Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015040.1 Kokia drynarioides strain JFW-HI SEQ_130084, 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: 158092
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 63 characters in sequence are not A, C, G, or T
Found at i:2590 original size:5 final size:5
Alignment explanation
Indices: 2580--2609 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2570 CCATTGATCT
2580 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA
1 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA
2610 ATTGTGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
TCTCA
Found at i:2862 original size:25 final size:26
Alignment explanation
Indices: 2830--2880 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2820 TTAAATACTT
2830 AATATGA-TT-AATTATTTCA-ATCAA
1 AATATGATTTCAATT-TTTCATATCAA
2854 AATATTGATTTCAATTTTTCATATCAA
1 AATA-TGATTTCAATTTTTCATATCAA
2881 CATTATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.17
25 3 0.13
26 7 0.30
27 9 0.39
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (26 bp):
AATATGATTTCAATTTTTCATATCAA
Found at i:8287 original size:18 final size:18
Alignment explanation
Indices: 8264--8318 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
8254 GTGCACTAAA
8264 AACCATGATTTAGTGATG
1 AACCATGATTTAGTGATG
8282 AACCATGATTTAGTGATG
1 AACCATGATTTAGTGATG
8300 AACCATGATTTAGTGATG
1 AACCATGATTTAGTGATG
8318 A
1 A
8319 TATTTTAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
AACCATGATTTAGTGATG
Found at i:9580 original size:4 final size:4
Alignment explanation
Indices: 9571--9618 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
9561 TTGTTTAGAT
* * *
9571 TTAA TTAA TTAA TTAAA TTAA CTAAA TTAA TTTA TTAA TTAA ATAA TT
1 TTAA TTAA TTAA TT-AA TTAA -TTAA TTAA TTAA TTAA TTAA TTAA TT
9619 TTCTCAATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 29 0.81
5 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (4 bp):
TTAA
Found at i:26133 original size:23 final size:23
Alignment explanation
Indices: 26093--26144 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
26083 AAATTGAGTC
*
26093 TATAATTGCTATAATTTACAGCA
1 TATAATTGCTACAATTTACAGCA
* * * *
26116 TATAATTTCTACATTTTAGAGCC
1 TATAATTGCTACAATTTACAGCA
26139 TATAAT
1 TATAAT
26145 CCCTATAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
TATAATTGCTACAATTTACAGCA
Found at i:29793 original size:23 final size:23
Alignment explanation
Indices: 29757--29829 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
29747 ACAAAGTACT
*
29757 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
29780 GAGCACATACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
*
29803 GAGCACACACAGTGTTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
29826 GAGC
1 GAGC
29830 GCGCTAGTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:52457 original size:25 final size:25
Alignment explanation
Indices: 52423--52473 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52413 CGAAGTACTT
52423 AACAGAAGCGCATAAGTGCTGGGAA
1 AACAGAAGCGCATAAGTGCTGGGAA
52448 AACAGAAGCGCATAAGTGCTGGGAA
1 AACAGAAGCGCATAAGTGCTGGGAA
52473 A
1 A
52474 CAGTAGGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.31, T:0.12
Consensus pattern (25 bp):
AACAGAAGCGCATAAGTGCTGGGAA
Found at i:82328 original size:21 final size:20
Alignment explanation
Indices: 82295--82343 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
82285 TATCAAAGAT
82295 AAAAA-ATATAAAAATAGA-
1 AAAAATATATAAAAATAGAG
*
82313 AATAAATATATGAAAAATTGAG
1 AA-AAATATAT-AAAAATAGAG
82335 AAAAATATA
1 AAAAATATA
82344 AAGTTTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 4 0.15
21 15 0.58
22 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
AAAAATATATAAAAATAGAG
Found at i:82543 original size:25 final size:26
Alignment explanation
Indices: 82484--82543 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
82474 AAAATGTTTA
*
82484 AATTTTATTAAAAAAATATAAAACTAT
1 AATTTT-TTAAAAAAATATAAAACAAT
*
82511 AATATTTTAAAAAAA-ATAAAA-AAT
1 AATTTTTTAAAAAAATATAAAACAAT
82535 CAATTTTTT
1 -AATTTTTT
82544 TTTTACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 13 0.45
26 9 0.31
27 5 0.17
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTTTTTAAAAAAATATAAAACAAT
Found at i:90493 original size:38 final size:38
Alignment explanation
Indices: 90422--90494 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
90412 ATGAAGTATA
*
90422 TCCATACGAACTTACCTAACCAAAACTATCACAAGAAG
1 TCCATACGAACTTACCTAACCAAAACTACCACAAGAAG
*
90460 TCCATACGAACTTATCTAACCAAAAC-ACCCACAAG
1 TCCATACGAACTTACCTAACCAAAACTA-CCACAAG
90495 CACGACTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.44, C:0.32, G:0.07, T:0.18
Consensus pattern (38 bp):
TCCATACGAACTTACCTAACCAAAACTACCACAAGAAG
Found at i:92697 original size:35 final size:35
Alignment explanation
Indices: 92628--92697 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
92618 ACACGATACA
*
92628 GCCCAGAAGGACCTATAAACCATTTACACCGTGTC
1 GCCCAGAAGGACCTATAAACCAGTTACACCGTGTC
* * * * *
92663 GCCCTGAATGACCTATAAATCAGTTATACGGTGTC
1 GCCCAGAAGGACCTATAAACCAGTTACACCGTGTC
92698 TGTAACACCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (35 bp):
GCCCAGAAGGACCTATAAACCAGTTACACCGTGTC
Found at i:100285 original size:21 final size:21
Alignment explanation
Indices: 100238--100290 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
100228 TGTGCAGACT
*
100238 TCTACCGATACAAGTATGATT
1 TCTACCGATACAAGTATGATA
100259 TCTACCGATACAAGTCATGCA-A
1 TCTACCGATACAAGT-ATG-ATA
100281 T-TACCGATAC
1 TCTACCGATAC
100291 CAAAAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 24 0.83
22 4 0.14
23 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTATGATA
Found at i:101329 original size:2 final size:2
Alignment explanation
Indices: 101322--101366 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
101312 TACATTGACA
*
101322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101364 AT A
1 AT A
101367 CATGTACAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104108 original size:54 final size:54
Alignment explanation
Indices: 104026--104133 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
104016 GGAGATGGTG
104026 AGTGAGTTTAGTTGTCCTAGGCCTCAAGGGACTTTTGAACCTATTCCTCCATGT
1 AGTGAGTTTAGTTGTCCTAGGCCTCAAGGGACTTTTGAACCTATTCCTCCATGT
104080 AGTGAGTTTAGTTGTCCTAGGCCTCAAGGGACTTTTGAACCTATTCCTCCATGT
1 AGTGAGTTTAGTTGTCCTAGGCCTCAAGGGACTTTTGAACCTATTCCTCCATGT
104134 TTGATCAAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (54 bp):
AGTGAGTTTAGTTGTCCTAGGCCTCAAGGGACTTTTGAACCTATTCCTCCATGT
Found at i:109660 original size:6 final size:6
Alignment explanation
Indices: 109649--109678 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
109639 TGTTTTATAT
109649 AATAGG AATAGG AATAGG AATAGG AATAGG
1 AATAGG AATAGG AATAGG AATAGG AATAGG
109679 TATGATTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (6 bp):
AATAGG
Found at i:121328 original size:30 final size:30
Alignment explanation
Indices: 121283--121519 Score: 227
Period size: 30 Copynumber: 7.9 Consensus size: 30
121273 AAAAATTATA
*
121283 TTTTAACCCTCAAACTTCCTAAAATTTCAT
1 TTTTAACCCTCAAACTTTCTAAAATTTCAT
* * * *
121313 TTTTGACCCTTAAACTTTATAAAACTTCA-
1 TTTTAACCCTCAAACTTTCTAAAATTTCAT
121342 TTTTAACCC-CTAAACTTTCTAAAATTTCAT
1 TTTTAACCCTC-AAACTTTCTAAAATTTCAT
* * * *
121372 TTTTGACCCCTCGAACTTTATAAAATTCCAT
1 TTTT-AACCCTCAAACTTTCTAAAATTTCAT
121403 TTTTAACCCTCAAACTTTCTAAAATTTCA-
1 TTTTAACCCTCAAACTTTCTAAAATTTCAT
* *
121432 -TTTAACCCCCAAACTTTCTAAAAATTGCAT
1 TTTTAACCCTCAAACTTTCT-AAAATTTCAT
* *
121462 TTTT-ATCC-CAAACTTTCTAGAAGATTGCA-
1 TTTTAACCCTCAAACTTTCTA-AA-ATTTCAT
* *
121491 TTTTAGCCCTCTAAAACTTTCCAAAATTT
1 TTTTAACCCTC--AAACTTTCTAAAATTT
121520 TGATTTTACC
Statistics
Matches: 170, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
28 19 0.11
29 48 0.28
30 60 0.35
31 31 0.18
32 3 0.02
33 9 0.05
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTTAACCCTCAAACTTTCTAAAATTTCAT
Found at i:121348 original size:59 final size:60
Alignment explanation
Indices: 121282--121494 Score: 242
Period size: 59 Copynumber: 3.6 Consensus size: 60
121272 CAAAAATTAT
* *
121282 ATTTTAACCCTCAAACTTCCTAAAATTTCATTTTTGA-CCCTTAAACTTTATAAAACTT-C
1 ATTTTAACCCTCAAACTTTCTAAAATTTCATTTTTGACCCCTCAAACTTTATAAAA-TTCC
*
121341 ATTTTAACCC-CTAAACTTTCTAAAATTTCATTTTTGACCCCTCGAACTTTATAAAATTCC
1 ATTTTAACCCTC-AAACTTTCTAAAATTTCATTTTTGACCCCTCAAACTTTATAAAATTCC
* * *
121401 ATTTTTAACCCTCAAACTTTCTAAAATTTCA--TTTAACCCC-CAAACTTTCTAAAAATTGC
1 A-TTTTAACCCTCAAACTTTCTAAAATTTCATTTTTGACCCCTCAAACTTTAT-AAAATTCC
* * *
121460 ATTTTTATCC-CAAACTTTCTAGAAGATTGCATTTT
1 ATTTTAACCCTCAAACTTTCTA-AA-ATTTCATTTT
121495 AGCCCTCTAA
Statistics
Matches: 134, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
57 11 0.08
58 18 0.13
59 57 0.43
60 18 0.13
61 29 0.22
62 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (60 bp):
ATTTTAACCCTCAAACTTTCTAAAATTTCATTTTTGACCCCTCAAACTTTATAAAATTCC
Found at i:130849 original size:77 final size:77
Alignment explanation
Indices: 130676--131356 Score: 759
Period size: 77 Copynumber: 9.0 Consensus size: 77
130666 TATTTTATAG
* * * * * *
130676 GTCTCTTACCCCGATCATGGGGCAGATCGAAGCATCCAAATCTTTTATCC-TAGTCAGAGGGTAG
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCC-AATCTCTTA-CCTTAATCAGAAGGCAG
*
130740 ATTTGAAGACA-GCC
64 A-TTGAAGACATGCA
* * * *
130754 GATCTCTTACCCCAATCATGGGGCAGATTTAAGAATCGAATCTCTTACCTTAATCAGAAGGCAAA
1 G-TCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGA
130819 TTGAAGACATGCA
65 TTGAAGACATGCA
* * ** * *
130832 GTCTCTTACCCCGATCATGGGGAAGATTGAAAAATCTGATCTCTT-CCTTAATGAGAAGACAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
*
130896 TGAAGACCTGC-
66 TGAAGACATGCA
* * *
130907 GATCTCTTACCCCGATCATGGGACAAACTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGA
1 G-TCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGA
*
130972 TTAAAGACATGCTA
65 TTGAAGACATGC-A
*
130986 -TCTCTTACCCCGATCATGGGACAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
* *
131050 TGAAAACATGAA
66 TGAAGACATGCA
* * * * *
131062 ATCTCTTACCCCGATCATAGGGCAGATTGAAGAATTCAATCTTTTACCTTAATTAGAAGGCAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
131127 TGAAGACATGCA
66 TGAAGACATGCA
*
131139 GTCTCTTACCCCGATCATGGGGCAAATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
131204 TGAAGACATGCA
66 TGAAGACATGCA
* * * * *
131216 ATCTCTTACCTCAATCATGGGGCAGATTG-A-AA---AATC-C--A----AATCAAAAGACAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
*
131269 TGAAGACAT-AA
66 TGAAGACATGCA
* * * * * * * * * *
131280 ATCTCTTACCTCGATCAAGAGGCAGATTGAAGCATTCAGTCTTTTACCCTAATCAGAGGGCAGAT
1 GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
131345 TGAAGACATGCA
66 TGAAGACATGCA
131357 ATCGTGGGGC
Statistics
Matches: 515, Mismatches: 67, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
64 27 0.05
65 23 0.04
66 1 0.00
69 4 0.01
71 1 0.00
72 5 0.01
75 3 0.01
76 86 0.17
77 311 0.60
78 23 0.04
79 31 0.06
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (77 bp):
GTCTCTTACCCCGATCATGGGGCAGATTGAAGAATCCAATCTCTTACCTTAATCAGAAGGCAGAT
TGAAGACATGCA
Found at i:131305 original size:64 final size:65
Alignment explanation
Indices: 131189--131310 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 65
131179 CTCTTACCTT
* * * * *
131189 AATCAGAAGGCAGATTGAAGACATGCAATCTCTTACCTCAATCATGGGGCAGATTGAAAAATCCA
1 AATCAAAAGACAGATTGAAGACATGAAATCTCTTACCTCAATCAAGAGGCAGATTGAAAAATCCA
*
131254 AATCAAAAGACAGATTGAAGACAT-AAATCTCTTACCTCGATCAAGAGGCAGATTGAA
1 AATCAAAAGACAGATTGAAGACATGAAATCTCTTACCTCAATCAAGAGGCAGATTGAA
131311 GCATTCAGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
64 29 0.57
65 22 0.43
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (65 bp):
AATCAAAAGACAGATTGAAGACATGAAATCTCTTACCTCAATCAAGAGGCAGATTGAAAAATCCA
Found at i:131306 original size:38 final size:38
Alignment explanation
Indices: 131254--131353 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 38
131244 GAAAAATCCA
* *
131254 AATCAAAAGACAGATTGAAGACATAAATCTCTTA-CCT
1 AATCAAGAGGCAGATTGAAGACATAAATCTCTTACCCT
* * * *
131291 CGATCAAGAGGCAGATTGAAG-CATTCAGTCTTTTACCCT
1 -AATCAAGAGGCAGATTGAAGACA-TAAATCTCTTACCCT
131330 AATC-AGAGGGCAGATTGAAGACAT
1 AATCAAGA-GGCAGATTGAAGACAT
131354 GCAATCGTGG
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
37 5 0.10
38 41 0.80
39 5 0.10
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (38 bp):
AATCAAGAGGCAGATTGAAGACATAAATCTCTTACCCT
Found at i:133104 original size:30 final size:30
Alignment explanation
Indices: 133023--133248 Score: 226
Period size: 30 Copynumber: 7.6 Consensus size: 30
133013 AAAATTATAA
* * *
133023 TTTAACCCCCAAACTTTTTAAAATTTAATT
1 TTTAACCCCTAAACTTTCTAAAATTTCATT
* * *
133053 TTT-A-CCCTCGAACTTTATAAAACTTCATT
1 TTTAACCCCT-AAACTTTCTAAAATTTCATT
*
133082 TTTAACCCCTAAACTTTCTAAAATTTTATT
1 TTTAACCCCTAAACTTTCTAAAATTTCATT
* *
133112 TTTGACCCCTAAACTTTCTAAAATTTTATT
1 TTTAACCCCTAAACTTTCTAAAATTTCATT
* * *
133142 TTTGACCCTTGAACTTTCTAAAATTTCATT
1 TTTAACCCCTAAACTTTCTAAAATTTCATT
* *
133172 TTTAACCCTTAAACTTTCTAAAACTTCATT
1 TTTAACCCCTAAACTTTCTAAAATTTCATT
* * * *
133202 TTTGACCCCCCAAACTTTTTGAAAATTACA-T
1 TTT-AACCCCTAAACTTTCT-AAAATTTCATT
*
133233 TTTAA-TCCTAAACTTT
1 TTTAACCCCTAAACTTT
133249 TTGGAAGATT
Statistics
Matches: 166, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.02
29 29 0.17
30 107 0.64
31 20 0.12
32 7 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTAACCCCTAAACTTTCTAAAATTTCATT
Found at i:133185 original size:90 final size:89
Alignment explanation
Indices: 133027--133228 Score: 296
Period size: 90 Copynumber: 2.2 Consensus size: 89
133017 TTATAATTTA
133027 ACCCCCAAACTTTTTAAAATTTAATTTTTACCCTCGAACTTTATAAAACTTCATTTTTAACCCCT
1 ACCCCCAAACTTTTTAAAATTTAATTTTTACCCTCGAACTTTATAAAACTTCATTTTTAACCCCT
* *
133092 AAACTTTCTAAAATTTTATTTTTG
66 AAACTTTCTAAAACTTCATTTTTG
* * * * * * *
133116 ACCCCTAAACTTTCTAAAATTTTATTTTTGACCCTTGAACTTTCTAAAATTTCATTTTTAACCCT
1 ACCCCCAAACTTTTTAAAATTTAATTTTT-ACCCTCGAACTTTATAAAACTTCATTTTTAACCCC
133181 TAAACTTTCTAAAACTTCATTTTTG
65 TAAACTTTCTAAAACTTCATTTTTG
133206 ACCCCCCAAACTTTTTGAAAATT
1 A-CCCCCAAACTTTTT-AAAATT
133229 ACATTTTAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
89 26 0.26
90 55 0.56
91 12 0.12
92 6 0.06
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (89 bp):
ACCCCCAAACTTTTTAAAATTTAATTTTTACCCTCGAACTTTATAAAACTTCATTTTTAACCCCT
AAACTTTCTAAAACTTCATTTTTG
Found at i:133517 original size:47 final size:47
Alignment explanation
Indices: 133465--133559 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
133455 TTTACCAAAA
133465 TCATCTTCTGTGTTTTGTTCCCTTTTTATGTTTAAATTAAGCCCCCT
1 TCATCTTCTGTGTTTTGTTCCCTTTTTATGTTTAAATTAAGCCCCCT
133512 TCATCTTCTGTGTTTTGTTCCCTTTTTATGTTTAAATTAAGCCCCCT
1 TCATCTTCTGTGTTTTGTTCCCTTTTTATGTTTAAATTAAGCCCCCT
133559 T
1 T
133560 ATTTTTTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.15, C:0.23, G:0.11, T:0.52
Consensus pattern (47 bp):
TCATCTTCTGTGTTTTGTTCCCTTTTTATGTTTAAATTAAGCCCCCT
Found at i:136893 original size:28 final size:28
Alignment explanation
Indices: 136853--136906 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
136843 AGAGGCGTTA
136853 AATGGGATTTTGGTATTTCCAGTGGATG
1 AATGGGATTTTGGTATTTCCAGTGGATG
136881 AATGGGATTTTGGTATTTCCAGTGGA
1 AATGGGATTTTGGTATTTCCAGTGGA
136907 AGCAGATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.07, G:0.31, T:0.39
Consensus pattern (28 bp):
AATGGGATTTTGGTATTTCCAGTGGATG
Found at i:140332 original size:52 final size:54
Alignment explanation
Indices: 140270--140376 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 54
140260 CACTTTTATG
140270 GTATAGTTACACTTCTAGT-C-CTTCTTTCTCATTTCACTTCAATTTAATCATT
1 GTATAGTTACACTTCTAGTCCTCTTCTTTCTCATTTCACTTCAATTTAATCATT
140322 GTATAGTTACACTTCTAGTCCTTCTTCTTTCTCATTTCACTTCAATTTAATCATT
1 GTATAGTTACACTTCTAGTCC-TCTTCTTTCTCATTTCACTTCAATTTAATCATT
140377 CATATTTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 19 0.37
53 1 0.02
55 32 0.62
ACGTcount: A:0.22, C:0.23, G:0.06, T:0.49
Consensus pattern (54 bp):
GTATAGTTACACTTCTAGTCCTCTTCTTTCTCATTTCACTTCAATTTAATCATT
Found at i:150339 original size:34 final size:35
Alignment explanation
Indices: 150297--150375 Score: 117
Period size: 34 Copynumber: 2.3 Consensus size: 35
150287 AACTTGATTC
* *
150297 TCTT-TTCTTTTTAGAGATTTGATTATTTATCTAT
1 TCTTGTTCTTTTTAGAGATCTGATTATCTATCTAT
150331 T-TTGTTCTTTTTAGAGATCTGATTATCTATCTAT
1 TCTTGTTCTTTTTAGAGATCTGATTATCTATCTAT
*
150365 TCTTGCTCTTT
1 TCTTGTTCTTT
150376 ATTGATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 2 0.05
34 30 0.75
35 8 0.20
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (35 bp):
TCTTGTTCTTTTTAGAGATCTGATTATCTATCTAT
Done.