignment explanation
Indices: 375199--375240 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
375189 AGTTTATTTT
375199 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
375220 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
375241 AACTTGTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:375277 original size:33 final size:33
Alignment explanation
Indices: 375235--375338 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
375225 TTTGTTTCAA
*
375235 TTATCGAACTTGTAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
375268 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
375301 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
375333 TTATCG
1 TTATCG
375339 TAAACTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 6 0.09
33 62 0.91
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:375526 original size:15 final size:17
Alignment explanation
Indices: 375500--375531 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
375490 GTCTATGGGA
375500 AAAAACCGAAT-CGGAT
1 AAAAACCGAATCCGGAT
375516 AAAAACC-AATCCGGAT
1 AAAAACCGAATCCGGAT
375532 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (17 bp):
AAAAACCGAATCCGGAT
Found at i:376422 original size:42 final size:43
Alignment explanation
Indices: 376352--376439 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 43
376342 TTTTCAAGAA
* * * *
376352 TGGTTTTAATATGTTAGTTTGATTTATTTGTGGATTGTTA-TT
1 TGGTTTTAATATATTAATGTGATATATTTGTGGATTGTTACTT
*
376394 TGGTTTTAATATATTAATGTGGTATATTTGTGGATTGTTACTT
1 TGGTTTTAATATATTAATGTGATATATTTGTGGATTGTTACTT
376437 TGG
1 TGG
376440 GGTTTAGATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 35 0.88
43 5 0.12
ACGTcount: A:0.20, C:0.01, G:0.23, T:0.56
Consensus pattern (43 bp):
TGGTTTTAATATATTAATGTGATATATTTGTGGATTGTTACTT
Found at i:383251 original size:15 final size:15
Alignment explanation
Indices: 383231--383278 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
383221 ATATTTAGCT
*
383231 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
383246 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
383261 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
383276 GGG
1 GGG
383279 TGGGTAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:391437 original size:22 final size:23
Alignment explanation
Indices: 391407--391450 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
391397 ATTAGATCAT
391407 ATAAGTTTATAATATAAAAATAA
1 ATAAGTTTATAATATAAAAATAA
* *
391430 ATAA-TTTATATTTTAAAAATA
1 ATAAGTTTATAATATAAAAATA
391451 TAACCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAGTTTATAATATAAAAATAA
Found at i:394200 original size:29 final size:29
Alignment explanation
Indices: 394167--394234 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
394157 CATTTTACAC
* *
394167 AAATAGCACCCTTTTTAAAATAATCACCA
1 AAATAGCACCCATTTCAAAATAATCACCA
* * *
394196 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATCACCA
*
394225 GAATAGCACC
1 AAATAGCACC
394235 AAAATCGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATCACCA
Found at i:394242 original size:29 final size:29
Alignment explanation
Indices: 394187--394292 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 29
394177 CTTTTTAAAA
* * * **
394187 TAATCACCAAAATAGCACCCATTTCGAAT
1 TAATTACCAGAATAGCACCAAAATCGAAT
394216 TAATTACCAGAATAGCACCAAAATCGAAT
1 TAATTACCAGAATAGCACCAAAATCGAAT
* *
394245 TATTTACCAGAATAACACCAAAA-CTGAAT
1 TAATTACCAGAATAGCACCAAAATC-GAAT
*
394274 TATTTACCAGAATAGCACC
1 TAATTACCAGAATAGCACC
394293 GATCAACGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 1 0.01
29 67 0.99
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (29 bp):
TAATTACCAGAATAGCACCAAAATCGAAT
Found at i:394322 original size:17 final size:18
Alignment explanation
Indices: 394300--394334 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
394290 ACCGATCAAC
394300 GGTCAAC-GATCGGGTCG
1 GGTCAACGGATCGGGTCG
*
394317 GGTCAACGGGTCGGGTCG
1 GGTCAACGGATCGGGTCG
394335 TGACCGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGATCGGGTCG
Found at i:401653 original size:29 final size:29
Alignment explanation
Indices: 401589--401669 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
401579 GCATCCATTT
* *
401589 CGAATTAATTACCAGAATAGCA-CAAAAT
1 CGAATTATTTACCAGAATAGCACCAAAAC
401617 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
401646 CGAATTATTTACTAGAATAGCACC
1 CGAATTATTTACCAGAATAGCACC
401670 GGTCAACGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 21 0.43
29 28 0.57
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.23
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:402115 original size:16 final size:16
Alignment explanation
Indices: 402096--402126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
402086 ACTCTTTTCA
402096 TTTTTATTTCATTTTG
1 TTTTTATTTCATTTTG
*
402112 TTTTTATTTTATTTT
1 TTTTTATTTCATTTT
402127 ACTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTATTTCATTTTG
Found at i:403650 original size:63 final size:63
Alignment explanation
Indices: 403513--403693 Score: 290
Period size: 63 Copynumber: 2.9 Consensus size: 63
403503 CGTCCCTTGT
* *
403513 TGCATTGCATTTCAAAGGATCATCAATTTTACATCTGCATTTTGCATTTTCGCATTCTGCATAA
1 TGCATTGCATGTCAAAGGATCATCAATTTTACATCTGTA-TTTGCATTTTCGCATTCTGCATAA
*
403577 TGCATTGCATGTCAAAGGATCATCAATTTTGCATCTGTATTTGCATTTTCGCATTCTGCATAA
1 TGCATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCATTCTGCATAA
* * * *
403640 TGCATTGCATGTCAAAGGATCATCACTTTTATATATGTATTTGCATGTTCGCAT
1 TGCATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCAT
403694 GATCATCATA
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 73 0.67
64 36 0.33
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (63 bp):
TGCATTGCATGTCAAAGGATCATCAATTTTACATCTGTATTTGCATTTTCGCATTCTGCATAA
Found at i:408229 original size:33 final size:31
Alignment explanation
Indices: 408173--408292 Score: 141
Period size: 32 Copynumber: 3.7 Consensus size: 31
408163 AAACAATAGA
408173 GGGCATCTTTGAAGATTCAACATCAAATGTT
1 GGGCATCTTTGAAGATTCAACATCAAATGTT
*
408204 GGTGCATCTTTGAAAAATTCAACATCAAATGTT
1 GG-GCATCTTTG-AAGATTCAACATCAAATGTT
* * * *
408237 AGGGCATATTTGGAGATTCAACATCAAATATCG
1 -GGGCATCTTTGAAGATTCAACATCAAATGT-T
**
408270 GGGCATCTTTGGGGATTCAACAT
1 GGGCATCTTTGAAGATTCAACAT
408293 TCTGATGCGA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
31 2 0.03
32 46 0.60
33 27 0.35
34 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
GGGCATCTTTGAAGATTCAACATCAAATGTT
Found at i:409001 original size:84 final size:84
Alignment explanation
Indices: 408819--409040 Score: 223
Period size: 84 Copynumber: 2.6 Consensus size: 84
408809 AGGAACTATT
* * * * *
408819 TACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAAACCTTCAAGCTCGACTACACTCA
1 TACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAACC-AAACCTTCAAGTTCGACTACACTCA
*
408884 GCTCAAAAGCATACCAAATT
65 GCTCAAAAGCATACCAAATC
* * * * * *
408904 TACAGCATTACTCAAGGTAATAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGA-TTCTATTCA
1 TACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGACTAC-ACTCA
* **
408968 GCTC-AAGGACATGTCAAATC
65 GCTCAAAAG-CATACCAAATC
* * * *
408988 TACAACATAACTCAAGGCGAGAAGGGTTATCCGTCAACGAACACCTTCGAGTT
1 TACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAA-ACCTTCAAGTT
409041 TTGATTCCAT
Statistics
Matches: 113, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
83 5 0.04
84 65 0.58
85 43 0.38
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (84 bp):
TACAACATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAACCTTCAAGTTCGACTACACTCAG
CTCAAAAGCATACCAAATC
Found at i:409964 original size:375 final size:365
Alignment explanation
Indices: 409249--410088 Score: 1150
Period size: 375 Copynumber: 2.2 Consensus size: 365
409239 AGTTGAATTT
* *
409249 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACTCTCAGACAATCAGACTTCCTAA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
409314 TCACGAAGGAACCGTATTGTCCCCAAATTATCTCTTGATTGACCCAATTTCCTCATCACGAAGGA
66 TCACGAAGGAACCGTATTGTCCCC-----A-----TGATTGACCCAATTTCCTCATCACGAAGGA
* ** *
409379 ACAGATTCATAATCGAAAATGACCCGATCTCTTCATCGAGGATGAGCAGTGTCGTCTTCAACATC
121 ACAGACTCATAATAAAAAATAACCCGATCTCTTCATCGAGGATGAGCAGTGTCGTCTTCAACATC
* * * * *
409444 AAATCGACCAGATCTCCTCATCACGAAGGAGCATCGTCACCCTCAGACAATCAGACTTTCTCATC
186 AAACCGACCAGATCTCCTAATCACGAAGGAGCATCGTCACCCTCAAACAATCAAACTTCCTCATC
* *
409509 ACGAAGGAAACGTATTATCCCCAAATTGACCCGATTCCCTCATCAAGAAGAAACAACGTCATAAT
251 ACGAAAGAAACGTATTATCCCAAAATTGACCCGATTCCCTCATCAAGAAGAAACAACGTCATAAT
* *
409574 TGAAAATAACCCGATCTCTTTATCGCGGATGAGCAGTATCGTCTTCAACA
316 CGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
*
409624 TCAAACCGACCCGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
*
409689 TCACGAAGGAACCGTATTGTCCCCA-GATTGGCCCGAA-TTCCTCATCACGAAGGAACA-ACCTC
66 TCACGAAGGAACCGTATTGTCCCCATGATTGACCC-AATTTCCTCATCACGAAGGAACAGA-CTC
409751 ATAATAAAAAATAACCCGATCTCTTCATCGCA-GATGAGCAGTGTCGTCTTCAACATCAAACCGA
129 ATAATAAAAAATAACCCGATCTCTTCATCG-AGGATGAGCAGTGTCGTCTTCAACATCAAACCGA
*
409815 CCCGATCTCCTAATCACGAAGGAGCAAT-GTCACCCTCAAACAATCAAACTTCCTCATCACGAAA
193 CCAGATCTCCTAATCACGAAGGAGC-ATCGTCACCCTCAAACAATCAAACTTCCTCATCACGAAA
* * * * * *
409879 GAACCGTATTGTCCTCAAATTATCTCTTGACTGACCCGATTTCCTCATCACGAAGGAACATCGTC
257 GAAACGTATTATCC-CAAA--A-----T---TGACCCGATTCCCTCATCAAGAAGAAACAACGTC
* *
409944 ATAATCGAAAATGACCCGATCTCTTCATCGCGGATGAGCAGTGTCGTCTTCAACA
311 ATAATCGAAAATAACCCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
*
409999 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGGCAATCAGACTTCCTCA
1 TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
** *
410064 TCATAAAGGAACCGTATTGCCCCCA
66 TCACGAAGGAACCGTATTGTCCCCA
410089 AATTATCTCT
Statistics
Matches: 419, Mismatches: 31, Indels: 30
0.87 0.06 0.06
Matches are distributed among these distances:
363 1 0.00
364 155 0.37
365 8 0.02
367 1 0.00
370 1 0.00
372 1 0.00
375 252 0.60
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (365 bp):
TCAAACCGACCAGATCTCCTCATCACGAAGGAGCAGTGTCACCCTCAGACAATCAGACTTCCTCA
TCACGAAGGAACCGTATTGTCCCCATGATTGACCCAATTTCCTCATCACGAAGGAACAGACTCAT
AATAAAAAATAACCCGATCTCTTCATCGAGGATGAGCAGTGTCGTCTTCAACATCAAACCGACCA
GATCTCCTAATCACGAAGGAGCATCGTCACCCTCAAACAATCAAACTTCCTCATCACGAAAGAAA
CGTATTATCCCAAAATTGACCCGATTCCCTCATCAAGAAGAAACAACGTCATAATCGAAAATAAC
CCGATCTCTTCATCGCGGATGAGCAGTATCGTCTTCAACA
Done.