Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012314.1 Kokia drynarioides strain JFW-HI SEQ_127315, 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: 102620
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 181 characters in sequence are not A, C, G, or T
Found at i:6499 original size:208 final size:207
Alignment explanation
Indices: 5990--7090 Score: 1300
Period size: 208 Copynumber: 5.3 Consensus size: 207
5980 GACATCGAAT
* * * * * * **
5990 CCCATCTTCCCGATGAGATACAAAAAAGTAGGTCGAAATAATAAAGTGGTTATTTTCCTGAATAG
1 CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAACAATAAAGTGGTCATCTTCCTGACGAG
** * *
6055 ATGCAGAGAAGTGAACCAAATCTATCTTCTTGATAAGATACAGAGAAGTCGATTGAAACAATGAG
66 ATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGT-GATTAAAACAATGAG
* * * * * * *
6120 GCGGTTATCTTCCTGGTGAGATACTAAGAAGTATACCAAATCAATGAAACAAAGCTCAATGTGAG
130 ACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAG
6185 TGAAACTTCAAACC
195 TGAAACTTCAAA-C
* * * *
6199 CCCATCTTCATGATGAGATACAAAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTCCTGACGAG
1 CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAACAATAAAGTGGTCATCTTCCTGACGAG
* * * *
6264 ACGTAGAGAAGTGAACCAAAT-CGTCTTCTTGATGAGATACATAGAAGTGACTTAAAATAATGAG
66 ATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTGA-TTAAAACAATGAG
* * * **
6328 ACGGTCATCTTCTTGAAGAAATACTGAGAAGTAGACCAAATTGATGAAGCGAAGCTCAATGTGAG
130 ACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAG
6393 TGAAACTTCAAAC
195 TGAAACTTCAAAC
* * *
6406 CCAATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAACAATAATGTGGTCATCTTCCT-AGCGA
1 CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAACAATAAAGTGGTCATCTTCCTGA-CGA
* * * *
6470 GATGCAGAGAAGTGAACCAAATCCGTCTTCCTGATAAGACACAGAGAAGTGTATTTAAACAATGA
65 GATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTG-ATTAAAACAATGA
* * * *
6535 GGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGATCAAATCAATGAAGTGAAGCTCAATATGA
129 GACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGA
6600 GTGAAACTTCAAAC
194 GTGAAACTTCAAAC
* * * * *
6614 CCTCATCTTCCTGATGAGATACAGAAAAGTAGGTC-AAAGCAATAAAGCGATCACCTTCCTGATG
1 CC-CATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAA-CAATAAAGTGGTCATCTTCCTGACG
* *
6678 AGATACAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTGGATTAAACCAA-G
64 AGATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGT-GATTAAAACAATG
* * * * *
6742 A-AGTGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAACGAAGCGGAGCTCAATGT
128 AGA-CGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGT
**
6806 GAGTGAAACTTCCAATG
192 GAGTGAAACTT-CAAAC
* * * * * * *
6823 TCCATCTTCTTGATGAGATACAGAGAAGTAGGT-TAAAGCAATAAAGCGATCACCTTCCTGATGA
1 CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAA-CAATAAAGTGGTCATCTTCCTGACGA
* * * * *
6887 GATACAGAGAAGTGAACCAAATCCGTCTTCTTGATGAAATACAGAGAAGGGGATTAGATCAATGA
65 GATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAA-GTGATTAAAACAATGA
* * * *
6952 AACAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCCAAGC-CTAATGTG
129 GACGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTC-AATGTG
7016 AGTGAAACTTCAAACC
193 AGTGAAACTTCAAA-C
* ** * * * *
7032 CCCATTTTCCTGATGAGATACAGAGAAGCGGGTC-AAAAAATGAAGCGATCATCTTCCTG
1 CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAACAATAAAGTGGTCATCTTCCTG
7091 GTGAGATACA
Statistics
Matches: 775, Mismatches: 100, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
206 1 0.00
207 80 0.10
208 412 0.53
209 279 0.36
210 3 0.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (207 bp):
CCCATCTTCCTGATGAGATACAGAGAAGTAGGTCGAAACAATAAAGTGGTCATCTTCCTGACGAG
ATGCAGAGAAGTGAACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTGATTAAAACAATGAGA
CGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGT
GAAACTTCAAAC
Found at i:6577 original size:85 final size:85
Alignment explanation
Indices: 6410--6567 Score: 192
Period size: 85 Copynumber: 1.9 Consensus size: 85
6400 TCAAACCCAA
* * * * * *
6410 TCTTCCTGATGAGATACAGAGAAGTGGGTCGAAACAATAATGTGGTCATCTTCCTAGCGAGATGC
1 TCTTCCTGATAAGACACAGAGAAGTGGATCGAAACAATAAGGCGGTCATCTTCCTAGCGAGATAC
6475 AGAGAAGTGAACCAAATCCG
66 AGAGAAGTGAACCAAATCCG
* ** * *
6495 TCTTCCTGATAAGACACAGAGAAGTGTATTTAAACAATGAGGCGGTCATCTTCCT-GATGAGATA
1 TCTTCCTGATAAGACACAGAGAAGTGGATCGAAACAATAAGGCGGTCATCTTCCTAG-CGAGATA
*
6559 CTGAGAAGT
65 CAGAGAAGT
6568 AGATCAAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 1 0.02
85 59 0.98
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATAAGACACAGAGAAGTGGATCGAAACAATAAGGCGGTCATCTTCCTAGCGAGATAC
AGAGAAGTGAACCAAATCCG
Found at i:6782 original size:84 final size:85
Alignment explanation
Indices: 6619--6775 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 85
6609 CAAACCCTCA
*
6619 TCTTCCTGATGAGATACAGAAAAGTAGGTCAAAGCAATAAAGCGATCACCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAAAAGTAGGTCAAACCAATAAAGCGATCACCTTCCTGATGAGATAC
6684 AGAGAAGTGAACCAAATCCG
66 AGAGAAGTGAACCAAATCCG
* * * * * * *
6704 TCTTCTTGATGAGATACAGAGAAGT-GGATTAAACCAA-GAAGTGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAAAAGTAGG-TCAAACCAATAAAGCGATCACCTTCCTGATGAGATA
6767 CAGAGAAGT
65 CAGAGAAGT
6776 AGACCAATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 33 0.52
85 30 0.48
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAAAAGTAGGTCAAACCAATAAAGCGATCACCTTCCTGATGAGATAC
AGAGAAGTGAACCAAATCCG
Found at i:6970 original size:85 final size:85
Alignment explanation
Indices: 6827--6994 Score: 227
Period size: 85 Copynumber: 2.0 Consensus size: 85
6817 CCAATGTCCA
*
6827 TCTTCTTGATGAGATACAGAGAAGTAGGTTAAAGCAATAAAGCGATCACCTTCCTGATGAGATAC
1 TCTTCTTGATGAAATACAGAGAAGTAGGTTAAAGCAATAAAGCGATCACCTTCCTGATGAGATAC
6892 AGAGAAGT-GAACCAAATCCG
66 AGAGAAGTAG-ACCAAATCCG
* * * *
6912 TCTTCTTGATGAAATACAGAGAAG-GGGATTAGATCAATGAAA-C-AGTCATCTTCCTGATGAGA
1 TCTTCTTGATGAAATACAGAGAAGTAGG-TTAAAGCAAT-AAAGCGA-TCACCTTCCTGATGAGA
6974 TACAGAGAAGTAGACCAAATC
63 TACAGAGAAGTAGACCAAATC
6995 AATGAAGCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
84 3 0.04
85 67 0.91
86 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (85 bp):
TCTTCTTGATGAAATACAGAGAAGTAGGTTAAAGCAATAAAGCGATCACCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCCG
Found at i:9384 original size:41 final size:39
Alignment explanation
Indices: 9337--9438 Score: 109
Period size: 38 Copynumber: 2.6 Consensus size: 39
9327 TTTGATCTTG
* *
9337 AGTCGATGAGACACTGGGTGTCATCATTTTACTTCGGATA
1 AGTCGATGAGACACT-GGTGTCACCACTTTACTTCGGATA
* ** *
9377 GATTCGATGAGGTACTGG-GT-ACCACTTTACTTCGGCTA
1 -AGTCGATGAGACACTGGTGTCACCACTTTACTTCGGATA
9415 AGTCGATGAGACACTAGGTGTCAC
1 AGTCGATGAGACACT-GGTGTCAC
9439 TTTATTGCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
37 12 0.24
38 17 0.35
39 4 0.08
40 4 0.08
41 12 0.24
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (39 bp):
AGTCGATGAGACACTGGTGTCACCACTTTACTTCGGATA
Found at i:9440 original size:37 final size:38
Alignment explanation
Indices: 9336--9442 Score: 117
Period size: 37 Copynumber: 2.8 Consensus size: 38
9326 TTTTGATCTT
9336 GAGTCGATGAGACACTGGGTGTCATCATTTTACTTCGGATA
1 GAGTCGATGAGACACTGGGTGTCA-C--TTTACTTCGGATA
* ** ** *
9377 GATTCGATGAGGTACTGGGTACCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTGTCACTTTACTTCGGATA
*
9415 -AGTCGATGAGACACTAGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTGTCACTTTA
9443 TTGCTTCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 22 0.41
38 12 0.22
40 1 0.02
41 19 0.35
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTGTCACTTTACTTCGGATA
Found at i:11848 original size:25 final size:26
Alignment explanation
Indices: 11820--11889 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
11810 GTCATTCGAA
*
11820 CTTTATTTTTTTTTAATTCAATCCTCTT
1 CTTTATTTTTTTTTAAAT-AATCC-CTT
*
11848 -TTTA-TTTCTTTTAAATAATCCCTT
1 CTTTATTTTTTTTTAAATAATCCCTT
* *
11872 TTTTATGTTTTTTTAAAT
1 CTTTATTTTTTTTTAAAT
11890 TGGTCCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.08
25 9 0.25
26 20 0.56
27 4 0.11
ACGTcount: A:0.21, C:0.13, G:0.01, T:0.64
Consensus pattern (26 bp):
CTTTATTTTTTTTTAAATAATCCCTT
Found at i:12936 original size:3 final size:3
Alignment explanation
Indices: 12928--12958 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12918 TGTTGGATCC
12928 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12959 TATCCAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19401 original size:73 final size:73
Alignment explanation
Indices: 19315--19464 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
19305 GAAATTTCAT
19315 TTTGGGCAAATTTCATTTTCACATCCATTCACTTTGTTGCTATTGCAGCAATCGGATGTGAGTTG
1 TTTGGGCAAATTTCATTTTCACATCCATTCACTTTGTTGCTATTGCAGCAATCGGATGTGAGTTG
19380 AAACTAAA
66 AAACTAAA
19388 TTTGGGCAAATTTCATTTTCACATCCATTCACTTTGTTGCTATTGCAGCAATCGGATGTGAGTTG
1 TTTGGGCAAATTTCATTTTCACATCCATTCACTTTGTTGCTATTGCAGCAATCGGATGTGAGTTG
19453 AAACTAAA
66 AAACTAAA
19461 TTTG
1 TTTG
19465 ATCATGGGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (73 bp):
TTTGGGCAAATTTCATTTTCACATCCATTCACTTTGTTGCTATTGCAGCAATCGGATGTGAGTTG
AAACTAAA
Found at i:24261 original size:29 final size:29
Alignment explanation
Indices: 24226--24453 Score: 255
Period size: 30 Copynumber: 7.7 Consensus size: 29
24216 GAGACCCTGA
24226 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
24255 AACTTCCAAAAATTCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
*** *
24285 AACTTCCAAAAATTTTGTTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* ***
24314 AACTTCCAAAAATTCCATTTTCGACCCGAA
1 AACTTCCAAAAATTCCATTTT-TACCCTCG
*
24344 AACTTCCAAAAATTTCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
24373 AACTTCCAAAAATTCCATTTTCGA-CCTTG
1 AACTTCCAAAAATTCCATTTT-TACCCTCG
24402 AAACTTCCAAAAATTCCATTTTTGACCC-CTG
1 -AACTTCCAAAAATTCCATTTTT-ACCCTC-G
*
24433 AACTTCCAAAAAATCCATTTT
1 AACTTCCAAAAATTCCATTTT
24454 GACCTCCAAA
Statistics
Matches: 166, Mismatches: 24, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
29 73 0.44
30 90 0.54
31 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:24317 original size:59 final size:59
Alignment explanation
Indices: 24225--24470 Score: 343
Period size: 59 Copynumber: 4.2 Consensus size: 59
24215 AGAGACCCTG
* *
24225 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTCA
***
24284 AAACTTCCAAAAATTTTGTTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACC-CGA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTC-A
* * **
24343 AAACTTCCAAAAATTTCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTCGACCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTCA
* *
24402 AAACTTCCAAAAATTCCATTTTTGACCCCTGAACTTCCAAAAAATCCATTTT-GACCTCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATTCCATTTTCGACCT-CA
*
24462 AAATTTCCA
1 AAACTTCCA
24471 TTTTTGGCCT
Statistics
Matches: 166, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.01
59 132 0.80
60 33 0.20
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTCGACCTCA
Found at i:24488 original size:51 final size:52
Alignment explanation
Indices: 24407--24506 Score: 132
Period size: 51 Copynumber: 1.9 Consensus size: 52
24397 CCTTGAAACT
24407 TCCAAAAATTCCATTTTTGACCCCTGAACTTCCAAAAAAT-CCATTTTGACC
1 TCCAAAAATTCCATTTTTGACCCCTGAACTTCCAAAAAATACCATTTTGACC
* * * * *
24458 TCCAAAATTTCCATTTTTG-GCCTTGAAACTTTCAAAAATTACCATTTTG
1 TCCAAAAATTCCATTTTTGACCCCTG-AACTTCCAAAAAATACCATTTTG
24507 TCCCGGGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 4 0.10
51 30 0.71
52 8 0.19
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (52 bp):
TCCAAAAATTCCATTTTTGACCCCTGAACTTCCAAAAAATACCATTTTGACC
Found at i:26769 original size:41 final size:41
Alignment explanation
Indices: 26693--26770 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
26683 TTCAAGGTCT
*
26693 AATATGAGAACAATTGTCAAATTCAAAGACTAACTTGAACC
1 AATATGAGAACAATTGTCAAATTCAAAGAATAACTTGAACC
* *
26734 AATATGAGAATAATTG-CTAAGTTCAAA-AATAAACTTG
1 AATATGAGAACAATTGTC-AAATTCAAAGAAT-AACTTG
26771 GACAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 3 0.09
41 29 0.91
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (41 bp):
AATATGAGAACAATTGTCAAATTCAAAGAATAACTTGAACC
Found at i:28654 original size:15 final size:14
Alignment explanation
Indices: 28636--28666 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28626 TTGAAAACCC
*
28636 AAAACCCAAAAAAA
1 AAAAACCAAAAAAA
28650 AAAAACCAAAAAAA
1 AAAAACCAAAAAAA
28664 AAA
1 AAA
28667 TAAAGAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAACCAAAAAAA
Found at i:32912 original size:9 final size:9
Alignment explanation
Indices: 32888--32918 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
32878 TTCAATTATT
32888 TTTAATTTA
1 TTTAATTTA
32897 GTTTAATTTA
1 -TTTAATTTA
32907 TTTAATTTA
1 TTTAATTTA
32916 TTT
1 TTT
32919 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:32920 original size:10 final size:10
Alignment explanation
Indices: 32887--32921 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
32877 ATTCAATTAT
32887 TTTTAATTTA
1 TTTTAATTTA
*
32897 GTTTAATTTA
1 TTTTAATTTA
32907 -TTTAATTTA
1 TTTTAATTTA
32916 TTTTAA
1 TTTTAA
32922 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:34219 original size:27 final size:27
Alignment explanation
Indices: 34181--34240 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
34171 ATCGGAGTTA
*
34181 AAAATGTGATTTTTG-GATATCGGGGGC
1 AAAATGTGATTTTTGTCAT-TCGGGGGC
*
34208 AAAATGCT-ATTTTTGTCATTCGGGGGT
1 AAAATG-TGATTTTTGTCATTCGGGGGC
34235 AAAATG
1 AAAATG
34241 GCAATTTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.35
Consensus pattern (27 bp):
AAAATGTGATTTTTGTCATTCGGGGGC
Found at i:34357 original size:29 final size:29
Alignment explanation
Indices: 34230--34723 Score: 117
Period size: 29 Copynumber: 17.1 Consensus size: 29
34220 TTGTCATTCG
* **
34230 GGGGT-AAAATGGCAATTTTGGGAAAATTA
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTA
* * **
34259 GGGGTCAAAAACGGAATTTTT-AAACATTA
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
34288 GGGGT-AAAATGGTATTTTTTTTGGAAGGATT-
1 GGGGTAAAAATGG-A--ATTTTTGGAA-GTTTA
34319 GGGGTTAAAAATGGAATTTTTGGAAGTTTA
1 GGGG-TAAAAATGGAATTTTTGGAAGTTTA
* ***
34349 GGGGT-AAAATGGTAATCTTTGGAAAAAAAATA
1 GGGGTAAAAATGG-AATTTTTGG---AAGTTTA
* * **
34381 -AGGTCAAAAATGGAATTTTTAGAAGTTCG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* * *** *
34410 GGGGT-AAAATGGTAATCTTTGAAAAAGTC
1 GGGGTAAAAATGG-AATTTTTGGAAGTTTA
* * *
34439 GGTGTCAAAAATGGAATTTTTAGAAATTT-
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
**
34468 GAGGGT-AAAATGGTAA-TTTTGGAAAAATTA
1 G-GGGTAAAAATGG-AATTTTTGG-AAGTTTA
*
34498 -GGGTCAAAAATGGAA-TTTTGGAAAGTTCA
1 GGGGT-AAAAATGGAATTTTTGG-AAGTTTA
* * **
34527 -GGGTAAAAATGTAATTTTTGAATAAATTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
* *
34556 -GGGTCAAAATGGAA-TTTTGAAAGTTT-
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* * ** *** *
34582 GAGGGTAAAATTGTAATTTTTTTAAAAATC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
*
34612 GAGGTAAAAATGGAA-TTTTGGAAAGTTT-
1 GGGGTAAAAATGGAATTTTTGG-AAGTTTA
*
34640 --GG------TGTAATTTTTGGATAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
**
34662 -GGGTCAAAAGGGGAA-TTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTTGG-AAGTTTA
* *
34691 GGGGTAAAAATGTAATTTTTAGATAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
34721 GGG
1 GGG
34724 ACCTTTAGGG
Statistics
Matches: 342, Mismatches: 75, Indels: 95
0.67 0.15 0.19
Matches are distributed among these distances:
20 5 0.01
21 11 0.03
23 2 0.01
26 2 0.01
27 9 0.03
28 63 0.18
29 128 0.37
30 70 0.20
31 22 0.06
32 16 0.05
33 14 0.04
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:34480 original size:28 final size:29
Alignment explanation
Indices: 34386--34630 Score: 127
Period size: 29 Copynumber: 8.5 Consensus size: 29
34376 AAATAAGGTC
* * *
34386 AAAAATGGAATTTTTAGAAGTTCGGGGGT
1 AAAAATGGAATTTTTAGAAATTTGAGGGT
* * * * *
34415 -AAAATGGTAATCTTTGAAAAAGTCG-GTGT
1 AAAAATGG-AAT-TTTTAGAAATTTGAGGGT
34444 CAAAAATGGAATTTTTAGAAATTTGAGGGT
1 -AAAAATGGAATTTTTAGAAATTTGAGGGT
* *
34474 -AAAATGGTAA-TTTTGGAAAAATT-AGGGT
1 AAAAATGG-AATTTTTAG-AAATTTGAGGGT
* * *
34502 CAAAAATGGAA-TTTTGGAAAGTTCAGGGT
1 -AAAAATGGAATTTTTAGAAATTTGAGGGT
* *
34531 AAAAATGTAATTTTT-GAATAAATT-AGGGT
1 AAAAATGGAATTTTTAG-A-AATTTGAGGGT
*
34560 CAAAATGGAA-TTTT-GAAAGTTTGAGGGT
1 AAAAATGGAATTTTTAGAAA-TTTGAGGGT
* * * *
34588 AAAATTGTAATTTTTTTA-AAAATCGA-GGT
1 AAAAATGGAA--TTTTTAGAAATTTGAGGGT
34617 AAAAATGGAATTTT
1 AAAAATGGAATTTT
34631 GGAAAGTTTG
Statistics
Matches: 172, Mismatches: 25, Indels: 40
0.73 0.11 0.17
Matches are distributed among these distances:
26 2 0.01
27 7 0.04
28 56 0.33
29 64 0.37
30 29 0.17
31 14 0.08
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAATTTGAGGGT
Found at i:34536 original size:58 final size:56
Alignment explanation
Indices: 34231--34638 Score: 324
Period size: 61 Copynumber: 7.0 Consensus size: 56
34221 TGTCATTCGG
* * * * *
34231 GGGTAAAATGGCAATTTTGGGAAAATTAGGGGTCAAAAACGGAATTTTTAAACATT-A
1 GGGTAAAATGGTAATTTTGGAAAAATTA-GGGTCAAAAATGGAATTTTGAAA-GTTCA
* ** * * * *
34288 GGGGTAAAATGGTATTTTTTTTGGAAGGATTGGGGTTAAAAATGGAATTTTTGGAAGTTTA
1 -GGGTAAAATGGTA---ATTTTGGAAAAATTAGGGTCAAAAATGGAA-TTTTGAAAGTTCA
* * * *
34349 GGGGTAAAATGGTAATCTTTGGAAAAAAAATAAGGTCAAAAATGGAATTTTTAGAAGTTCGG
1 -GGGTAAAATGGTAAT-TTTGG--AAAAATTAGGGTCAAAAATGGAATTTTGA-AAGTTC-A
* * * *
34411 GGGTAAAATGGTAATCTTT-GAAAAAGTCGGTGTCAAAAATGGAATTTTTAGAAATTTGA
1 GGGTAAAATGGTAAT-TTTGGAAAAATTAGG-GTCAAAAATGGAA-TTTT-GAAAGTTCA
34470 GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCA
1 GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTT-GAAAGTTCA
* *
34527 GGGTAAAAAT-GTAATTTTTGAATAAATTAGGGTC-AAAATGGAATTTTGAAAGTTTGA
1 GGGT-AAAATGGTAATTTTGGAA-AAATTAGGGTCAAAAATGGAATTTTGAAAG-TTCA
* ** *
34584 GGGTAAAATTGTAATTTTTTTAAAAA-TCGAGGT-AAAAATGGAATTTTGGAAAGTT
1 GGGTAAAATGGTAA-TTTTGGAAAAATTAG-GGTCAAAAATGGAATTTT-GAAAGTT
34639 TGGTGTAATT
Statistics
Matches: 290, Mismatches: 38, Indels: 45
0.78 0.10 0.12
Matches are distributed among these distances:
56 12 0.04
57 71 0.24
58 64 0.22
59 42 0.14
60 28 0.10
61 73 0.25
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (56 bp):
GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGAAAGTTCA
Found at i:34565 original size:57 final size:56
Alignment explanation
Indices: 34231--34710 Score: 288
Period size: 57 Copynumber: 8.3 Consensus size: 56
34221 TGTCATTCGG
* * * * * *
34231 GGGTAAAATGGCAATTTTGGGAAAATTAGGGGTCAAAAACGGAATTTT-TAAACATT-A
1 GGGTAAAAT-GTAATTTTTGAAAAATTA-GGGTCAAAAATGGAATTTTGGAAA-GTTCA
* ** * * *
34288 GGGGTAAAATGGTATTTTTTTTGGAAGGATTGGGGTTAAAAATGGAATTTTTGG-AAGTTTA
1 -GGGTAAAAT-GTA--ATTTTT-GAAAAATTAGGGTCAAAAATGGAA-TTTTGGAAAGTTCA
* * * * *
34349 GGGGTAAAATGGTAATCTTTGGAAAAAAAATAAGGTCAAAAATGGAATTTT-TAGAAGTTCGG
1 -GGGTAAAAT-GTAAT-TTTTG--AAAAATTAGGGTCAAAAATGGAATTTTGGA-AAGTTC-A
* * * * * *
34411 GGGTAAAATGGTAATCTTTGAAAAAGTCGGTGTCAAAAATGGAATTTTTAGAAATTTGA
1 GGGTAAAAT-GTAATTTTTGAAAAATTAGG-GTCAAAAATGGAA-TTTTGGAAAGTTCA
*
34470 GGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCA
1 GGGTAAAAT-GTAATTTTTGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCA
*
34527 GGGTAAAAATGTAATTTTTGAATAAATTAGGGTC-AAAATGGAATTTT-GAAAGTTTGA
1 GGGT-AAAATGTAATTTTTGAA-AAATTAGGGTCAAAAATGGAATTTTGGAAAG-TTCA
* *
34584 GGGTAAAATTGTAATTTTTTTAAAAA-TCGAGGT-AAAAATGGAATTTTGGAAAGTT--
1 GGGTAAAA-TGTAA-TTTTTGAAAAATTAG-GGTCAAAAATGGAATTTTGGAAAGTTCA
* * ** ** *
34639 TGG-----TGTAATTTTTGGATAGTTTAGGGTCAAAAGGGGAATTTTGGAAAGTTTA
1 GGGTAAAATGTAATTTTT-GAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCA
34691 GGGGTAAAAATGTAATTTTT
1 -GGGT-AAAATGTAATTTTT
34711 AGATAGTTTA
Statistics
Matches: 336, Mismatches: 51, Indels: 69
0.74 0.11 0.15
Matches are distributed among these distances:
48 5 0.01
49 10 0.03
50 22 0.07
53 2 0.01
55 2 0.01
56 11 0.03
57 72 0.21
58 60 0.18
59 51 0.15
60 37 0.11
61 64 0.19
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (56 bp):
GGGTAAAATGTAATTTTTGAAAAATTAGGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:34721 original size:30 final size:31
Alignment explanation
Indices: 34642--34723 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 31
34632 GAAAGTTTGG
*
34642 TGTAATTTTTGGATAGTTTA-GGGTCAAAAG
1 TGTAATTTTTGGATAGTTTAGGGGTCAAAAA
* * *
34672 GGGAA-TTTTGGAAAGTTTAGGGGT-AAAAA
1 TGTAATTTTTGGATAGTTTAGGGGTCAAAAA
*
34701 TGTAATTTTTAGATAGTTTAGGG
1 TGTAATTTTTGGATAGTTTAGGG
34724 ACCTTTAGGG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.38
Consensus pattern (31 bp):
TGTAATTTTTGGATAGTTTAGGGGTCAAAAA
Found at i:35162 original size:17 final size:16
Alignment explanation
Indices: 35140--35242 Score: 107
Period size: 17 Copynumber: 6.1 Consensus size: 16
35130 CAGGCCCTTT
35140 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAA-A
*
35157 TTAAATGTATTTTAAA
1 TTAAATTTATTTTAAA
*
35173 TTTAGATTTATTTTAAA
1 -TTAAATTTATTTTAAA
* *
35190 TTCAAATTTAATTTAAGT
1 TT-AAATTTATTTTAA-A
35208 TTAAATTTATTTTAAA
1 TTAAATTTATTTTAAA
* *
35224 TTTAAAATTATTATAAA
1 -TTAAATTTATTTTAAA
35241 TT
1 TT
35243 TAAAATAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
16 5 0.07
17 65 0.90
18 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:35176 original size:6 final size:6
Alignment explanation
Indices: 35167--35246 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
35157 TTAAATGTAT
* * * *
35167 TTTAAA TTTAGA TTT-AT TTTAAA TTCAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
35213 TTT-AT TTTAAA TTTAAA ATT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
35247 ATAAATAATG
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 2 0.04
5 13 0.23
6 38 0.68
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:35187 original size:34 final size:33
Alignment explanation
Indices: 35139--35246 Score: 128
Period size: 34 Copynumber: 3.2 Consensus size: 33
35129 CCAGGCCCTT
35139 TTTAAATTTATTTTAAGATT-AAATGTATTTTAAA
1 TTTAAATTTATTTTAA-ATTAAAAT-TATTTTAAA
* * * *
35173 TTTAGATTTATTTTAAATTCAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATT-AAAATTATTTTAAA
*
35207 TTTAAATTTATTTTAAATTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA-TTAAAATTATTTTAAA
35241 TTTAAA
1 TTTAAA
35247 ATAAATAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
33 3 0.05
34 54 0.87
35 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (33 bp):
TTTAAATTTATTTTAAATTAAAATTATTTTAAA
Found at i:35196 original size:23 final size:23
Alignment explanation
Indices: 35170--35214 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35160 AATGTATTTT
*
35170 AAATTTAGATTT-ATTTTAAATTC
1 AAATTTA-ATTTAAGTTTAAATTC
35193 AAATTTAATTTAAGTTTAAATT
1 AAATTTAATTTAAGTTTAAATT
35215 TATTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
AAATTTAATTTAAGTTTAAATTC
Found at i:35198 original size:51 final size:51
Alignment explanation
Indices: 35142--35242 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
35132 GGCCCTTTTT
* * * *
35142 AAATTTATTTTAAGATTAAATGTATTTTAAATTTAGATTTATTTTAAATTC
1 AAATTTAATTTAAGATTAAATGTATTTTAAATTTAAAATTATTATAAATTC
* *
35193 AAATTTAATTTAAGTTTAAATTTATTTTAAATTTAAAATTATTATAAATT
1 AAATTTAATTTAAGATTAAATGTATTTTAAATTTAAAATTATTATAAATT
35243 TAAAATAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (51 bp):
AAATTTAATTTAAGATTAAATGTATTTTAAATTTAAAATTATTATAAATTC
Found at i:35985 original size:21 final size:21
Alignment explanation
Indices: 35949--36002 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
35939 CAATAAATGG
35949 CATTAATAAGTATTAATAAAAA
1 CATTAATAA-TATTAATAAAAA
* *
35971 TATTATTAATATTAATAAAAA
1 CATTAATAATATTAATAAAAA
35992 CATTAATAATA
1 CATTAATAATA
36003 ATAAAAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
CATTAATAATATTAATAAAAA
Found at i:37074 original size:29 final size:29
Alignment explanation
Indices: 37042--37221 Score: 179
Period size: 29 Copynumber: 6.1 Consensus size: 29
37032 TAAACTATTC
*
37042 AAAAATTACATTTTTACCCTCGAACTTCA
1 AAAAATTACATTTTTACCCTCAAACTTCA
* * *
37071 AAAAATTCCATTATTGA-CCTCGAAACTTCT
1 AAAAATTACATT-TTTACCCTC-AAACTTCA
* *
37101 GAAAATTACATTTTTACCCTCAAACTTCC
1 AAAAATTACATTTTTACCCTCAAACTTCA
* *
37130 AAAAATTCCATTTTTGA-CCTCAAAACTTCC
1 AAAAATTACATTTTT-ACCCTC-AAACTTCA
*
37160 AAAAATTACA-TTTTACCCCCAAACTTCA
1 AAAAATTACATTTTTACCCTCAAACTTCA
*
37188 AAAAATT-CTATTTTTAACCCTAAAACTTTCA
1 AAAAATTAC-ATTTTT-ACCCTCAAAC-TTCA
37219 AAA
1 AAA
37222 TTACCCTTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 16 0.13
29 53 0.42
30 49 0.39
31 7 0.06
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATTACATTTTTACCCTCAAACTTCA
Found at i:37106 original size:30 final size:29
Alignment explanation
Indices: 37042--37201 Score: 146
Period size: 30 Copynumber: 5.5 Consensus size: 29
37032 TAAACTATTC
* *
37042 AAAAATTACATTTTTACCCTCG-AACTTCA
1 AAAAATTCCATTTTGA-CCTCGAAACTTCA
*
37071 AAAAATTCCATTATTGACCTCGAAACTTCT
1 AAAAATTCCATT-TTGACCTCGAAACTTCA
* * * *
37101 GAAAATTACATTTTTACCCTC-AAACTTCC
1 AAAAATTCCATTTTGA-CCTCGAAACTTCA
* *
37130 AAAAATTCCATTTTTGACCTCAAAACTTCC
1 AAAAATTCCA-TTTTGACCTCGAAACTTCA
* * *
37160 AAAAATTACATTTT-ACCCCCAAACTTCA
1 AAAAATTCCATTTTGACCTCGAAACTTCA
*
37188 AAAAATTCTATTTT
1 AAAAATTCCATTTT
37202 TAACCCTAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 23 0.21
29 42 0.38
30 45 0.41
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTGACCTCGAAACTTCA
Found at i:37134 original size:59 final size:59
Alignment explanation
Indices: 37041--37235 Score: 243
Period size: 59 Copynumber: 3.3 Consensus size: 59
37031 CTAAACTATT
* *
37041 CAAAAATTACATTTTTACCCTCGAACTTCAAAAAATTCCATTATTGACCTCGAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTATTGACCTCAAAACTTC
** * *
37100 TGAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTC
1 CAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTATTGACCTCAAAACTTC
* * * * *
37159 CAAAAATTACA-TTTTACCCCCAAACTTCAAAAAATTCTATTTTTAACC-CTAAAACTTT
1 CAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTATTGACCTC-AAAACTTC
**
37217 C-AAAATTACCCTTTTACCC
1 CAAAAATTACATTTTTACCC
37236 CATATGTCCC
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
57 9 0.08
58 49 0.41
59 62 0.52
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTCAAACTTCAAAAAATTCCATTATTGACCTCAAAACTTC
Found at i:38670 original size:17 final size:18
Alignment explanation
Indices: 38633--38670 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
38623 TTTCAGGTTT
38633 AAACTAAATTTAAATTTA
1 AAACTAAATTTAAATTTA
38651 AAAC-AAATTTAAATTTA
1 AAACTAAATTTAAATTTA
38668 AAA
1 AAA
38671 ATGAAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AAACTAAATTTAAATTTA
Found at i:40873 original size:3 final size:3
Alignment explanation
Indices: 40865--40893 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
40855 CAAGCCGAGA
40865 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
40894 TTAAGGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:41604 original size:23 final size:22
Alignment explanation
Indices: 41560--41604 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
41550 AATATATATA
**
41560 TATAACATTATATATTTGAATT
1 TATAACATTATATATTCAAATT
*
41582 TATAATATATATATATTCAAATT
1 TATAACAT-TATATATTCAAATT
41605 AAATTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TATAACATTATATATTCAAATT
Found at i:49976 original size:18 final size:18
Alignment explanation
Indices: 49919--49976 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
49909 TAATAAATTA
*
49919 TAAAAATATTTAAAACCA-
1 TAAAAATATTTAAAA-AAT
* *
49937 TAAAAACGTATTGAAAAGAT
1 TAAAAA--TATTTAAAAAAT
49957 TAAAAATATTTAAAAAAT
1 TAAAAATATTTAAAAAAT
49975 TA
1 TA
49977 TTAAATAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 18 0.55
19 1 0.03
20 14 0.42
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
TAAAAATATTTAAAAAAT
Found at i:54210 original size:26 final size:28
Alignment explanation
Indices: 54179--54230 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
54169 TTTTTCTAAA
*
54179 TATTTTTATTATTTTT-AATT-TTTGAC
1 TATTTTTATAATTTTTGAATTATTTGAC
54205 TATTTTTATAATTTTTGAATTATTTG
1 TATTTTTATAATTTTTGAATTATTTG
54231 TTAACGTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 4 0.17
28 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (28 bp):
TATTTTTATAATTTTTGAATTATTTGAC
Found at i:54653 original size:31 final size:31
Alignment explanation
Indices: 54585--54654 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
54575 AATAGGTCCT
* * ***
54585 AGAAAATTTTTAAAATTTTCATTTAGGTCCT
1 AGAAAATTTTTAAAATTTTAAATTAGGTAAA
54616 AGAAAATTTTTAAAATTTTAAATTA-GTAAA
1 AGAAAATTTTTAAAATTTTAAATTAGGTAAA
54646 AGTAAAATT
1 AG-AAAATT
54655 ACATTTTGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (31 bp):
AGAAAATTTTTAAAATTTTAAATTAGGTAAA
Found at i:56058 original size:30 final size:30
Alignment explanation
Indices: 56022--56116 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 30
56012 AAGTTAAAAC
*
56022 TTTTAAAATGGTTAAATAACGTTAAATTTT
1 TTTTAAAATGATTAAATAACGTTAAATTTT
* * *
56052 TTTTAAATATGCTCAAATAACGCCTAAA-TTT
1 TTTTAAA-ATGATTAAATAACG-TTAAATTTT
** * *
56083 TTCGAAAATAATTAAATAAAGGTTAAATTTT
1 TTTTAAAATGATTAAAT-AACGTTAAATTTT
56114 TTT
1 TTT
56117 CGAGTACGCT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
30 18 0.36
31 28 0.56
32 4 0.08
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (30 bp):
TTTTAAAATGATTAAATAACGTTAAATTTT
Found at i:66728 original size:30 final size:29
Alignment explanation
Indices: 66690--66837 Score: 172
Period size: 30 Copynumber: 5.0 Consensus size: 29
66680 TAGTAAAACG
*
66690 GGGTTAAATTTTAATTTTTGAAAACTTTA
1 GGGTTAAATTTGAATTTTTGAAAACTTTA
*
66719 GGCGTTAAATTTGAATTTTTGGAAA-TTTAAA
1 GG-GTTAAATTTGAATTTTTGAAAACTTT--A
*
66750 GGGTCAAATTTGAATTTTTGAAAACTTTA
1 GGGTTAAATTTGAATTTTTGAAAACTTTA
* *
66779 GGGATTAAATTTGAATTTTTGAAAAATTTGG
1 GGG-TTAAATTTGAATTTTTGAAAACTTT-A
* **
66810 GGGTCAAATTTGAATTTTAAAAAACTTT
1 GGGTTAAATTTGAATTTTTGAAAACTTT
66838 GGGGGTCAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.09
30 84 0.82
31 9 0.09
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (29 bp):
GGGTTAAATTTGAATTTTTGAAAACTTTA
Found at i:66788 original size:60 final size:60
Alignment explanation
Indices: 66690--66837 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
66680 TAGTAAAACG
* * *
66690 GGGTTAAATTTTAATTTTTGAAAACTTTAGGCGTTAAATTTGAATTTTTG-GAAATTTAAA
1 GGGTCAAATTTGAATTTTTGAAAACTTTAGGCGTTAAATTTGAATTTTTGAAAAATTT-AA
**
66750 GGGTCAAATTTGAATTTTTGAAAACTTTAGG-GATTAAATTTGAATTTTTGAAAAATTTGG
1 GGGTCAAATTTGAATTTTTGAAAACTTTAGGCG-TTAAATTTGAATTTTTGAAAAATTTAA
**
66810 GGGTCAAATTTGAATTTTAAAAAACTTT
1 GGGTCAAATTTGAATTTTTGAAAACTTT
66838 GGGGGTCAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 72 0.91
61 6 0.08
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43
Consensus pattern (60 bp):
GGGTCAAATTTGAATTTTTGAAAACTTTAGGCGTTAAATTTGAATTTTTGAAAAATTTAA
Found at i:66839 original size:30 final size:30
Alignment explanation
Indices: 66750--66847 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
66740 GAAATTTAAA
** *
66750 GGGTCAAATTTGAATTTTTGAAAACTTTAG
1 GGGTCAAATTTGAATTTTAAAAAACTTTGG
* * *
66780 GGATTAAATTTGAATTTTTGAAAAA-TTTGG
1 GGGTCAAATTTGAA-TTTTAAAAAACTTTGG
66810 GGGTCAAATTTGAATTTTAAAAAACTTTGG
1 GGGTCAAATTTGAATTTTAAAAAACTTTGG
66840 GGGTCAAA
1 GGGTCAAA
66848 AAAATGATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.16
30 41 0.71
31 8 0.14
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTAAAAAACTTTGG
Found at i:68465 original size:50 final size:50
Alignment explanation
Indices: 68407--68584 Score: 275
Period size: 50 Copynumber: 3.6 Consensus size: 50
68397 TACAAGTTTT
* * * *
68407 AATTTGCCCCTCTATTACTTTAGGGGTATAAGATTTACTTTTATAGCTTC
1 AATTTGCCCCTCTGTAACTTTAGGGGTATAAGATTTGCTTTTGTAGCTTC
*
68457 AATTTGCCCCTCTGTAACTTTAGGGGTATAAGATTTGCTTTTGTAGCTTT
1 AATTTGCCCCTCTGTAACTTTAGGGGTATAAGATTTGCTTTTGTAGCTTC
* * * *
68507 AATTTTCCCTTCTGTATCTTTAGGGGTATAATATTTGCTTTTGTAGCTTC
1 AATTTGCCCCTCTGTAACTTTAGGGGTATAAGATTTGCTTTTGTAGCTTC
68557 AATTTGCCCCTCTGTAACTTTAGGGGTA
1 AATTTGCCCCTCTGTAACTTTAGGGGTA
68585 AAAAATTAGA
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 115 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (50 bp):
AATTTGCCCCTCTGTAACTTTAGGGGTATAAGATTTGCTTTTGTAGCTTC
Found at i:68655 original size:40 final size:39
Alignment explanation
Indices: 68593--68753 Score: 166
Period size: 40 Copynumber: 4.1 Consensus size: 39
68583 TAAAAAATTA
* * * *
68593 GATTGT-TTCAACCCGCCTCATGGTCGGGTTAAGAGATTG
1 GATTGTCTTCAATCTGCCCCATGGTAGGG-TAAGAGATTG
*
68632 GATTGTCTTCAATCTGCCCCATGGTTGGGGTAAGAGATTG
1 GATTGTCTTCAATCTGCCCCATGG-TAGGGTAAGAGATTG
* *
68672 GATTGTCTTCAATCTGCCCTC-TGATTAGGGTAAAAGATTG
1 GATTGTCTTCAATCTGCCC-CATG-GTAGGGTAAGAGATTG
**
68712 GA-TGATCTTCAATCTGCCCTTTGGTTAGGGTAAGAGATTG
1 GATTG-TCTTCAATCTGCCCCATGG-TAGGGTAAGAGATTG
68752 GA
1 GA
68754 GGTTGTAATT
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
39 8 0.08
40 92 0.88
41 5 0.05
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (39 bp):
GATTGTCTTCAATCTGCCCCATGGTAGGGTAAGAGATTG
Found at i:68868 original size:50 final size:51
Alignment explanation
Indices: 68806--68934 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
68796 CGTCCTTGCA
*
68806 CTTCAATATGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCC-ATTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCTATTGCGG
* * *
68856 CTTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTTGCGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCTATTGCGG
* ** *
68907 TTTCAATCTGTACCTCTATAGCTTTAGG
1 CTTCAATCTGCCCCTCTACAGCTTTAGG
68935 GTAAAAGATT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
50 40 0.58
51 29 0.42
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (51 bp):
CTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCTATTGCGG
Found at i:68944 original size:50 final size:49
Alignment explanation
Indices: 68806--68951 Score: 150
Period size: 50 Copynumber: 2.9 Consensus size: 49
68796 CGTCCTTGCA
* *
68806 CTTCAATATGCCCCTCTACAGCTTTA-GGTGAATGAGATTTGCCATTGCGG
1 CTTCAATCTGCACCTCTACAGCTTTAGGGT-AA-GAGATTTGCCATTGCGG
* * * *
68856 CTTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCTTTTGCGG
1 CTTCAATCTGCACCTCTACAGCTTTAGG-GTAAGAGATTTGCC-ATTGCGG
* * * * *
68907 TTTCAATCTGTACCTCTATAGCTTTAGGGTAAAAGATTTGTCATT
1 CTTCAATCTGCACCTCTACAGCTTTAGGGTAAGAGATTTGCCATT
68952 CTATTGCCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.03
50 45 0.56
51 31 0.39
52 2 0.03
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.38
Consensus pattern (49 bp):
CTTCAATCTGCACCTCTACAGCTTTAGGGTAAGAGATTTGCCATTGCGG
Found at i:80502 original size:31 final size:29
Alignment explanation
Indices: 80431--80616 Score: 174
Period size: 30 Copynumber: 6.2 Consensus size: 29
80421 ACATTAAAAC
*
80431 GGGGTTAAATTTTAATTTTTGAAAACTTTA
1 GGGGTTAAATTTGAATTTTTGAAAA-TTTA
**
80461 ACGGTTAAATTTGAATTTTTGGAAAATTTAA
1 GGGGTTAAATTTGAATTTTT-GAAAATTT-A
* *
80492 GGGGTCAAATTTGAATTTTTGAAAACTTTT
1 GGGGTTAAATTTGAATTTTTGAAAA-TTTA
* * *
80522 GGGATTAAATTTGAATTTTTGGAAATCTTG
1 GGGGTTAAATTTGAATTTTTGAAAAT-TTA
* *
80552 GGGGTGAAATATGAATTTTTAGAAAATTTA
1 GGGGTTAAATTTGAATTTTT-GAAAATTTA
** * * *
80582 GGGGTCCAATTTAAATTTTTAAAAACTTTG
1 GGGGTTAAATTTGAATTTTTGAAAA-TTTA
80612 GGGGT
1 GGGGT
80617 CAAAAAAATG
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
29 5 0.04
30 92 0.72
31 31 0.24
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.41
Consensus pattern (29 bp):
GGGGTTAAATTTGAATTTTTGAAAATTTA
Found at i:80530 original size:61 final size:60
Alignment explanation
Indices: 80431--80581 Score: 182
Period size: 61 Copynumber: 2.5 Consensus size: 60
80421 ACATTAAAAC
* *
80431 GGGGTTAAATTTTAATTTTTGAAAACTTTAACGGTTAAATTTGAATTTTTGGAAAAT-TTAA
1 GGGGTCAAATTTGAATTTTTGAAAACTTTAACGGTTAAATTTGAATTTTTGG-AAATCTT-A
** *
80492 GGGGTCAAATTTGAATTTTTGAAAACTTT-TGGGATTAAATTTGAATTTTTGGAAATCTTG
1 GGGGTCAAATTTGAATTTTTGAAAACTTTAACGG-TTAAATTTGAATTTTTGGAAATCTTA
* *
80552 GGGGTGAAATATGAATTTTTAGAAAA-TTTA
1 GGGGTCAAATTTGAATTTTT-GAAAACTTTA
80582 GGGGTCCAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
60 27 0.34
61 52 0.66
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (60 bp):
GGGGTCAAATTTGAATTTTTGAAAACTTTAACGGTTAAATTTGAATTTTTGGAAATCTTA
Found at i:95479 original size:7 final size:7
Alignment explanation
Indices: 95469--95495 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
95459 GGCTTTGGGC
95469 TGGGGAG
1 TGGGGAG
95476 TGGGGAG
1 TGGGGAG
95483 TGGGGAG
1 TGGGGAG
95490 TGGGGA
1 TGGGGA
95496 AATATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.70, T:0.15
Consensus pattern (7 bp):
TGGGGAG
Found at i:98717 original size:89 final size:89
Alignment explanation
Indices: 98517--98695 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
98507 TGAAAAAATA
98517 TTCTAAAACCAAATAAAAAATTATGATAAAAGGAACAAAAATTTTGCTCAAAAAGAAACACACAT
1 TTCTAAAACCAAATAAAAAATTATGATAAAAGGAACAAAAATTTTGCTCAAAAAGAAACACACAT
*
98582 ACGAATCGGGGGACAACACACGTG
66 ACGAATCGGGGGACAACACAAGTG
98606 TTCTAAAACCAAATAAAAAATTATGATAAAAGGAACAAAAATTTTGCTCAAAAAGAAACACACAT
1 TTCTAAAACCAAATAAAAAATTATGATAAAAGGAACAAAAATTTTGCTCAAAAAGAAACACACAT
98671 ACGAATCGGGGGACAACACAAGTG
66 ACGAATCGGGGGACAACACAAGTG
98695 T
1 T
98696 GTTGGAATTT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (89 bp):
TTCTAAAACCAAATAAAAAATTATGATAAAAGGAACAAAAATTTTGCTCAAAAAGAAACACACAT
ACGAATCGGGGGACAACACAAGTG
Found at i:99902 original size:13 final size:13
Alignment explanation
Indices: 99881--99914 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
99871 ACAATATAAT
99881 AATAATAATCCTA
1 AATAATAATCCTA
*
99894 AATATTAATCCTA
1 AATAATAATCCTA
*
99907 AAAAATAA
1 AATAATAA
99915 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:100922 original size:16 final size:16
Alignment explanation
Indices: 100888--100927 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
100878 TTTTTTTCAA
100888 TTTTTTTCTTTTTGACT
1 TTTTTTTCTTTTT-ACT
100905 TTTTTTTCTTCTTT-CT
1 TTTTTTTCTT-TTTACT
100921 TTTTTTT
1 TTTTTTT
100928 TTAAACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 10 0.45
18 3 0.14
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTTTTTACT
Found at i:100928 original size:17 final size:17
Alignment explanation
Indices: 100844--100928 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 17
100834 CACTTTTGTC
100844 TTCTTTTTTTTGTCTT-T
1 TTCTTTTTTTT-TCTTCT
100861 TTCTTTTTTTTTC-TCAAT
1 TTCTTTTTTTTTCTTC--T
100879 TT-TTTTCAATTTTT-TTCT
1 TTCTTTT---TTTTTCTTCT
*
100897 TTTTGACTTTTTTTTCTTCT
1 TTCT---TTTTTTTTCTTCT
100917 TTCTTTTTTTTT
1 TTCTTTTTTTTT
100929 TAAACAATAA
Statistics
Matches: 55, Mismatches: 1, Indels: 24
0.69 0.01 0.30
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 23 0.42
18 6 0.11
19 6 0.11
20 14 0.25
22 3 0.05
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (17 bp):
TTCTTTTTTTTTCTTCT
Found at i:101864 original size:45 final size:44
Alignment explanation
Indices: 101815--101952 Score: 104
Period size: 45 Copynumber: 3.1 Consensus size: 44
101805 AGATAATAAT
101815 TAAAAAAAAAACAACCATGAGAATAAAAATAGTGTATGATTAAAA
1 TAAAAAAAAAACAACCATGAGAATAAAAATAGTG-ATGATTAAAA
* * * * * * * * *
101860 TAAAATTAAAAATAA-AAAGACAAGT-CAGAGAG-GAAGA-TAATAA
1 TAAAA-AAAAAACAACCATGAGAA-TAAAAATAGTGATGATTAA-AA
* *
101903 TTAAAAAACAACAACCATGAGAATAAAAATAGTGCATGATTAAAA
1 TAAAAAAAAAACAACCATGAGAATAAAAATAGTG-ATGATTAAAA
101948 TAAAA
1 TAAAA
101953 TTAAAAATAA
Statistics
Matches: 64, Mismatches: 21, Indels: 16
0.63 0.21 0.16
Matches are distributed among these distances:
42 10 0.16
43 18 0.28
44 2 0.03
45 23 0.36
46 11 0.17
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (44 bp):
TAAAAAAAAAACAACCATGAGAATAAAAATAGTGATGATTAAAA
Found at i:101942 original size:88 final size:89
Alignment explanation
Indices: 101777--101965 Score: 326
Period size: 88 Copynumber: 2.1 Consensus size: 89
101767 AACTAAAAAG
*
101777 AAAATAGACAAAGACAAGTCAGAGAGGGAGATAATAATTAAAAAAAAAACAACCATGAGAATAAA
1 AAAATA-A-AAAGACAAGTCAGAGAGGAAGATAATAATTAAAAAAAAAACAACCATGAGAATAAA
*
101842 AATAGTGTATGATTAAAATAAAATTA
64 AATAGTGCATGATTAAAATAAAATTA
*
101868 AAAATAAAAAGACAAGTCAGAGAGGAAGATAATAATT-AAAAAACAACAACCATGAGAATAAAAA
1 AAAATAAAAAGACAAGTCAGAGAGGAAGATAATAATTAAAAAAAAAACAACCATGAGAATAAAAA
101932 TAGTGCATGATTAAAATAAAATTA
66 TAGTGCATGATTAAAATAAAATTA
101956 AAAATAAAAA
1 AAAATAAAAA
101966 AATAAAAAAG
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
88 59 0.62
89 29 0.31
90 1 0.01
91 6 0.06
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (89 bp):
AAAATAAAAAGACAAGTCAGAGAGGAAGATAATAATTAAAAAAAAAACAACCATGAGAATAAAAA
TAGTGCATGATTAAAATAAAATTA
Found at i:102014 original size:19 final size:19
Alignment explanation
Indices: 101990--102037 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
101980 TAAATATACT
101990 AATTTTTTTTAACTTTTCA
1 AATTTTTTTTAACTTTTCA
* * **
102009 AATTTTTTTAAATTTTTTT
1 AATTTTTTTTAACTTTTCA
102028 AATTTTTTTT
1 AATTTTTTTT
102038 TTCAACTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTTTTAACTTTTCA
Found at i:102036 original size:9 final size:9
Alignment explanation
Indices: 101993--102036 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
101983 ATATACTAAT
101993 TTTTTTTAA
1 TTTTTTTAA
* **
102002 CTTTTCAAA
1 TTTTTTTAA
102011 TTTTTTTAAA
1 TTTTTTT-AA
102021 TTTTTTTAA
1 TTTTTTTAA
102030 TTTTTTT
1 TTTTTTT
102037 TTTCAACTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
9 19 0.68
10 9 0.32
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:102037 original size:10 final size:10
Alignment explanation
Indices: 101990--102036 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
101980 TAAATATACT
*
101990 AATTTTTTTT
1 AATTTTTTTA
* *
102000 AA-CTTTTCA
1 AATTTTTTTA
102009 AATTTTTTTA
1 AATTTTTTTA
102019 AATTTTTTT-
1 AATTTTTTTA
102028 AATTTTTTT
1 AATTTTTTT
102037 TTTCAACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:102080 original size:19 final size:18
Alignment explanation
Indices: 102049--102085 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
102039 TCAACTTTTT
*
102049 TAAAAAATGAAAATAAAA
1 TAAAAAATAAAAATAAAA
102067 TAAATAAATAAAAATAAAA
1 TAAA-AAATAAAAATAAAA
102086 ACACTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (18 bp):
TAAAAAATAAAAATAAAA
Done.