Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011748.1 Kokia drynarioides strain JFW-HI SEQ_126742, 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: 52460
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:480 original size:20 final size:20
Alignment explanation
Indices: 415--501 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
405 TAAGAATATA
*
415 AAAAAATTA-ATAAAA-AAT
1 AAAAAATTATAGAAAATAAT
433 AAAAAA-TATA-AAAA-AACTT
1 AAAAAATTATAGAAAATAA--T
* *
452 CAAAGAATTATTGAAAATAAT
1 -AAAAAATTATAGAAAATAAT
**
473 AAAAAATTATAGAAAATTGT
1 AAAAAATTATAGAAAATAAT
493 AAAAAATTA
1 AAAAAATTA
502 CAATAAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
17 8 0.14
18 7 0.12
19 1 0.02
20 30 0.54
21 4 0.07
22 4 0.07
23 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAAAATTATAGAAAATAAT
Found at i:655 original size:23 final size:24
Alignment explanation
Indices: 611--655 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
601 TTTTCCCGAC
*
611 AAAAAATAAAACAAAATTTATACT
1 AAAAAATAAAACAAAATATATACT
* *
635 AAAAACTAAAATAAAA-ATATA
1 AAAAAATAAAACAAAATATATA
656 AAAAATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAAATAAAACAAAATATATACT
Found at i:7531 original size:14 final size:15
Alignment explanation
Indices: 7503--7531 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7493 TTTGTGCTAA
7503 AATTTTTAATATATT
1 AATTTTTAATATATT
7518 AATTTTTAAT-TATT
1 AATTTTTAATATATT
7532 TTTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTTAATATATT
Found at i:8831 original size:4 final size:4
Alignment explanation
Indices: 8822--8865 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
8812 TGATTTTATA
*
8822 ATGT ATGT ATTT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
8866 GCTATAACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATGT
Found at i:16004 original size:26 final size:27
Alignment explanation
Indices: 15948--16004 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
15938 CTATTTTCTA
*
15948 ATTTTCAATTTATTTAATTTATTAACT
1 ATTTTCAATTTATTTAAATTATTAACT
*
15975 -TTTT-AATTTATTTTAAATTGTTAA-T
1 ATTTTCAATTTA-TTTAAATTATTAACT
16000 ATTTT
1 ATTTT
16005 TTAGAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTCAATTTATTTAAATTATTAACT
Found at i:17045 original size:21 final size:22
Alignment explanation
Indices: 17020--17061 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17010 CGATCTTCTT
*
17020 TTAGA-TCCAGGCTAGATCTAA
1 TTAGATTCCAGCCTAGATCTAA
*
17041 TTAGATTCGAGCCTAGATCTA
1 TTAGATTCCAGCCTAGATCTA
17062 TGTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (22 bp):
TTAGATTCCAGCCTAGATCTAA
Found at i:17645 original size:30 final size:30
Alignment explanation
Indices: 17609--17717 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
17599 TTAAATATCC
17609 AAAAATT-ATATTTTGACCCTCGAACTTTCT
1 AAAAATTCATA-TTTGACCCTCGAACTTTCT
* * * *
17639 AAAAATTCAAATTTCACCCTCGAAGTTTAT
1 AAAAATTCATATTTGACCCTCGAACTTTCT
* * *
17669 AAAAATTCGTATTTGACCCTTGAACTTTCCA
1 AAAAATTCATATTTGACCCTCGAACTTT-CT
*
17700 AAAAATT-AGATTTGACCC
1 AAAAATTCATATTTGACCC
17718 CTAAAATTCC
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 55 0.86
31 9 0.14
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (30 bp):
AAAAATTCATATTTGACCCTCGAACTTTCT
Found at i:17761 original size:29 final size:29
Alignment explanation
Indices: 17609--17764 Score: 107
Period size: 30 Copynumber: 5.2 Consensus size: 29
17599 TTAAATATCC
* * * *
17609 AAAAATTATATTTTGACCCTCGAACTTTCT
1 AAAAATTAGA-TTTGACCCTTGAACTTCCA
* * * * *
17639 AAAAATTCAAATTTCACCCTCGAAGTT-TA
1 AAAAATT-AGATTTGACCCTTGAACTTCCA
*
17668 TAAAAATTCGTATTTGACCCTTGAACTTTCCA
1 -AAAAATTAG-ATTTGACCCTTGAAC-TTCCA
* * * *
17700 AAAAATTAGATTTGACCCCTAAAATTCCT
1 AAAAATTAGATTTGACCCTTGAACTTCCA
* * *
17729 AAAATTTAGATTTGACCCTTGAACTACCC
1 AAAAATTAGATTTGACCCTTGAACTTCCA
17758 AAAAATT
1 AAAAATT
17765 TGAATTTAGC
Statistics
Matches: 98, Mismatches: 23, Indels: 11
0.74 0.17 0.08
Matches are distributed among these distances:
29 33 0.34
30 52 0.53
31 12 0.12
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAAATTAGATTTGACCCTTGAACTTCCA
Found at i:17765 original size:30 final size:29
Alignment explanation
Indices: 17679--17765 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
17669 AAAAATTCGT
*
17679 ATTTGACCCTTGAACTTTCCAAAAAATTAG
1 ATTTGACCCTTGAAC-TTCCAAAAATTTAG
* * * *
17709 ATTTGACCCCTAAAATTCCTAAAATTTAG
1 ATTTGACCCTTGAACTTCCAAAAATTTAG
*
17738 ATTTGACCCTTGAACTACCCAAAAATTT
1 ATTTGACCCTTGAACT-TCCAAAAATTT
17766 GAATTTAGCC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (29 bp):
ATTTGACCCTTGAACTTCCAAAAATTTAG
Found at i:17840 original size:19 final size:20
Alignment explanation
Indices: 17818--17855 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17808 GTTTTTCCTT
17818 ATTTTCATATTT-TTTCAAA
1 ATTTTCATATTTGTTTCAAA
*
17837 ATTTTCATTTTTGTTTCAA
1 ATTTTCATATTTGTTTCAA
17856 TTTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTCATATTTGTTTCAAA
Found at i:21952 original size:18 final size:18
Alignment explanation
Indices: 21926--21986 Score: 81
Period size: 17 Copynumber: 3.4 Consensus size: 18
21916 AAAAAAGAGG
*
21926 AAAAGAAGAAAGAAAGAA
1 AAAAAAAGAAAGAAAGAA
21944 AAAAAAAGAAA-AAAGAA
1 AAAAAAAGAAAGAAAGAA
*
21961 AAAAAAA-AGAGAAAGAA
1 AAAAAAAGAAAGAAAGAA
21978 AAAGAAAAG
1 AAA-AAAAG
21987 GAACGAGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
18 14 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAGAAAGAA
Found at i:21958 original size:17 final size:17
Alignment explanation
Indices: 21916--21986 Score: 72
Period size: 17 Copynumber: 4.0 Consensus size: 17
21906 TGAGGTCACA
* *
21916 AAAAAAGAGGAAAAGAAG
1 AAAAAAGA-AAAAAAAAG
21934 AAAGAAAGAAAAAAAAAG
1 AAA-AAAGAAAAAAAAAG
21952 AAAAAAGAAAAAAAAA-
1 AAAAAAGAAAAAAAAAG
*
21968 AGAGAAAGAAAAAGAAAAG
1 A-AAAAAGAAAAA-AAAAG
21987 GAACGAGATG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
16 1 0.02
17 23 0.50
18 17 0.37
19 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAAG
Found at i:21986 original size:11 final size:11
Alignment explanation
Indices: 21925--21986 Score: 74
Period size: 11 Copynumber: 5.5 Consensus size: 11
21915 AAAAAAAGAG
21925 GAAAAGAAGAAA
1 GAAAAGAA-AAA
21937 G-AAAGAAAAA
1 GAAAAGAAAAA
21947 -AAAAGAAAAAA
1 GAAAAG-AAAAA
*
21958 GAAAAAAAAAA
1 GAAAAGAAAAA
21969 GAGAAAGAAAAA
1 GA-AAAGAAAAA
21981 GAAAAG
1 GAAAAG
21987 GAACGAGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
10 7 0.16
11 22 0.50
12 15 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:22071 original size:14 final size:15
Alignment explanation
Indices: 22045--22079 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
22035 CAAGGAAAAG
22045 GAAAAGAAAAAGAAA
1 GAAAAGAAAAAGAAA
*
22060 GCAAAG-AAAAGAAA
1 GAAAAGAAAAAGAAA
22074 GAAAAG
1 GAAAAG
22080 TCAAGATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAAGAAA
Found at i:22989 original size:32 final size:33
Alignment explanation
Indices: 22950--23068 Score: 145
Period size: 33 Copynumber: 3.7 Consensus size: 33
22940 AAGAGAGAAA
*
22950 AAAAAAGAA-AAGAAAACGGAAACACAAAAAAG
1 AAAAAAGAAGAAGAAAAAGGAAACACAAAAAAG
*** * *
22982 AAAAAAGAAGAAGAAAAAGGAAGGTC-AAGATG
1 AAAAAAGAAGAAGAAAAAGGAAACACAAAAAAG
*
23014 AAAAAAAGAA-AAGAAAACGGAAACACAAAAAAG
1 -AAAAAAGAAGAAGAAAAAGGAAACACAAAAAAG
23047 AAAAAAGAAGAAGAAAAAGGAA
1 AAAAAAGAAGAAGAAAAAGGAA
23069 GGTCAAGATG
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
32 34 0.49
33 36 0.51
ACGTcount: A:0.72, C:0.06, G:0.20, T:0.02
Consensus pattern (33 bp):
AAAAAAGAAGAAGAAAAAGGAAACACAAAAAAG
Found at i:23036 original size:20 final size:20
Alignment explanation
Indices: 23013--23050 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23003 AGGTCAAGAT
23013 GAAA-AAAAGAAAAGAAAACG
1 GAAACAAAA-AAAAGAAAACG
*
23033 GAAACACAAAAAAGAAAA
1 GAAACAAAAAAAAGAAAA
23051 AAGAAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (20 bp):
GAAACAAAAAAAAGAAAACG
Found at i:23082 original size:32 final size:32
Alignment explanation
Indices: 22981--23082 Score: 125
Period size: 32 Copynumber: 3.2 Consensus size: 32
22971 ACACAAAAAA
22981 GAAAAAAGAAGAAGAAAAAGGAAGGTCAAGAT
1 GAAAAAAGAAGAAGAAAAAGGAAGGTCAAGAT
* *** * *
23013 GAAAAAAAGAA-AAGAAAACGGAAACACAAAAAA
1 G-AAAAAAGAAGAAGAAAAAGGAAGGTC-AAGAT
23046 GAAAAAAGAAGAAGAAAAAGGAAGGTCAAGAT
1 GAAAAAAGAAGAAGAAAAAGGAAGGTCAAGAT
23078 GAAAA
1 GAAAA
23083 CTTGTAAAGG
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.04
Consensus pattern (32 bp):
GAAAAAAGAAGAAGAAAAAGGAAGGTCAAGAT
Found at i:23112 original size:65 final size:65
Alignment explanation
Indices: 22949--23082 Score: 268
Period size: 65 Copynumber: 2.1 Consensus size: 65
22939 AAAGAGAGAA
22949 AAAAAAAGAAAAGAAAACGGAAACACAAAAAAGAAAAAAGAAGAAGAAAAAGGAAGGTCAAGATG
1 AAAAAAAGAAAAGAAAACGGAAACACAAAAAAGAAAAAAGAAGAAGAAAAAGGAAGGTCAAGATG
23014 AAAAAAAGAAAAGAAAACGGAAACACAAAAAAGAAAAAAGAAGAAGAAAAAGGAAGGTCAAGATG
1 AAAAAAAGAAAAGAAAACGGAAACACAAAAAAGAAAAAAGAAGAAGAAAAAGGAAGGTCAAGATG
23079 AAAA
1 AAAA
23083 CTTGTAAAGG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 69 1.00
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.03
Consensus pattern (65 bp):
AAAAAAAGAAAAGAAAACGGAAACACAAAAAAGAAAAAAGAAGAAGAAAAAGGAAGGTCAAGATG
Found at i:24056 original size:48 final size:49
Alignment explanation
Indices: 23973--24187 Score: 222
Period size: 49 Copynumber: 4.4 Consensus size: 49
23963 TGCAATGACA
* * * *
23973 AATCTTATACCTTAGAGAT-TGATGGGAAAGGTTGAAGCCGCAACGATA
1 AATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGGTG
* * *
24021 AACCTTATACCTTAGTGATGTGAAGGG-AAGATTGAAGGCGCAACGGTG
1 AATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGGTG
* * * * *
24069 AATCTTATACCTTAAAGATG-AAGAGGGACAAG-TGGAAGCCTCAATGGTG
1 AATCTTATACCTTAGAGATGTGA-AGGGA-AAGATTGAAGCCGCAACGGTG
* * **
24118 AACCTTATACCCTAGAGATGTGAAGGGAAAGATTGAAATCGCAACGGTG
1 AATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGGTG
* *
24167 AATCTTATACCCTAAAGATGT
1 AATCTTATACCTTAGAGATGT
24188 AGAGAAGCAG
Statistics
Matches: 135, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
47 1 0.01
48 58 0.43
49 72 0.53
50 4 0.03
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (49 bp):
AATCTTATACCTTAGAGATGTGAAGGGAAAGATTGAAGCCGCAACGGTG
Found at i:24200 original size:49 final size:49
Alignment explanation
Indices: 24049--24207 Score: 146
Period size: 49 Copynumber: 3.2 Consensus size: 49
24039 TGTGAAGGGA
* * * *
24049 AGATTGAAGGCGCAACGGTGAATCTTATACCTTAAAGATGAAGAG-GGAC
1 AGATTGAAGCCGCAACGGTGAATCTTATACCCTAAAGATGTAGAGAAG-C
* * * * * *
24098 A-AGTGGAAGCCTCAATGGTGAACCTTATACCCTAGAGATGTGAAGGGAA--
1 AGA-TTGAAGCCGCAACGGTGAATCTTATACCCTAAAGATGT--AGAGAAGC
**
24147 AGATTGAAATCGCAACGGTGAATCTTATACCCTAAAGATGTAGAGAAGC
1 AGATTGAAGCCGCAACGGTGAATCTTATACCCTAAAGATGTAGAGAAGC
24196 AGATTGAAGCCG
1 AGATTGAAGCCG
24208 GAAAGGTAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
47 5 0.06
48 1 0.01
49 73 0.88
50 1 0.01
51 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (49 bp):
AGATTGAAGCCGCAACGGTGAATCTTATACCCTAAAGATGTAGAGAAGC
Found at i:24566 original size:46 final size:46
Alignment explanation
Indices: 24435--24613 Score: 197
Period size: 46 Copynumber: 4.0 Consensus size: 46
24425 TAAAGTTACA
* * * * *
24435 TCATCATCCAATCATTTACCCTTAA-TCT-AGAGAGGCAGGTTTAAG
1 TCATCATCCAATCTTTTACCCCTAAGT-TAAGAGGGGCAGATTGAAG
* * *
24480 TCAT--TCTAATATTTTACCCCTAA-TTAAGAGGGGCAAATTGAAG
1 TCATCATCCAATCTTTTACCCCTAAGTTAAGAGGGGCAGATTGAAG
* * *
24523 TCATCATCCACTCTTTTACCCCTAAGTTAAGAGAGACAGATTGAAG
1 TCATCATCCAATCTTTTACCCCTAAGTTAAGAGGGGCAGATTGAAG
* *
24569 TGATCATCCAATCTTTTACCCCTAAGTTAATAGGGGCAGATTGAA
1 TCATCATCCAATCTTTTACCCCTAAGTTAAGAGGGGCAGATTGAA
24614 ACTATTATCT
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 33 0.30
45 20 0.18
46 57 0.51
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (46 bp):
TCATCATCCAATCTTTTACCCCTAAGTTAAGAGGGGCAGATTGAAG
Found at i:24777 original size:76 final size:75
Alignment explanation
Indices: 24636--24807 Score: 202
Period size: 76 Copynumber: 2.3 Consensus size: 75
24626 CTCAAGTTGT
* * * * * *
24636 AGTGGATCAAAAAAAATGAAGTGAAACTCAACATGAGTGAAACTTCAAATCTCATCTTCTTGATG
1 AGTGGATC-AAAACAATGAAGCGAAACTCAACATGAGAGAAACTTCAAACCCCATCTTCCTGATG
*
24701 AGTTACAGAGA
65 AGATACAGAGA
* ** *
24712 AGTGGATCAAGACAATGAAGCGAAGTTCAACGTGAGAGAAACTTCAAAACCCCATCTTCCTGATG
1 AGTGGATCAAAACAATGAAGCGAAACTCAACATGAGAGAAACTTC-AAACCCCATCTTCCTGATG
*
24777 AGATATAGAGA
65 AGATACAGAGA
24788 AGTGTG-TCAAAACAATGAAG
1 AGTG-GATCAAAACAATGAAG
24808 TGGTCATCTT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 30 0.37
76 50 0.62
77 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (75 bp):
AGTGGATCAAAACAATGAAGCGAAACTCAACATGAGAGAAACTTCAAACCCCATCTTCCTGATGA
GATACAGAGA
Found at i:24820 original size:48 final size:48
Alignment explanation
Indices: 24764--24855 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
24754 TTCAAAACCC
* * **
24764 CATCTTCCTGATGAGATATAGAGAAGT-GTGTCAAAACAATGAAGTGGT
1 CATCTTCCTGATGAGATACAAAGAAGTAG-ACCAAAACAATGAAGTGGT
24812 CATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAG
1 CATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAG
24856 CAAAGCTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGTGGT
Found at i:25065 original size:124 final size:123
Alignment explanation
Indices: 24687--25891 Score: 926
Period size: 124 Copynumber: 9.9 Consensus size: 123
24677 ACTTCAAATC
* * * * * * *
24687 TCATCTTCTTGATGAGTTACAGAGAAGTGGATCAAGACAATGAAGCGAAGTTCAACGTGAGAGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAA
* *
24752 ACTTCAAAACCCCATCTTCCTGATGAGATATAGAGAAGTGTG-TCAAAACAATGAAGTGG
66 ACTTC-AAACCCCATCTTCCTGATGAGATACAGAGAAGTG-GATCAAAATAATGAAGTGG
* * * *
24811 TCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCA-AAGCTCAATGCGAGTGA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAG-AGAAGCTCAATGTGAGTGA
* * * * * * *
24875 AACTTCAAACCCCACCTTCCTAATGAGATATAGAGAAAT-GAGTCAAAACAAAGAAGCGG
65 AACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGA-TCAAAATAATGAAGTGG
* * ** * *
24934 TCATCTTCTTGAAT-ATATACAGAGATGTGGACCAAATTAATGAAGAGGAGTTCAATGTGAGTGA
1 TCATCTTCTTG-ATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGA
* * *
24998 AACTTCAAAACCCCATTTTCTTGATGAGATACAGAGAAGT-GAGTCAAAATAATGAAGTGA
65 AACTTC-AAACCCCATCTTCCTGATGAGATACAGAGAAGTGGA-TCAAAATAATGAAGTGG
* * * ** *
25058 TCATCTTCTTGATGAGATACATATATGTAAACCAAAACAATGAAGCA-AAGCTCAATGTGGGTGA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAG-AGAAGCTCAATGTGAGTGA
* * * * *
25122 AACTTCAAACTCGATCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGG
65 AACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
* * * * * *
25181 TTAACTTCTTGATGAGATACTGAAAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAA
* * * * * * *
25246 ACTTCAAACCCCTACCTTCCTAATGAGATATAGATAAATAGATCAAAATGATGAA-TCGG
66 ACTTCAAACCCC-ATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGT-GG
* * *
25305 TCATCTTCCTT-ATGAAATACAGAGAAGTGGACCAAAACAATGAAGCA-AAGTTCAATGTGAGTT
1 TCATCTT-CTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAG-AGAAGCTCAATGTGAGTG
* * ***
25368 AAACTTCAAACCCTCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGCAA
64 AAACTTCAAACCC-CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
* * * * *
25429 CCATCTTCCTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAA
* * *
25494 ACTTCAAATCCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATG-A--GA
66 ACTTCAAA-CCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
****** * * * * * * * * * ** *
25550 T-A-CAGAGAAATGA-A-CCA-AAATAATGAAGCAAAGC--TCAATATG-AG-TGAAACT---TC
1 TCATCTTCTTGATGAGATACAGAGA-AGTGGACCAAAACAATGAAGA-GAAGCTCAATGTGAGTG
** * * *
25603 AAA--T----CCCTGTCTTCCTGATAG-GATACAGAAAAGTGGATCAAAACAATGAAGCGG
64 AAACTTCAAACCCCATCTTCCTGAT-GAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
* * * ** * * *
25657 TCATCTTCCTGATGAGATAGAGAGAAGTAGACCGAGTA-AATGAAGCGAAGCTCAATTTGAGTAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACC-AAAACAATGAAGAGAAGCTCAATGTGAGTGA
* * * * * *
25721 AACTTCAAACTCCATCTTTCTGATTAGATACAGAAAAGTGGATAAAAAAAATGAAGTGG
65 AACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
* * * * * * * **
25780 TCACCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATAAAGAAAAACTCAATACGAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAA
** * * * * *
25845 ACTTCAAATGCCATCTTCCTAATAAGATACAAAAAAGAGGATCAAAA
66 ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAA
25892 GATGAAGATA
Statistics
Matches: 854, Mismatches: 181, Indels: 93
0.76 0.16 0.08
Matches are distributed among these distances:
104 36 0.04
105 2 0.00
107 2 0.00
108 1 0.00
109 6 0.01
110 1 0.00
111 9 0.01
112 4 0.00
113 5 0.01
114 8 0.01
115 5 0.01
116 3 0.00
117 15 0.02
118 1 0.00
119 6 0.01
120 1 0.00
121 2 0.00
122 2 0.00
123 344 0.40
124 393 0.46
125 8 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (123 bp):
TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGAGAAGCTCAATGTGAGTGAA
ACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGTGG
Found at i:25124 original size:247 final size:248
Alignment explanation
Indices: 24687--25891 Score: 1209
Period size: 247 Copynumber: 5.0 Consensus size: 248
24677 ACTTCAAATC
* * * * * *
24687 TCATCTTCTTGATGAGTTACAGAGAAGTGGATCAAGACAATGAAGCGAAGTTCAACGTGAGAGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
* * *
24752 ACTTCAAAACCCCATCTTCCTGATGAGATATAGAGAAGTGTG-TCAAAACAATGAAGTGGTCATC
66 ACTTCAAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGTGGTCATC
* *
24816 TTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGCGAGTGAAACTTC
131 TTCTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTC
* * * * * *
24881 AAACCCCACCTTCCTAATGAGATATAGAGAAAT-GAGTCAAAACAAAGAAGCGG
196 AAACCCCATCTTCCTGATGAGATACAAAGAAGTGGA-TCAAAACAATGAAGCGG
* * ** * * *
24934 TCATCTTCTTGAAT-ATATACAGAGATGTGGACCAAATTAATGAAGAGGAGTTCAATGTGAGTGA
1 TCATCTTCTTG-ATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGA
* * *
24998 AACTTCAAAACCCCATTTTCTTGATGAGATACAGAGAAGTGAG-TCAAAATAATGAAGTGATCAT
65 AACTTCAAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGTGGTCAT
* * * * *
25062 CTTCTTGATGAGATACATATATGTAAACCAAAACAATGAAGCAAAGCTCAATGTGGGTGAAACTT
130 CTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTT
* * * *
25127 CAAACTCGATCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGG
195 CAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGG
* * * * *
25181 TTAACTTCTTGATGAGATACTGAAAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
* * * * * *
25246 ACTTC-AAACCCCTACCTTCCTAATGAGATATAGATAAAT-AGATCAAAATGATGAA-TCGGTCA
66 ACTTCAAAACCCC-ATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGT-GGTCA
* * * * *
25308 TCTTCCTT-ATGAAATACAGAGAAGTGGACCAAAACAATGAAGCAAAGTTCAATGTGAGTTAAAC
129 TCTT-CTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAAC
** **
25372 TTCAAACCCTCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGCAA
193 TTCAAACCC-CATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGG
* * * *
25429 CCATCTTCCTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
* * *
25494 ACTTCAAATCCCCATCTTCCTGATGAGATACAAAGAAGTG-GATCAAAATGATG-A---G--A--
66 ACTTCAAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGTGGTCATC
* * * *
25550 TAC---A-GAG-----AA-ATG-A-ACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTC
131 TTCTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTC
**
25603 AAATCCCTGTCTTCCTGAT-AGGATACAGAA-AAGTGGATCAAAACAATGAAGCGG
196 AAA-CCCCATCTTCCTGATGA-GATACA-AAGAAGTGGATCAAAACAATGAAGCGG
* * * ** * *
25657 TCATCTTCCTGATGAGATAGAGAGAAGTAGACCGAGTA-AATGAAGCGAAGCTCAATTTGAGTAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGGACC-AAAACAATGAAGCGAAGCTCAATGTGAGTGA
* * * * * * *
25721 AACTTC-AAACTCCATCTTTCTGATTAGATACAGAAAAGTG-GATAAAAAAAATGAAGTGGTCAC
65 AACTTCAAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGTGGTCAT
* * * * * * **
25784 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATAAAGAAAAACTCAATACGAGTGAAACTT
130 CTTCTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTT
** * * * *
25849 CAAATGCCATCTTCCTAATAAGATACAAAAAAGAGGATCAAAA
195 CAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAA
25892 GATGAAGATA
Statistics
Matches: 787, Mismatches: 135, Indels: 73
0.79 0.14 0.07
Matches are distributed among these distances:
227 39 0.05
228 135 0.17
229 7 0.01
230 2 0.00
231 2 0.00
233 1 0.00
235 2 0.00
236 2 0.00
237 1 0.00
238 1 0.00
239 4 0.01
240 1 0.00
242 1 0.00
244 2 0.00
245 4 0.01
246 41 0.05
247 395 0.50
248 141 0.18
249 6 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (248 bp):
TCATCTTCTTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
ACTTCAAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGATCAAAATAATGAAGTGGTCATC
TTCTTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGTGAGTGAAACTTC
AAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGG
Found at i:25374 original size:371 final size:369
Alignment explanation
Indices: 24687--25891 Score: 1148
Period size: 371 Copynumber: 3.3 Consensus size: 369
24677 ACTTCAAATC
* * * * * * *
24687 TCATCTTCTTGATGAGTTACAGAGAAGTGGATCAAGACAATGAAGCGAAGTTCAACGTGAGAGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
* * *
24752 ACTTCAAAACCCCATCTTCCTGATGAGATATAGAGAAGTGTG-TCAAAACAATGAAGTGGTCATC
66 ACTTC-AAACCCCATCTTCCTGATGAGATACAAAGAAGTG-GATCAAAACAATGAAGTGGTCAAC
*
24816 TTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGCGAGTGAAACTTC
129 TTCCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGCAAGTGAAACTTC
24881 AAACCCCACCTTCCTAATGAGATATAGAGAAATGAGTCAAAACAAAGAAGCGGTCATCTTCTTGA
194 AAACCCCACCTTCCTAATGAGATATAGAGAAATGAGTCAAAACAAAGAAGCGGTCATCTTCTT-A
* * ** *
24946 ATATATACAGAGATGTGGACCAAATTAATGAAGAGGAGTTCAATGTGAGTGAAACTTCAAAACCC
258 ATAAATACAGAGAAGTGGACCAAAACAATGAAGAGAAGTTCAATGTGAGTGAAACTTC-AAACCC
* * * **
25011 -CATTTTCTTGATGAGATACAGAGAAGT-GAGTCAAAATAATGAAGTGA
322 TCATCTTCCTGATGAGATACAAAGAAGTGGA-TCAAAATAATGAAGCAA
* * * * * *
25058 TCATCTTCTTGATGAGATACATATATGTAAACCAAAACAATGAAGCAAAGCTCAATGTGGGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
* * * *
25123 ACTTCAAACTCGATCTTCTTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGGTTAACTT
66 ACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGGTCAACTT
* * * * *
25188 CTTGATGAGATACTGAA-AAGTGGACCAAAACAATGAAGCGAAGCTCAATGTAAGTGAAACTTCA
131 CCTGATGAGATAC-AAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGCAAGTGAAACTTCA
* ** * *
25252 AACCCCTACCTTCCTAATGAGATATAGATAAAT-AGATCAAAATGATGAATCGGTCATCTTCCTT
195 AACCCC-ACCTTCCTAATGAGATATAGAGAAATGAG-TCAAAACAAAGAAGCGGTCATCTT-CTT
*
25316 -ATGAAATACAGAGAAGTGGACCAAAACAATGAAGCA-AAGTTCAATGTGAGTTAAACTTCAAAC
257 AAT-AAATACAGAGAAGTGGACCAAAACAATGAAG-AGAAGTTCAATGTGAGTGAAACTTCAAAC
*
25379 CCTCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGCAA
320 CCTCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATAATGAAGCAA
* * *
25429 CCATCTTCCTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAA
1 TCATCTTCTTGATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
25494 ACTTCAAATCCCCATCTTCCTGATGAGATACAAAGAAGTGGAT-----C----AA------AA--
66 ACTTCAAA-CCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGGTCAACT
* * * ***
25542 ---TGATGAGATACAGAGAAAT-GAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTC
130 TCCTGATGAGATACAAAGAAGTAG-ACCAAAACAATGAAGCAAAGCTCAATGCAAGTGAAACTTC
*** * * *
25603 AAATCCCTGTCTTCCTGAT-AGGATACAGA-AAAGTG-GATCAAAACAATGAAGCGGTCATCTTC
194 AAA-CCCCACCTTCCTAATGA-GATATAGAGAAA-TGAG-TCAAAACAAAGAAGCGGTCATCTTC
* * * * * ** * * * *
25665 CTGATGAGATAGAGAGAAGTAGACCGAGTA-AATGAAGCGAAGCTCAATTTGAGTAAAACTTCAA
255 TTAAT-AAATACAGAGAAGTGGACC-AAAACAATGAAGAGAAGTTCAATGTGAGTGAAACTTCAA
* * * * * ***
25729 ACTC-CATCTTTCTGATTAGATACAGAA-AAGTGGATAAAAAAAATGAAGTGG
318 ACCCTCATCTTCCTGATGAGATACA-AAGAAGTGGATCAAAATAATGAAGCAA
* * * * ** * **
25780 TCACCTTCCTGATGAGATACAGAGAAGT-AGACCAAATCAATAAAGAAAAACTCAATACGAGTGA
1 TCATCTTCTTGATGAGATACAGAGAAGTGA-ACCAAAACAATGAAGCGAAGCTCAATGTGAGTGA
** * * * *
25844 AACTTCAAATGCCATCTTCCTAATAAGATACAAAAAAGAGGATCAAAA
65 AACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAA
25892 GATGAAGATA
Statistics
Matches: 703, Mismatches: 105, Indels: 68
0.80 0.12 0.08
Matches are distributed among these distances:
350 29 0.04
351 105 0.15
352 145 0.21
353 5 0.01
357 2 0.00
363 2 0.00
367 1 0.00
369 1 0.00
370 122 0.17
371 254 0.36
372 37 0.05
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (369 bp):
TCATCTTCTTGATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGTGAGTGAA
ACTTCAAACCCCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGTGGTCAACTT
CCTGATGAGATACAAAGAAGTAGACCAAAACAATGAAGCAAAGCTCAATGCAAGTGAAACTTCAA
ACCCCACCTTCCTAATGAGATATAGAGAAATGAGTCAAAACAAAGAAGCGGTCATCTTCTTAATA
AATACAGAGAAGTGGACCAAAACAATGAAGAGAAGTTCAATGTGAGTGAAACTTCAAACCCTCAT
CTTCCTGATGAGATACAAAGAAGTGGATCAAAATAATGAAGCAA
Found at i:25438 original size:48 final size:48
Alignment explanation
Indices: 25382--25474 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
25372 TTCAAACCCT
* * *
25382 CATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGCAAC
1 CATCTTCCTGATGAGATACAAAGAAGTGAACCAAAATAATGAAGCAAC
*
25430 CATCTTCCTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGC
1 CATCTTCCTGATGAGATACAAAGAAGTGAACCAAAATAATGAAGC
25475 GAAGCTCAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAAAGAAGTGAACCAAAATAATGAAGCAAC
Found at i:25568 original size:28 final size:28
Alignment explanation
Indices: 25514--25575 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
25504 CCCATCTTCC
* * *
25514 TGATGAGATACAAAGAAGTGGATCAAAA
1 TGATGAGATACAAAGAAATGAACCAAAA
*
25542 TGATGAGATACAGAGAAATGAACCAAAA
1 TGATGAGATACAAAGAAATGAACCAAAA
*
25570 TAATGA
1 TGATGA
25576 AGCAAAGCTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.23, T:0.18
Consensus pattern (28 bp):
TGATGAGATACAAAGAAATGAACCAAAA
Found at i:25618 original size:104 final size:104
Alignment explanation
Indices: 25438--25645 Score: 339
Period size: 104 Copynumber: 2.0 Consensus size: 104
25428 ACCATCTTCC
* * *
25438 TGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAAT
1 TGATGAGATACAGAGAAATGAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAAT
25503 CCCCATCTTCCTGAT-GAGATACA-AAGAAGTGGATCAAAA
66 CCCCATCTTCCTGATAG-GATACAGAA-AAGTGGATCAAAA
25542 TGATGAGATACAGAGAAATGAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAAT
1 TGATGAGATACAGAGAAATGAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAAT
**
25607 CCCTGTCTTCCTGATAGGATACAGAAAAGTGGATCAAAA
66 CCCCATCTTCCTGATAGGATACAGAAAAGTGGATCAAAA
25646 CAATGAAGCG
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
104 94 0.97
105 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (104 bp):
TGATGAGATACAGAGAAATGAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAAT
CCCCATCTTCCTGATAGGATACAGAAAAGTGGATCAAAA
Found at i:25726 original size:228 final size:227
Alignment explanation
Indices: 25316--25768 Score: 603
Period size: 228 Copynumber: 2.0 Consensus size: 227
25306 CATCTTCCTT
* * * * *
25316 ATGAAATACAGAGAAGTGGACCAAAACAATGAAGCAAAGTTCAATGTGAGTTAAACTTCAAACCC
1 ATGAAATACAGAGAAATGAACCAAAACAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAACCC
**
25381 TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAATGATGAAGCAACCATCTTCCTGATGAGA
66 TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCAACCATCTTCCTGATGAGA
*
25446 TACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCT
131 TACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAA-CCCCATCT
*
25511 TCCTGATGAGATACA-AAGAAGTGGATCAAAATG
195 TCCTGATGAGATACAGAA-AAGTGGATAAAAATG
* *
25544 ATGAGATACAGAGAAATGAACCAAAATAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAATCC
1 ATGAAATACAGAGAAATGAACCAAAACAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAA-CC
* ***
25609 CT-GTCTTCCTGAT-AGGATACAGAA-AAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATG
65 CTCATCTTCCTGATGA-GATACA-AAGAAGTGGATCAAAACAATGAAGCAACCATCTTCCTGATG
* * * * *
25671 AGATAGAGAGAAGT-AGACC-GAGTAAATGAAGCGAAGCTCAATTTGAGTAAAACTTCAAACTCC
128 AGATACAGAGAAGTGA-ACCAAAAT-AATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAACCCC
* *
25734 ATCTTTCTGATTAGATACAGAAAAGTGGATAAAAA
191 ATCTTCCTGATGAGATACAGAAAAGTGGATAAAAA
25769 AAATGAAGTG
Statistics
Matches: 197, Mismatches: 22, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
227 36 0.18
228 155 0.79
229 6 0.03
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.22
Consensus pattern (227 bp):
ATGAAATACAGAGAAATGAACCAAAACAATGAAGCAAAGCTCAATATGAGTGAAACTTCAAACCC
TCATCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCAACCATCTTCCTGATGAGA
TACAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAACCCCATCTT
CCTGATGAGATACAGAAAAGTGGATAAAAATG
Found at i:25797 original size:123 final size:124
Alignment explanation
Indices: 25571--25891 Score: 380
Period size: 123 Copynumber: 2.6 Consensus size: 124
25561 GAACCAAAAT
* *
25571 AATGAAGCAAAGCTCAATATGAGTGAAACTTCAAATCCCTGTCTTCCTGATAGGATACAGAAAAG
1 AATGAAGCAAAGCTCAATATGAGTAAAACTTCAAATCCCTATCTTCCTGATAGGATACAGAAAAG
* * * *
25636 TGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGATAGAGAGAAGTAGACCGAGTA
66 TGGATAAAAAAAATGAAGCGGTCACCTTCCTGATGAGATACAGAGAAGTAGACCGAGTA
* * *
25695 AATGAAGCGAAGCTCAATTTGAGTAAAACTTCAAA-CTCC-ATCTTTCTGATTA-GATACAGAAA
1 AATGAAGCAAAGCTCAATATGAGTAAAACTTCAAATC-CCTATCTTCCTGA-TAGGATACAGAAA
* * * *
25757 AGTGGATAAAAAAAATGAAGTGGTCACCTTCCTGATGAGATACAGAGAAGTAGACCAAATC
64 AGTGGATAAAAAAAATGAAGCGGTCACCTTCCTGATGAGATACAGAGAAGTAGACCGAGTA
* * * * * * * * *
25818 AATAAAGAAAAACTCAATACGAGTGAAACTTCAAATGCC-ATCTTCCTAATAAGATACAAAAAAG
1 AATGAAGCAAAGCTCAATATGAGTAAAACTTCAAATCCCTATCTTCCTGATAGGATACAGAAAAG
* *
25882 AGGATCAAAA
66 TGGATAAAAA
25892 GATGAAGATA
Statistics
Matches: 167, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
122 2 0.01
123 129 0.77
124 36 0.22
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.22
Consensus pattern (124 bp):
AATGAAGCAAAGCTCAATATGAGTAAAACTTCAAATCCCTATCTTCCTGATAGGATACAGAAAAG
TGGATAAAAAAAATGAAGCGGTCACCTTCCTGATGAGATACAGAGAAGTAGACCGAGTA
Found at i:26959 original size:25 final size:26
Alignment explanation
Indices: 26931--26984 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
26921 CAAAGAGAAC
* *
26931 AAAAGATAAC-AAAATAGATTATATA
1 AAAAGATAACTAAAACAGATTATAGA
* *
26956 AAAATATAACTAAGACAGATTATAGA
1 AAAAGATAACTAAAACAGATTATAGA
26982 AAA
1 AAA
26985 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.22
Consensus pattern (26 bp):
AAAAGATAACTAAAACAGATTATAGA
Found at i:27708 original size:29 final size:29
Alignment explanation
Indices: 27654--27847 Score: 153
Period size: 29 Copynumber: 6.6 Consensus size: 29
27644 ATTTAACCCC
* * *
27654 CAAACTATCTAAAAATTATGTTTTGACTCT
1 CAAACTTTCCAAAAATTAT-ATTTGACTCT
* * *
27684 CGAAGTTTCCAAAAATTATATTTGA-TCCC
1 CAAACTTTCCAAAAATTATATTTGACT-CT
* *
27713 CAAACTTTCCAAAAATTTAGATTTGACCCT
1 CAAACTTTCCAAAAA-TTATATTTGACTCT
* * *
27743 CAAAGTTTTCAAAAATTATATTTGA-TCCA
1 CAAACTTTCCAAAAATTATATTTGACT-CT
*
27772 CAAACTTTCCAAAAATTTAAATTTGAC-CT
1 CAAACTTTCCAAAAA-TTATATTTGACTCT
* * * *
27801 CTAAAC-TTCCTAAAATTTAGATTTGACCCC
1 C-AAACTTTCC-AAAAATTATATTTGACTCT
27831 CAAACTTTCCAAAAATT
1 CAAACTTTCCAAAAATT
27848 TAAAATTTGA
Statistics
Matches: 130, Mismatches: 24, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
28 1 0.01
29 68 0.52
30 61 0.47
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (29 bp):
CAAACTTTCCAAAAATTATATTTGACTCT
Found at i:27729 original size:59 final size:58
Alignment explanation
Indices: 27637--27859 Score: 243
Period size: 59 Copynumber: 3.8 Consensus size: 58
27627 TTTTATTTAG
* * * * * *
27637 AAATTACATTTAACCCCCAAACTATCTAAAAA-TTATGTTTTGACTCTCGAAGTTTCCAA
1 AAATTATATTTGACCCCCAAACTTTCCAAAAATTTA-GATTTGAC-CTCAAAGTTTCCAA
* *
27696 AAATTATATTTGATCCCCAAACTTTCCAAAAATTTAGATTTGACCCTCAAAGTTTTCAA
1 AAATTATATTTGACCCCCAAACTTTCCAAAAATTTAGATTTGA-CCTCAAAGTTTCCAA
* * * *
27755 AAATTATATTTGATCCACAAACTTTCCAAAAATTTAAATTTGACCTCTAAA-CTTCCTAA
1 AAATTATATTTGACCCCCAAACTTTCCAAAAATTTAGATTTGACCTC-AAAGTTTCC-AA
* * *
27814 AATTTAGATTTGACCCCCAAACTTTCCAAAAATTTAAAATTTGACC
1 AAATTATATTTGACCCCCAAACTTTCCAAAAATTT-AGATTTGACC
27860 CTTAAACTTC
Statistics
Matches: 143, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
58 7 0.05
59 122 0.85
60 14 0.10
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.35
Consensus pattern (58 bp):
AAATTATATTTGACCCCCAAACTTTCCAAAAATTTAGATTTGACCTCAAAGTTTCCAA
Found at i:27848 original size:30 final size:30
Alignment explanation
Indices: 27644--27860 Score: 199
Period size: 30 Copynumber: 7.3 Consensus size: 30
27634 TAGAAATTAC
* * *
27644 ATTTAACCCCCAAACTATCTAAAAA-TTATG
1 ATTTGACCCCCAAACTTTCCAAAAATTTA-G
* * * * * *
27674 TTTTGACTCTCGAAGTTTCCAAAAA-TTAT
1 ATTTGACCCCCAAACTTTCCAAAAATTTAG
*
27703 ATTTGATCCCCAAACTTTCCAAAAATTTAG
1 ATTTGACCCCCAAACTTTCCAAAAATTTAG
* * * *
27733 ATTTGACCCTCAAAGTTTTCAAAAA-TTAT
1 ATTTGACCCCCAAACTTTCCAAAAATTTAG
* * *
27762 ATTTGATCCACAAACTTTCCAAAAATTTAA
1 ATTTGACCCCCAAACTTTCCAAAAATTTAG
* * *
27792 ATTTGACCTCTAAAC-TTCCTAAAATTTAG
1 ATTTGACCCCCAAACTTTCCAAAAATTTAG
*
27821 ATTTGACCCCCAAACTTTCCAAAAATTTAAA
1 ATTTGACCCCCAAACTTTCCAAAAATTT-AG
27852 ATTTGACCC
1 ATTTGACCC
27861 TTAAACTTCT
Statistics
Matches: 147, Mismatches: 36, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
29 68 0.46
30 69 0.47
31 10 0.07
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
ATTTGACCCCCAAACTTTCCAAAAATTTAG
Found at i:27876 original size:30 final size:29
Alignment explanation
Indices: 27714--27878 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 29
27704 TTTGATCCCC
* * *
27714 AAACTTTCCAAAAATTTAGATTTGACCCTC
1 AAAC-TTCCTAAAATTTAAATTTGACCCTT
* * * * * **
27744 AAAGTT-TTCAAAAATTATATTTGATCCAC
1 AAACTTCCT-AAAATTTAAATTTGACCCTT
*
27773 AAACTTTCCAAAAATTTAAATTTGA-CCTCT
1 AAAC-TTCCTAAAATTTAAATTTGACCCT-T
* **
27803 AAACTTCCTAAAATTTAGATTTGACCCCC
1 AAACTTCCTAAAATTTAAATTTGACCCTT
*
27832 AAACTTTCCAAAAATTTAAAATTTGACCCTT
1 AAAC-TTCCTAAAATTT-AAATTTGACCCTT
*
27863 AAACTTCTTAAAATTT
1 AAACTTCCTAAAATTT
27879 TCAATTTAGC
Statistics
Matches: 104, Mismatches: 24, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
29 45 0.43
30 45 0.43
31 14 0.13
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (29 bp):
AAACTTCCTAAAATTTAAATTTGACCCTT
Found at i:27885 original size:30 final size:30
Alignment explanation
Indices: 27773--27908 Score: 109
Period size: 30 Copynumber: 4.5 Consensus size: 30
27763 TTTGATCCAC
*
27773 AAACTTTCC-AAAAATTTAAATTTGA-CCTCT
1 AAAC-TTCCTAAAATTTTAAATTTGACCCT-T
* **
27803 AAACTTCCTAAAA-TTTAGATTTGACCCCC
1 AAACTTCCTAAAATTTTAAATTTGACCCTT
* *
27832 AAACTTTCCAAAAATTTAAAATTTGACCCTT
1 AAAC-TTCCTAAAATTTTAAATTTGACCCTT
* * **
27863 AAACTTCTTAAAATTTTCAATTT-AGCCCCA
1 AAACTTCCTAAAATTTTAAATTTGA-CCCTT
*
27893 AAACTTTCTAAAATTT
1 AAACTTCCTAAAATTT
27909 CATTTTTGCC
Statistics
Matches: 85, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
29 19 0.22
30 50 0.59
31 16 0.19
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTCCTAAAATTTTAAATTTGACCCTT
Found at i:27908 original size:60 final size:59
Alignment explanation
Indices: 27690--27905 Score: 196
Period size: 59 Copynumber: 3.6 Consensus size: 59
27680 CTCTCGAAGT
* * * *
27690 TTCC-AAAAATTATATTTGATCCCC-AAACTTTCCAAAAATTTAGATTTGACC-CTCAAAG
1 TTCCTAAAATTTAGATTTGA-CCCCAAAACTTTCCAAAAATTTAAATTTGACCTCT-AAAC
* * * *
27748 TT-TTCAAAAATTATATTTGA-TCCACAAACTTTCCAAAAATTTAAATTTGACCTCTAAAC
1 TTCCT-AAAATTTAGATTTGACCCCA-AAACTTTCCAAAAATTTAAATTTGACCTCTAAAC
*
27807 TTCCTAAAATTTAGATTTGACCCCCAAACTTTCCAAAAATTTAAAATTTGACC-CTTAAAC
1 TTCCTAAAATTTAGATTTGACCCCAAAACTTTCCAAAAATTT-AAATTTGACCTC-TAAAC
* *
27867 TTCTTAAAATTTTCA-ATTT-AGCCCCAAAACTTTCTAAAA
1 TTCCTAAAA-TTT-AGATTTGA-CCCCAAAACTTTCCAAAA
27906 TTTCATTTTT
Statistics
Matches: 134, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
57 2 0.01
58 2 0.01
59 77 0.57
60 29 0.22
61 23 0.17
62 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (59 bp):
TTCCTAAAATTTAGATTTGACCCCAAAACTTTCCAAAAATTTAAATTTGACCTCTAAAC
Found at i:31810 original size:12 final size:12
Alignment explanation
Indices: 31793--31818 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31783 TGTTATCATG
31793 ATGAATCCTATT
1 ATGAATCCTATT
31805 ATGAATCCTATT
1 ATGAATCCTATT
31817 AT
1 AT
31819 TTCTTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
ATGAATCCTATT
Found at i:47842 original size:21 final size:21
Alignment explanation
Indices: 47811--47858 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
47801 GACTGGTGAA
**
47811 TTATC-TTTTTATCCTCTTTT
1 TTATCTTTTTTATCCTCCCTT
47831 TTATCTTTTTTATCCTCCCTT
1 TTATCTTTTTTATCCTCCCTT
47852 TTATCTT
1 TTATCTT
47859 CTTTGTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATCTTTTTTATCCTCCCTT
Found at i:49774 original size:4 final size:4
Alignment explanation
Indices: 49761--49803 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
49751 AAAGTTGAAG
*
49761 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
49804 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:50216 original size:20 final size:21
Alignment explanation
Indices: 50175--50217 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
50165 TAATTTACTT
50175 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
50196 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
50216 TA
1 TA
50218 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:50509 original size:29 final size:28
Alignment explanation
Indices: 50477--50586 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 28
50467 TAAGCCTAGC
*
50477 TAATTAATTATTAAAATTTAATATAAAAA
1 TAATTAATTATCAAAA-TTAATATAAAAA
* **
50506 TAATTAATTATCAAAA-TAATATCATCA
1 TAATTAATTATCAAAATTAATATAAAAA
* *
50533 TCATATTATTTACCAAAATATAATATAAAAAA
1 T-A-ATTAATTATCAAAAT-TAATAT-AAAAA
*
50565 TAATTAATTATGAAAA-TAATAT
1 TAATTAATTATCAAAATTAATAT
50587 CCCCATCATA
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
27 9 0.14
28 7 0.11
29 27 0.42
30 11 0.17
31 7 0.11
32 3 0.05
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (28 bp):
TAATTAATTATCAAAATTAATATAAAAA
Found at i:50581 original size:59 final size:58
Alignment explanation
Indices: 50489--50610 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 58
50479 ATTAATTATT
* *
50489 AAAATTTAATATAAAAATAATTAATTATCAAAATAATATCATCATCATATTATTTACC
1 AAAATATAATATAAAAATAATTAATTATCAAAATAATATCACCATCATATTATTTACC
* *
50547 AAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCATATTATTTACC
1 AAAATATAATAT-AAAAATAATTAATTATCAAAATAATATCACCATCATATTATTTACC
50606 AAAAT
1 AAAAT
50611 GATACAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 11 0.19
59 48 0.81
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (58 bp):
AAAATATAATATAAAAATAATTAATTATCAAAATAATATCACCATCATATTATTTACC
Done.