Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011978.1 Kokia drynarioides strain JFW-HI SEQ_126976, 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: 107681
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:4229 original size:27 final size:28
Alignment explanation
Indices: 4187--4239 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
4177 CTAAATAAAA
4187 TAAAAAAATTGGAACCCT-TAAAAGTTGG
1 TAAAAAAATTGGAA-CCTATAAAAGTTGG
*
4215 TAAAAAAATT-TAACCTATAAAAGTT
1 TAAAAAAATTGGAACCTATAAAAGTT
4240 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 10 0.43
28 10 0.43
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.28
Consensus pattern (28 bp):
TAAAAAAATTGGAACCTATAAAAGTTGG
Found at i:4294 original size:30 final size:31
Alignment explanation
Indices: 4216--4294 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
4206 AAAAGTTGGT
*
4216 AAAAAAATTTA-A-CCTATAAAAGTTAAAAAA
1 AAAAAAATTTAGATCCT-TAAAAATTAAAAAA
* *
4246 AAAAAAAATTGGACTCCTTAAAAATT-AAAAA
1 AAAAAAATTTAGA-TCCTTAAAAATTAAAAAA
4277 AAAAAAATTTAGATCCTT
1 AAAAAAATTTAGATCCTT
4295 TTAACCTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
30 14 0.34
31 17 0.41
32 7 0.17
33 3 0.07
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAAAAATTTAGATCCTTAAAAATTAAAAAA
Found at i:8747 original size:17 final size:17
Alignment explanation
Indices: 8727--8762 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
8717 CTCTGATTTA
8727 TTTTTATAATTA-ATTAT
1 TTTTTAT-ATTATATTAT
8744 TTTTTATATTATATTAT
1 TTTTTATATTATATTAT
8761 TT
1 TT
8763 AAAAAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATATTATATTAT
Found at i:9900 original size:20 final size:21
Alignment explanation
Indices: 9854--9914 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 21
9844 TTCATTTTTT
*
9854 ATTATTTTAAAAATATAATAT
1 ATTATTTTAAAAATATAATAC
* *
9875 A-CATTTT-AAATTATAATAC
1 ATTATTTTAAAAATATAATAC
* *
9894 ATTATTTGAATAATATCAATA
1 ATTATTTTAAAAATAT-AATA
9915 ATTTATAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
19 11 0.37
20 9 0.30
21 6 0.20
22 4 0.13
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTATTTTAAAAATATAATAC
Found at i:13698 original size:74 final size:74
Alignment explanation
Indices: 13556--13697 Score: 241
Period size: 74 Copynumber: 1.9 Consensus size: 74
13546 AATAATTAAG
* *
13556 TTTATTTTTTATTCAATTAAGTATTTATACTTTTAAAATGCATAAAAAAATCTTCAAATTTTTAT
1 TTTATTTATTATTCAATTAAATATTTATACTTTTAAAATGCATAAAAAAATCTTCAAATTTTTAT
13621 TTTTATTTA
66 TTTTATTTA
* *
13630 TTTATTTATTATTCAATTAAATATTTATACTTTTAAAATGCAT-AAAAAATCTTTAAATTTTTCT
1 TTTATTTATTATTCAATTAAATATTTATACTTTTAAAATGCATAAAAAAATCTTCAAATTTTTAT
13694 TTTT
66 TTTT
13698 TTTTTTCATC
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 23 0.36
74 41 0.64
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (74 bp):
TTTATTTATTATTCAATTAAATATTTATACTTTTAAAATGCATAAAAAAATCTTCAAATTTTTAT
TTTTATTTA
Found at i:13958 original size:20 final size:21
Alignment explanation
Indices: 13932--13981 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
13922 AAATAAAAAA
13932 TATAAAAATTA-TT-AAATTT
1 TATAAAAATTATTTAAAATTT
13951 TAATAAAAA-TATTTAAAATTT
1 T-ATAAAAATTATTTAAAATTT
*
13972 TCTAAAAATT
1 TATAAAAATT
13982 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 8 0.31
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAAAAATTATTTAAAATTT
Found at i:14007 original size:20 final size:19
Alignment explanation
Indices: 13974--14017 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
13964 TAAAATTTTC
*
13974 TAAAAATTGAAAAAGAAATA
1 TAAAAATCGAAAAA-AAATA
* *
13994 TAAAAATCGTAAAAACATA
1 TAAAAATCGAAAAAAAATA
14013 TAAAA
1 TAAAA
14018 GATTTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (19 bp):
TAAAAATCGAAAAAAAATA
Found at i:23898 original size:63 final size:63
Alignment explanation
Indices: 23814--23943 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 63
23804 TTGACCATCT
* * *
23814 TGAAGAATCTGACATGCTTGTTAATGATGAAAAAGGTGCTGAAGTTGA-TTACAGTGAGGAAGA
1 TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGTGCTGAAGCTGATTTA-AGTGAGGAAGA
* ** *
23877 TGAACAATCTGACTTGCTTGTTAATGAAGAAAAATTTGCTGAAGCTGATTTAAGTGATGAAGA
1 TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGTGCTGAAGCTGATTTAAGTGAGGAAGA
23940 TGAA
1 TGAA
23944 GATTATCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 56 0.95
64 3 0.05
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (63 bp):
TGAACAATCTGACATGCTTGTTAATGAAGAAAAAGGTGCTGAAGCTGATTTAAGTGAGGAAGA
Found at i:31338 original size:28 final size:28
Alignment explanation
Indices: 31298--31355 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
31288 TTCATGGGCT
*
31298 TCAATTTGCGAGAGACTTGGGATTCTCG
1 TCAATTTGCGAGAGACCTGGGATTCTCG
*
31326 TCAATTTGTGAGAGACCTGGGATTCTCG
1 TCAATTTGCGAGAGACCTGGGATTCTCG
31354 TC
1 TC
31356 GATCTTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (28 bp):
TCAATTTGCGAGAGACCTGGGATTCTCG
Found at i:41308 original size:20 final size:20
Alignment explanation
Indices: 41283--41322 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
41273 TTCATAGTCT
41283 ATATT-ATTATAATTTTTAAA
1 ATATTAATTA-AATTTTTAAA
41303 ATATTAAATTAAATTTTTAA
1 ATATT-AATTAAATTTTTAA
41323 TATTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTAATTAAATTTTTAAA
Found at i:41889 original size:17 final size:18
Alignment explanation
Indices: 41858--41898 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
41848 ATCTTCTTTT
*
41858 TTTTTTTATTCAATTTAA
1 TTTTTTTATTCAATTAAA
41876 TCTTTTTT-TT-AATTAAA
1 T-TTTTTTATTCAATTAAA
41893 TTTTTT
1 TTTTTT
41899 CATTAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 3 0.14
19 6 0.29
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTATTCAATTAAA
Found at i:43410 original size:29 final size:31
Alignment explanation
Indices: 43353--43431 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
43343 ATCTTAAAAT
* *
43353 TATATATGAATTTTAATTTAATGTGTAATTA
1 TATATATAAATTTTAATTTAATGTATAATTA
43384 TATATATAAATTTTAATTT-A-GTATAATTA
1 TATATATAAATTTTAATTTAATGTATAATTA
*
43413 TACACGTA-AAATTTTAATT
1 TATA--TATAAATTTTAATT
43432 ATGTTTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.26
30 12 0.28
31 20 0.47
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TATATATAAATTTTAATTTAATGTATAATTA
Found at i:46150 original size:42 final size:42
Alignment explanation
Indices: 46088--46172 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
46078 TGTCTTTTGC
46088 TTTACAATTATTTACCCAAACATAATATAAAAGTTTT-ATTAA
1 TTTACAATTATTTACCCAAACATAATATAAAA-TTTTCATTAA
*
46130 TTTACAATTATTTACTCAAACATAATATAAAATTTTCATTAA
1 TTTACAATTATTTACCCAAACATAATATAAAATTTTCATTAA
46172 T
1 T
46173 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (42 bp):
TTTACAATTATTTACCCAAACATAATATAAAATTTTCATTAA
Found at i:61738 original size:49 final size:48
Alignment explanation
Indices: 61654--61747 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
61644 ATTTATTATA
* * *
61654 TAAAACAAAATTAAACAATATATAATATATCAAATAAACTTAAAAACAG
1 TAAAACAAAATTAAAAAATAAATAATATATAAAATAAA-TTAAAAACAG
* *
61703 TAAAACAAACATTAAAAAATAAATAA-ATTTAAAATACATTAAAAA
1 TAAAACAAA-ATTAAAAAATAAATAATATATAAAATAAATTAAAAA
61748 TTATTTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 7 0.18
49 18 0.46
50 14 0.36
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.24
Consensus pattern (48 bp):
TAAAACAAAATTAAAAAATAAATAATATATAAAATAAATTAAAAACAG
Found at i:61918 original size:12 final size:12
Alignment explanation
Indices: 61903--61975 Score: 92
Period size: 12 Copynumber: 6.1 Consensus size: 12
61893 AAAAAAACAG
*
61903 AAAAACAGCAAC
1 AAAAATAGCAAC
* *
61915 AAAAATAACAGC
1 AAAAATAGCAAC
61927 AAAAATAGCAAC
1 AAAAATAGCAAC
* *
61939 AAAAATAACAGC
1 AAAAATAGCAAC
61951 AAAAATAGCAAC
1 AAAAATAGCAAC
*
61963 AAAAATAACAAC
1 AAAAATAGCAAC
61975 A
1 A
61976 TCAAAACAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATAGCAAC
Found at i:61919 original size:24 final size:24
Alignment explanation
Indices: 61881--62007 Score: 121
Period size: 24 Copynumber: 5.2 Consensus size: 24
61871 TCAAACAACC
* *
61881 AAAACAGTAGCAAAAAAAACAG-A
1 AAAACAGCAACAAAAAAAACAGCA
*
61904 AAAACAGCAACAAAAATAACAGCA
1 AAAACAGCAACAAAAAAAACAGCA
* *
61928 AAAATAGCAACAAAAATAACAGCA
1 AAAACAGCAACAAAAAAAACAGCA
* * *
61952 AAAATAGCAACAAAAATAACAACA
1 AAAACAGCAACAAAAAAAACAGCA
* *
61976 TCAAAACAGTAAAAAAACCAAAACAGCA
1 --AAAACAGCAACAAAA--AAAACAGCA
62004 AAAA
1 AAAA
62008 AAAACCAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
23 19 0.21
24 47 0.53
26 16 0.18
28 7 0.08
ACGTcount: A:0.69, C:0.17, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAACAGCAACAAAAAAAACAGCA
Found at i:61999 original size:17 final size:17
Alignment explanation
Indices: 61977--62009 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
61967 ATAACAACAT
*
61977 CAAAACAGTAAAAAAAC
1 CAAAACAGCAAAAAAAC
61994 CAAAACAGCAAAAAAA
1 CAAAACAGCAAAAAAA
62010 AACCAAAATA
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:0.73, C:0.18, G:0.06, T:0.03
Consensus pattern (17 bp):
CAAAACAGCAAAAAAAC
Found at i:62028 original size:19 final size:19
Alignment explanation
Indices: 61986--62022 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61976 TCAAAACAGT
61986 AAAAAAACCAAAACAGCAA
1 AAAAAAACCAAAACAGCAA
*
62005 AAAAAAACCAAAATAGCA
1 AAAAAAACCAAAACAGCA
62023 CCAAAACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.19, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAACCAAAACAGCAA
Found at i:64502 original size:19 final size:19
Alignment explanation
Indices: 64474--64512 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64464 GATCTGATCG
64474 TTTTTCTTTT-GTATTTTGT
1 TTTTTCTTTTGGT-TTTTGT
*
64493 TTTTTTTTTTGGTTTTTGT
1 TTTTTCTTTTGGTTTTTGT
64512 T
1 T
64513 GGCTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTGGTTTTTGT
Found at i:70531 original size:2 final size:2
Alignment explanation
Indices: 70488--70518 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
70478 CTCTCTCTCT
70488 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
70519 GGAGAGACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:71913 original size:57 final size:57
Alignment explanation
Indices: 71861--72003 Score: 268
Period size: 57 Copynumber: 2.5 Consensus size: 57
71851 TGGATCTGGT
*
71861 GATGCAACCAAAGATTCTAGTTGGGGGAAGAGAAGTGACTGGAACTCAGGATCTTCA
1 GATGCAACCAATGATTCTAGTTGGGGGAAGAGAAGTGACTGGAACTCAGGATCTTCA
71918 GATGCAACCAATGATTCTAGTTGGGGGAAGAGAAGTGACTGGAACTCAGGATCTTCA
1 GATGCAACCAATGATTCTAGTTGGGGGAAGAGAAGTGACTGGAACTCAGGATCTTCA
*
71975 GATGCAACCAATGATTCTAGTTTGGGGAA
1 GATGCAACCAATGATTCTAGTTGGGGGAA
72004 AAAGGGATCA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 84 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.23
Consensus pattern (57 bp):
GATGCAACCAATGATTCTAGTTGGGGGAAGAGAAGTGACTGGAACTCAGGATCTTCA
Found at i:72113 original size:93 final size:92
Alignment explanation
Indices: 71996--72288 Score: 484
Period size: 93 Copynumber: 3.2 Consensus size: 92
71986 TGATTCTAGT
*
71996 TTGGGG-AAAAAGGGATC-AGCAGATGCAAGTCAGGATTCTAACTGGGGTAAGAAAAGTTGGGGC
1 TTGGGGCAAAAAAGGATCGA-CAGATGCAAGTCAGGATTC-AACTGGGGTAAGAAAAGTTGGGG-
*
72059 T-CTGGAAATGATGCTGGCCAAGACTCTGG
63 TACTGGAAATGATTCTGGCCAAGACTCTGG
72088 TTGGGGCAAAAAAGGATCGACAGATGCAAGTCAGGATTCAAGCTGGGGTAAGAAAAGTTGGGGTA
1 TTGGGGCAAAAAAGGATCGACAGATGCAAGTCAGGATTCAA-CTGGGGTAAGAAAAGTTGGGGTA
72153 CTGGAAATGATTCTGGCCAAGACTCTGG
65 CTGGAAATGATTCTGGCCAAGACTCTGG
* *
72181 TTGGGGCAAAAAAGGATCGGCAGATGCAAGTCAGGATTCAAACTGGGGTAAGAAAAGTTGGGGTG
1 TTGGGGCAAAAAAGGATCGACAGATGCAAGTCAGGATTC-AACTGGGGTAAGAAAAGTTGGGGTA
72246 CTGGAAATGATTCTGGCCAAGACTCTGG
65 CTGGAAATGATTCTGGCCAAGACTCTGG
72274 TTGGGGCAAAAAAGG
1 TTGGGGCAAAAAAGG
72289 TGGTTGGAAC
Statistics
Matches: 192, Mismatches: 4, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
92 9 0.05
93 180 0.94
94 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (92 bp):
TTGGGGCAAAAAAGGATCGACAGATGCAAGTCAGGATTCAACTGGGGTAAGAAAAGTTGGGGTAC
TGGAAATGATTCTGGCCAAGACTCTGG
Found at i:72630 original size:30 final size:30
Alignment explanation
Indices: 72596--72723 Score: 184
Period size: 30 Copynumber: 4.3 Consensus size: 30
72586 TTTTGGTGGC
72596 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
* *
72626 AGAGGCGGTGATGGTGGAGGCTATGGAGGT
1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
*
72656 AGAGGCGGTGATGGTGGAGGCTACGGAGGT
1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
** * * *
72686 AGAGGTGGTGACAGAGGTGGCTACAGAGGT
1 AGAGGTGGTGATGGTGGAGGCTACGGAGGT
72716 AGAGGTGG
1 AGAGGTGG
72724 AAGAGGTGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.22, C:0.08, G:0.52, T:0.18
Consensus pattern (30 bp):
AGAGGTGGTGATGGTGGAGGCTACGGAGGT
Found at i:72676 original size:15 final size:15
Alignment explanation
Indices: 72597--72676 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
72587 TTTGGTGGCA
*
72597 GAGGTGGTGATGGTG
1 GAGGCGGTGATGGTG
* *
72612 GAGGCTACG-GA-GGTA
1 GAGGC--GGTGATGGTG
72627 GAGGCGGTGATGGTG
1 GAGGCGGTGATGGTG
** *
72642 GAGGCTATGGA-GGTA
1 GAGGCGGT-GATGGTG
72657 GAGGCGGTGATGGTG
1 GAGGCGGTGATGGTG
72672 GAGGC
1 GAGGC
72677 TACGGAGGTA
Statistics
Matches: 48, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
13 1 0.02
14 4 0.08
15 38 0.79
16 4 0.08
17 1 0.02
ACGTcount: A:0.19, C:0.07, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGGCGGTGATGGTG
Found at i:72994 original size:120 final size:121
Alignment explanation
Indices: 72826--73082 Score: 372
Period size: 120 Copynumber: 2.1 Consensus size: 121
72816 ATAAGTCTTT
**
72826 TGGCTGGAACAAAGAGGGGGGGAACCAGGGCTGGAATGGTGGAACAAGTGGAGGTGGAGGTAAGA
1 TGGCTGGAACAAAGA--GGGGGAACCAGGGCTGGAATGGTGGAACAAGTGGAGGTGGAGCCAAGA
* ** * * *
72891 GTTGGAATCAATCTGGTGCTGATCAAGGAGGCCATTCCTCCAGTTGGAGTCAGTCTGG
64 CTTGGAATCAATCCAGTGCTGATCAAGGAGGCCAATCCTCCAGTTGGAATCAATCTGG
* *
72949 TGGCTGGAACAAAGA-GGGGAACCAGGGGTGGAATGGTGGATCAAGTGGAGGTGGAGCCAAGACT
1 TGGCTGGAACAAAGAGGGGGAACCAGGGCTGGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACT
*
73013 TGGAATCAATCCAGTGCTGATCAAGGAGGCCAATCCTGCAGTTGGAATCAATCTGG
66 TGGAATCAATCCAGTGCTGATCAAGGAGGCCAATCCTCCAGTTGGAATCAATCTGG
* *
73069 TGGGTGGAGCAAAG
1 TGGCTGGAACAAAG
73083 GCTCTAGTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
120 106 0.88
123 15 0.12
ACGTcount: A:0.28, C:0.15, G:0.39, T:0.19
Consensus pattern (121 bp):
TGGCTGGAACAAAGAGGGGGAACCAGGGCTGGAATGGTGGAACAAGTGGAGGTGGAGCCAAGACT
TGGAATCAATCCAGTGCTGATCAAGGAGGCCAATCCTCCAGTTGGAATCAATCTGG
Found at i:75687 original size:15 final size:15
Alignment explanation
Indices: 75667--75700 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
75657 GCTGCAACCA
75667 AATT-AATAAATAATT
1 AATTAAATAAA-AATT
75682 AATTAAATAAAAATT
1 AATTAAATAAAAATT
75697 AATT
1 AATT
75701 GAGTCAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTAAATAAAAATT
Found at i:75870 original size:15 final size:16
Alignment explanation
Indices: 75850--75879 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
75840 TTTAACTAAT
75850 AAATTAA-AACAAATG
1 AAATTAACAACAAATG
75865 AAATTAACAACAAAT
1 AAATTAACAACAAAT
75880 ACACTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.20
Consensus pattern (16 bp):
AAATTAACAACAAATG
Found at i:77627 original size:18 final size:18
Alignment explanation
Indices: 77604--77640 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
77594 ATATAACATT
77604 TAACTTACAGTAGTGTTA
1 TAACTTACAGTAGTGTTA
77622 TAACTTACAGTAGTGTTA
1 TAACTTACAGTAGTGTTA
77640 T
1 T
77641 GAAATTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (18 bp):
TAACTTACAGTAGTGTTA
Found at i:79011 original size:24 final size:23
Alignment explanation
Indices: 78984--79029 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
78974 AATTAATCAT
78984 ATTT-ATTAAATTATAAACACTTTA
1 ATTTAATT-AATTATAAAC-CTTTA
*
79008 ATTTAATTAATTCTAAACCTTT
1 ATTTAATTAATTATAAACCTTT
79030 TAATACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 13 0.65
25 3 0.15
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTAATTATAAACCTTTA
Found at i:80261 original size:5 final size:5
Alignment explanation
Indices: 80251--80279 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
80241 ACACTTGTTG
80251 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
80280 GCCTTTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:101129 original size:18 final size:18
Alignment explanation
Indices: 101099--101145 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
101089 AGAACACATT
* *
101099 TGACGATCTCACATAAAG
1 TGACGAGCTCACAGAAAG
* *
101117 TGGCGAGCTCACAGGAAG
1 TGACGAGCTCACAGAAAG
101135 TGACGAGCTCA
1 TGACGAGCTCA
101146 TTAATTTTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (18 bp):
TGACGAGCTCACAGAAAG
Found at i:104130 original size:5 final size:5
Alignment explanation
Indices: 104116--104145 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
104106 GTTTTCAAAC
104116 AAAAG AAAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAA
104146 ACATAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Done.