Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014268.1 Kokia drynarioides strain JFW-HI SEQ_129301, 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: 45927
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:3182 original size:17 final size:18
Alignment explanation
Indices: 3152--3191 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3142 TTTTTTTTTT
*
3152 TTAAATGAGCATTTTAAA
1 TTAAATGAGAATTTTAAA
*
3170 TTAAAT-AGAATTTTAAT
1 TTAAATGAGAATTTTAAA
3187 TTAAA
1 TTAAA
3192 ATTTTATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (18 bp):
TTAAATGAGAATTTTAAA
Found at i:3820 original size:40 final size:39
Alignment explanation
Indices: 3713--4298 Score: 537
Period size: 40 Copynumber: 15.0 Consensus size: 39
3703 GATTGGGTTG
*
3713 TGGTTTCAA-CTTGTCCCATGATCGGGGTAAGAGATTGGA
1 TGGTTTCAATC-TGCCCCATGATCGGGGTAAGAGATTGGA
* * **
3752 TGGTTGT-GATCTACCCCATGATCGGGGTAAGAGATCAGA
1 TGGTT-TCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
3791 TGGTTTTTAATCTGCCCCATAATTGGGGTAAGAGATTAGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
3831 TGGCTGT-GATCTGCCCCATGATCAGGGTAAGAGATCGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
3870 TGGTTTTCTATTTGTCCCATGATCGGGGTAAGAGATTAGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * * * *
3910 TGGCTGCGATCTGCCTCATGATCGGGATAAGAGATTGGG
1 TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
3949 TGGTTTTAAATCTGTCCCATGATCAGTGTAAGAGATTGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
*
3989 TGG-TT---T-T-CCCCATGATCGGGATAAGAGATTGGA
1 TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
4022 TGGTTGCGATCTACCCCATGATCGAGGT-AGAGATTGGA
1 TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* *
4060 TGGTTTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
4100 TGGATGCGATCTACCCCATGATCGGGGTAAGAGATCT-GA
1 TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGAT-TGGA
* *
4139 TGGTTTTCAATCTGCCCCGTGATCGAGGTAAGAGATTGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * *
4179 TGGTTTTCAATCTACCCCTTGATCGGGGTAAGTGATTGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * * * * *
4219 TGGTTGCGATCTGCCCTATGATTGGGGTAAAAGATCGTA
1 TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
*
4258 TGGTTTTCAATCTGCCCGATGATCGGGGTAAGAGATTGGA
1 TGG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
4298 T
1 T
4299 TTGATGTCGA
Statistics
Matches: 440, Mismatches: 89, Indels: 35
0.78 0.16 0.06
Matches are distributed among these distances:
33 25 0.06
34 2 0.00
35 1 0.00
37 1 0.00
38 16 0.04
39 191 0.43
40 204 0.46
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (39 bp):
TGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGA
Found at i:3821 original size:79 final size:79
Alignment explanation
Indices: 3727--4298 Score: 597
Period size: 79 Copynumber: 7.3 Consensus size: 79
3717 TTCAACTTGT
* **
3727 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTACCCCATGATCGGGGTAAGAGATCAGAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
*
3792 GGTTTTTAATCTGC
66 GGTTTTCAATCTGC
* * * * * *
3806 CCCATAATTGGGGTAAGAGATTAGATGGCTGTGATCTGCCCCATGATCAGGGTAAGAGATCGGAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * *
3871 GGTTTTCTATTTGT
66 GGTTTTCAATCTGC
* * * * * *
3885 CCCATGATCGGGGTAAGAGATTAGATGGCTGCGATCTGCCTCATGATCGGGATAAGAGATTGGGT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* *
3950 GGTTTTAAATCTGT
66 GGTTTTCAATCTGC
* * *
3964 CCCATGATCAGTGTAAGAGATTGGATGG-T-T--T-T-CCCCATGATCGGGATAAGAGATTGGAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
* * *
4023 GG-TTGCGATCTAC
66 GGTTTTCAATCTGC
* * * * *
4036 CCCATGATCGAGGT-AGAGATTGGATGGTTTTCAATCTGCCCCATGATCGAGGTAAAAGATTGGA
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGT-GATCTGCCCCATGATCGGGGTAAGAGATTGGA
* * * *
4100 TGG-ATGCGATCTAC
65 TGGTTTTCAATCTGC
* * * *
4114 CCCATGATCGGGGTAAGAGATCT-GATGGTTTTCAATCTGCCCCGTGATCGAGGTAAGAGATTGG
1 CCCATGATCGGGGTAAGAGAT-TGGATGGTTGT-GATCTGCCCCATGATCGGGGTAAGAGATTGG
*
4178 ATGGTTTTCAATCTAC
64 ATGGTTTTCAATCTGC
* * * * * * * *
4194 CCCTTGATCGGGGTAAGTGATTGGATGGTTGCGATCTGCCCTATGATTGGGGTAAAAGATCGTAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
4259 GGTTTTCAATCTGC
66 GGTTTTCAATCTGC
*
4273 CCGATGATCGGGGTAAGAGATTGGAT
1 CCCATGATCGGGGTAAGAGATTGGAT
4299 TTGATGTCGA
Statistics
Matches: 420, Mismatches: 62, Indels: 22
0.83 0.12 0.04
Matches are distributed among these distances:
71 13 0.03
72 18 0.04
73 28 0.07
74 1 0.00
75 1 0.00
76 1 0.00
77 1 0.00
78 50 0.12
79 272 0.65
80 35 0.08
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (79 bp):
CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAGAGATTGGAT
GGTTTTCAATCTGC
Found at i:4014 original size:33 final size:32
Alignment explanation
Indices: 3964--4067 Score: 111
Period size: 33 Copynumber: 3.0 Consensus size: 32
3954 TTAAATCTGT
*
3964 CCCATGATCAGTGTAAGAGATTGGATGGTTTTC
1 CCCATGATC-GGGTAAGAGATTGGATGGTTTTC
3997 CCCATGATCGGGATAAGAGATTGGATGGTTGCGATCTAC
1 CCCATGATCGGG-TAAGAGATTGGATGGTT----T-T-C
4036 CCCATGATCGAGGT-AGAGATTGGATGGTTTTC
1 CCCATGATCG-GGTAAGAGATTGGATGGTTTTC
4068 AATCTGCCCC
Statistics
Matches: 62, Mismatches: 1, Indels: 17
0.77 0.01 0.21
Matches are distributed among these distances:
32 3 0.05
33 27 0.44
34 1 0.02
37 1 0.02
38 16 0.26
39 12 0.19
40 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (32 bp):
CCCATGATCGGGTAAGAGATTGGATGGTTTTC
Found at i:4227 original size:119 final size:119
Alignment explanation
Indices: 3727--4298 Score: 614
Period size: 119 Copynumber: 4.9 Consensus size: 119
3717 TTCAACTTGT
* *
3727 CCCATGATCGGGGTAAGAGATTGGATGGTTGTGATCTACCCCATGATCGGGGTAAGAGATCAGAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGCGATCTACCCCATGATCGGGGTAAGAGATCTGAT
* * * * * * * *
3792 GGTTTTTAATCTGCCCCATAATTGGGGTAAGAGATTAGATGGCTGT-GATCTGC
66 GGTTTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTTTCAATCTGC
* * * * * **
3845 CCCATGATCAGGGTAAGAGATCGGATGGTTTTCTATTTGTCCCATGATCGGGGTAAGAGAT-TAG
1 CCCATGATCGGGGTAAGAGATTGGATGG-TTGCGATCTACCCCATGATCGGGGTAAGAGATCT-G
* * * * * * *
3909 ATGG-CTGCGATCTGCCTCATGATCG-GGATAAGAGATTGGGTGGTTTTAAATCTGT
64 ATGGTTTTCAATCTGCCCCATGATCGAGG-TAAGAGATTGGATGGTTTTCAATCTGC
* * *
3964 CCCATGATCAGTGTAAGAGATTGGATGGTT----T-T-CCCCATGATCGGGATAAGAGAT-TGGA
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGCGATCTACCCCATGATCGGGGTAAGAGATCT-GA
* * *
4022 TGG-TTGCGATCTACCCCATGATCGAGGT-AGAGATTGGATGGTTTTCAATCTGC
65 TGGTTTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTTTCAATCTGC
* * *
4075 CCCATGATCGAGGTAAAAGATTGGATGGATGCGATCTACCCCATGATCGGGGTAAGAGATCTGAT
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGCGATCTACCCCATGATCGGGGTAAGAGATCTGAT
* *
4140 GGTTTTCAATCTGCCCCGTGATCGAGGTAAGAGATTGGATGGTTTTCAATCTAC
66 GGTTTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTTTCAATCTGC
* * * * * *
4194 CCCTTGATCGGGGTAAGTGATTGGATGGTTGCGATCTGCCCTATGATTGGGGTAAAAGATC-GTA
1 CCCATGATCGGGGTAAGAGATTGGATGGTTGCGATCTACCCCATGATCGGGGTAAGAGATCTG-A
* *
4258 TGGTTTTCAATCTGCCCGATGATCGGGGTAAGAGATTGGAT
65 TGGTTTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGAT
4299 TTGATGTCGA
Statistics
Matches: 383, Mismatches: 56, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
111 47 0.12
112 45 0.12
113 3 0.01
114 1 0.00
115 1 0.00
116 1 0.00
117 28 0.07
118 80 0.21
119 177 0.46
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (119 bp):
CCCATGATCGGGGTAAGAGATTGGATGGTTGCGATCTACCCCATGATCGGGGTAAGAGATCTGAT
GGTTTTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGGTTTTCAATCTGC
Found at i:4733 original size:50 final size:51
Alignment explanation
Indices: 4507--4722 Score: 214
Period size: 50 Copynumber: 4.4 Consensus size: 51
4497 TTCATCGTTG
* *
4507 CGGCCTCAAT-CATTCCCATCACATTTTCTAAGGTA-CTGGGTTCGCCATTA
1 CGGCCTCAATCCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCGCCATTA
*
4557 CGGCCTCAATCC-TTCTCATCACATCTTCTAAGGTATCGGGTTCGCCATTA
1 CGGCCTCAATCCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCATTA
* * * * * * * * * *
4607 CGGCCTTAA-CCTTTCCCTTTATATCTTC-ATGGTGTCGGATTTGCTATTG
1 CGGCCTCAATCCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCATTA
* * *
4656 CAGCCTCAATCCTTGT--CATCACATCTTCTAAGGTATCGGGTTTGCCATTG
1 CGGCCTCAATCCTT-TCCCATCACATCTTCTAAGGTATCGGGTTCGCCATTA
4706 CGGCCTCAA-CCTTTCCC
1 CGGCCTCAATCCTTTCCC
4723 TTTATGTCTT
Statistics
Matches: 135, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
48 1 0.01
49 37 0.27
50 94 0.70
51 3 0.02
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.34
Consensus pattern (51 bp):
CGGCCTCAATCCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCATTA
Found at i:6590 original size:18 final size:18
Alignment explanation
Indices: 6569--6603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6559 TGACTTTCCT
6569 TTCTTTTCTTTCTTTTTC
1 TTCTTTTCTTTCTTTTTC
* *
6587 TTCTTTTTTTTGTTTTT
1 TTCTTTTCTTTCTTTTT
6604 TTTGTATTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TTCTTTTCTTTCTTTTTC
Found at i:10665 original size:3 final size:3
Alignment explanation
Indices: 10657--10684 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10647 TGATATGCTG
10657 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10685 CCAATAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17914 original size:151 final size:150
Alignment explanation
Indices: 17705--17999 Score: 527
Period size: 151 Copynumber: 2.0 Consensus size: 150
17695 ATGTCAATAG
17705 ACAGGCGAAAAGGGTGGACGACACTATCGCTACTAAAAGTTAGAGAAGAGGAGAAGAGTTTTACC
1 ACAGGCGAAAAGGGTGGACGACACTATCGCTACTAAAAGTTAGAGAAGAGGAGAAGAGTTTTACC
*
17770 TGCTTGGATTAGTGTCAAAATATATAGCAAAAGGCTCTGGCAAATGACTCGATTCAAGAAACATA
66 TGCTTGGATTAGTGTCAAAATATATAGC-AAAGGCTCTGGCAAATGACTCGATTCAAGAAACAGA
17835 TTGAAGAATGAAGAATGAAGA
130 TTGAAGAATGAAGAATGAAGA
* *
17856 ACAGGCGAAAAGGGTGGACGACACTATCGTTACTAAAAGTTTGAGAAGAGGAGAAGAGTTTTACC
1 ACAGGCGAAAAGGGTGGACGACACTATCGCTACTAAAAGTTAGAGAAGAGGAGAAGAGTTTTACC
* * *
17921 TGCTTGGATTAGTGTCAAGATATGTAGCAAAGGCTCTGGCAAATGACTCGATTCAAGAAGCAGAT
66 TGCTTGGATTAGTGTCAAAATATATAGCAAAGGCTCTGGCAAATGACTCGATTCAAGAAACAGAT
17986 TGAAGAATGAAGAA
131 TGAAGAATGAAGAA
18000 CAAAGAGAAT
Statistics
Matches: 138, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
150 49 0.36
151 89 0.64
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (150 bp):
ACAGGCGAAAAGGGTGGACGACACTATCGCTACTAAAAGTTAGAGAAGAGGAGAAGAGTTTTACC
TGCTTGGATTAGTGTCAAAATATATAGCAAAGGCTCTGGCAAATGACTCGATTCAAGAAACAGAT
TGAAGAATGAAGAATGAAGA
Found at i:25285 original size:25 final size:25
Alignment explanation
Indices: 25241--25288 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
25231 GTGTTTCATT
*
25241 TTTTTTCTTTATTTTCAATTTTTTC
1 TTTTGTCTTTATTTTCAATTTTTTC
25266 TTTTGTCTCTTATTTT-AATTTTT
1 TTTTGTCT-TTATTTTCAATTTTT
25289 AATTAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTGTCTTTATTTTCAATTTTTTC
Found at i:33957 original size:23 final size:23
Alignment explanation
Indices: 33914--33957 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
33904 ATATTTTAAT
* *
33914 TTGTTATTGCTTTTTTGTATTGA
1 TTGTTATTGCTTTTATATATTGA
33937 TTGTTATTGCTTTTATATATT
1 TTGTTATTGCTTTTATATATT
33958 ACAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.66
Consensus pattern (23 bp):
TTGTTATTGCTTTTATATATTGA
Found at i:35184 original size:115 final size:116
Alignment explanation
Indices: 34967--35230 Score: 329
Period size: 115 Copynumber: 2.3 Consensus size: 116
34957 TTTGGTCCTA
* ** * *
34967 TTTCTAGCTTTGTTC-ACTATTTCCCGCGCTTTGCCTTTCTTTGTCCAAGCTAAGTCATCATACG
1 TTTCTAGCTTTGTCCTA-TATTTCATGTGCTTTGCCTTTCTTTGTCCAAGCTAAATCATCATACG
* * * * *
35031 CAATCTATTTTGAGTCGTTTACTACTTTGTTGACCAAACTCTTTTGGTCTCG
65 CAATCTATTCTAAGTCATTGACTACTCTGTTGACCAAACTCTTTTGGTCTCG
** *
35083 TTTCTAGCTTTGTCCTATATTTTTTGTGCTTTGCCTTT-TTTGTCCAAG-TCAAATCATCATACT
1 TTTCTAGCTTTGTCCTATATTTCATGTGCTTTGCCTTTCTTTGTCCAAGCT-AAATCATCATACG
* *
35146 TAAT-TCATTCTAAGTCATTGACTACTCTGTTGACCAAACTCTTTTGGTCTTG
65 CAATCT-ATTCTAAGTCATTGACTACTCTGTTGACCAAACTCTTTTGGTCTCG
*
35198 TTTCTAGCTTTGTCCTCTATTTCATGTGCTTTG
1 TTTCTAGCTTTGTCCTATATTTCATGTGCTTTG
35231 ACTATTTGTT
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
114 2 0.02
115 94 0.73
116 31 0.24
117 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.46
Consensus pattern (116 bp):
TTTCTAGCTTTGTCCTATATTTCATGTGCTTTGCCTTTCTTTGTCCAAGCTAAATCATCATACGC
AATCTATTCTAAGTCATTGACTACTCTGTTGACCAAACTCTTTTGGTCTCG
Found at i:36700 original size:116 final size:116
Alignment explanation
Indices: 36462--36710 Score: 261
Period size: 116 Copynumber: 2.1 Consensus size: 116
36452 AGCTCTGTCC
** * * *
36462 TCTATTTCTTATGCTTTTTCTTTCTTCGTCCAAGTCGATTTATCATATGCAACCCATTCTAAGTC
1 TCTATTTCTCGTGCTTTTCCTTTCTTCGTCCAAGTCGAGTCATCATATGCAACCCATTCTAAGTC
* *
36527 ATTGAATACTCTATTAACCAAACTCTTTTGGTCCCATTTTCAGCTTGATCC
66 ATTGAAGACTCTATTAACCAAACTCTTTTGGTCCCATTTTCAGCTTGATCA
* * ** * *
36578 TTTATTTTTCGTGCTTTTCCTTTCTTTTTCCAAGTCGAGTCATCATACT-CAATCCATTCTGAGT
1 TCTATTTCTCGTGCTTTTCCTTTCTTCGTCCAAGTCGAGTCATCATA-TGCAACCCATTCTAAGT
* * ** *** *
36642 CGTTGACGACTCTATTGGCCAAACTCTTTTGGTCTTGTTTGT-ATCTTTG-TCA
65 CATTGAAGACTCTATTAACCAAACTCTTTTGGTCCCATTT-TCAGC-TTGATCA
36694 TCTATTTCTCGTGCTTT
1 TCTATTTCTCGTGCTTT
36711 GGCTATTTGT
Statistics
Matches: 107, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
116 102 0.95
117 5 0.05
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.46
Consensus pattern (116 bp):
TCTATTTCTCGTGCTTTTCCTTTCTTCGTCCAAGTCGAGTCATCATATGCAACCCATTCTAAGTC
ATTGAAGACTCTATTAACCAAACTCTTTTGGTCCCATTTTCAGCTTGATCA
Found at i:39574 original size:115 final size:116
Alignment explanation
Indices: 39388--39717 Score: 432
Period size: 116 Copynumber: 2.9 Consensus size: 116
39378 GTTTCTATCT
* * *
39388 TTGTCCTCTGTTTCAC-GTGCTTTGCCTTCCTTTGTCCAAGTCGATTCATCATACACAATTCATT
1 TTGTCCTCTGTTTC-CTGTGCTTTGCCTTTCTTTGTCCAAGTTGATTCATCATACACAATCCATT
* * * * **
39452 CTAAGTCGTTGACTCCTCTGCTGACCAAACTCTTT-GGTCTTTTTTCAAGCA
65 TTGAGTCGTTGACTACTCTGTTGACCAAACTCTTTCGGTCTCCTTTCAAGCA
* * *
39503 TTGTCCTCTGTTTCCTATGCTTTGCCTTTCTTTGCCCAAGTTGATTCATCATGCACAATCCATTT
1 TTGTCCTCTGTTTCCTGTGCTTTGCCTTTCTTTGTCCAAGTTGATTCATCATACACAATCCATTT
*
39568 TGAGTCGTTGACTACTCTGTTGACCAAACTCTTTCGGTCTCCTTTCTAGCA
66 TGAGTCGTTGACTACTCTGTTGACCAAACTCTTTCGGTCTCCTTTCAAGCA
* * * * * *
39619 TTGTCCTCTATTT-TTCGTGCTTTGCCTTTCTTTGTCCAAGTTAAGTAATCATACTCAATCCATT
1 TTGTCCTCTGTTTCCT-GTGCTTTGCCTTTCTTTGTCCAAGTTGATTCATCATACACAATCCATT
* *
39683 TTGAGTCGTTAACTACTCTATTGACCAAACTCTTT
65 TTGAGTCGTTGACTACTCTGTTGACCAAACTCTTT
39718 TTTTCTTGTT
Statistics
Matches: 188, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
114 1 0.01
115 88 0.47
116 99 0.53
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.42
Consensus pattern (116 bp):
TTGTCCTCTGTTTCCTGTGCTTTGCCTTTCTTTGTCCAAGTTGATTCATCATACACAATCCATTT
TGAGTCGTTGACTACTCTGTTGACCAAACTCTTTCGGTCTCCTTTCAAGCA
Found at i:39739 original size:116 final size:116
Alignment explanation
Indices: 39368--39747 Score: 426
Period size: 116 Copynumber: 3.3 Consensus size: 116
39358 TTTTTTCCCT
* * * * * *
39368 TTTTGGT-TCTGTTTCTATCTTTGTCCTCTGTTTCACGTGCTTTGCCTTCCTTTGTCCAAGTCGA
1 TTTTGGTCT-TGTTTCTAGCATTGTCCTCTATTTTACGTGCTTTGCCTTTCTTTGTCCAAGTTGA
* * * * *
39432 TTCATCATACACAATTCATTCTAAGTCGTTGACTCCTCTGCTGACCAAACTC
65 TTCATCATACACAATCCATTTTGAGTCGTTGACTACTCTGTTGACCAAACTC
* * * *
39484 -TTTGGTCTTTTTTCAAGCATTGTCCTCTGTTTCCTA--TGCTTTGCCTTTCTTTGCCCAAGTTG
1 TTTTGGTCTTGTTTCTAGCATTGTCCTCTATTT--TACGTGCTTTGCCTTTCTTTGTCCAAGTTG
*
39546 ATTCATCATGCACAATCCATTTTGAGTCGTTGACTACTCTGTTGACCAAACTC
64 ATTCATCATACACAATCCATTTTGAGTCGTTGACTACTCTGTTGACCAAACTC
* ** * * *
39599 TTTCGGTCTCCTTTCTAGCATTGTCCTCTATTTTTCGTGCTTTGCCTTTCTTTGTCCAAGTTAAG
1 TTTTGGTCTTGTTTCTAGCATTGTCCTCTATTTTACGTGCTTTGCCTTTCTTTGTCCAAGTTGAT
* * * *
39664 TAATCATACTCAATCCATTTTGAGTCGTTAACTACTCTATTGACCAAACTC
66 TCATCATACACAATCCATTTTGAGTCGTTGACTACTCTGTTGACCAAACTC
** * * *
39715 TTTTTTTCTTGTTTTTAGCTTTGTCTTCTATTT
1 TTTTGGTCTTGTTTCTAGCATTGTCCTCTATTT
39748 CCCTGCTTTG
Statistics
Matches: 222, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
114 1 0.00
115 96 0.43
116 124 0.56
117 1 0.00
ACGTcount: A:0.17, C:0.25, G:0.13, T:0.45
Consensus pattern (116 bp):
TTTTGGTCTTGTTTCTAGCATTGTCCTCTATTTTACGTGCTTTGCCTTTCTTTGTCCAAGTTGAT
TCATCATACACAATCCATTTTGAGTCGTTGACTACTCTGTTGACCAAACTC
Found at i:40541 original size:5 final size:5
Alignment explanation
Indices: 40531--40562 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
40521 CATAATTAAT
40531 TCATA TCATA TCATA TCATA TCATA TCATA TC
1 TCATA TCATA TCATA TCATA TCATA TCATA TC
40563 TTTCCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (5 bp):
TCATA
Found at i:41406 original size:49 final size:49
Alignment explanation
Indices: 41330--41801 Score: 359
Period size: 49 Copynumber: 9.6 Consensus size: 49
41320 GGTTTGTCAC
* *
41330 TGCGGCCTC-ACCTTTCCCTTCATATCTTCATGGTACCGGATTTGCTGT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCTGT
* ** * *
41378 TGCGGCCTCAATCC-TTCCCTTCACATCTTCTAAAGTATCGGGTTTG-TCGT
1 TGCGGCCTCAA-CCTTTCCCTTCATATCTTC-ATGGTACCGGGTTCGCT-GT
* * * * * *
41428 TGCAGCTTCGACCTTTCCTTTCATATGC-TCATGGTACCGGGTTCACCGT
1 TGCGGCCTCAACCTTTCCCTTCATAT-CTTCATGGTACCGGGTTCGCTGT
* *
41477 TGTGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCGGGTTCG-TCGT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCT-GT
* * * * *
41526 TGCAGCCTCAA-CTTTTCCTATCACATCTTCATGGTACCGGATTCGCCGT
1 TGCGGCCTCAACCTTTCCCT-TCATATCTTCATGGTACCGGGTTCGCTGT
* * ** * *
41575 TACGGCCTCAATCC-TTCCTTTCACT-TCTTCTAAAGTACCGGGTTAG-TCAT
1 TGCGGCCTCAA-CCTTTCCCTTCA-TATCTTC-ATGGTACCGGGTTCGCT-GT
* * * * *
41625 TGCAGCCTCAACCTTTCCTTTCATATCCTCATGGTACCAGGTTCGCTAT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCTGT
* * * * * * *
41674 CGCGGCCTTATCCTTTCCCATCATATCTTCATGATACTGGGTTCGCCGT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCTGT
* * * * * * * * *
41723 TGTGGCATCAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTTGCCGT
1 TGCGGCCTCAACCTTTCCCTTCATATC-TTCATGGTACCGGGTTCGCTGT
41773 TGCGGCCTCAACCTTTCCCTTCATATCTT
1 TGCGGCCTCAACCTTTCCCTTCATATCTT
41802 AGTATTTTTT
Statistics
Matches: 327, Mismatches: 77, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
48 17 0.05
49 195 0.60
50 113 0.35
51 2 0.01
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (49 bp):
TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCTGT
Found at i:41613 original size:148 final size:147
Alignment explanation
Indices: 41330--41801 Score: 368
Period size: 148 Copynumber: 3.2 Consensus size: 147
41320 GGTTTGTCAC
* * * *
41330 TGCGGCCTC-ACCTTTCCCTTCATATCTTCATGGTACC-GGATTTGCTGTTGCGGCCTCAATCC-
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGG-TTCGCTATCGCAGCCTCAA-CCT
* * * * * * * * * * ** *
41392 TTCCCTTCACATCTTC-TAAAGTATCGGGTTTGTCGTTGCAGCTTCGACCTTTCCTTTCATATGC
64 TTCCCATCACATCTTCAT-GA-TACCGGATTCGCCGTTACGGCATCAACCTTTCCCATCACAT-C
**
41456 -TC-ATGGTACCGGGTTCACCGT
126 TTCTAAAGTACCGGGTT-ACCGT
* * * *
41477 TGTGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCGGGTTCGTCGT-T-GCAGCCTCAACTT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCG-C-TATCGCAGCCTCAACCT
* * * ** *
41540 TTCCTATCACATCTTCATGGTACCGGATTCGCCGTTACGGCCTCAATCC-TTCCTTTCACTTCTT
64 TTCCCATCACATCTTCATGATACCGGATTCGCCGTTACGGCATCAA-CCTTTCCCATCACATCTT
* *
41604 CTAAAGTACCGGGTTAGTCAT
128 CTAAAGTACCGGGTTA-CCGT
* * * * * *
41625 TGCAGCCTCAACCTTTCCTTTCATATCCTCATGGTACCAGGTTCGCTATCGCGGCCTTATCCTTT
1 TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCGCTATCGCAGCCTCAACCTTT
* * * ** *
41690 CCCATCATATCTTCATGATACTGGGTTCGCCGTTGTGGCATCAACCTTTCCCATCACATCTTTTA
66 CCCATCACATCTTCATGATACCGGATTCGCCGTTACGGCATCAACCTTTCCCATCACATCTTCTA
* * *
41755 AGGTATCGGGTTTGCCGT
131 AAGTACCGGG-TTACCGT
41773 TGCGGCCTCAACCTTTCCCTTCATATCTT
1 TGCGGCCTCAACCTTTCCCTTCATATCTT
41802 AGTATTTTTT
Statistics
Matches: 258, Mismatches: 53, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
146 2 0.01
147 44 0.17
148 204 0.79
149 7 0.03
150 1 0.00
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (147 bp):
TGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCAGGTTCGCTATCGCAGCCTCAACCTTT
CCCATCACATCTTCATGATACCGGATTCGCCGTTACGGCATCAACCTTTCCCATCACATCTTCTA
AAGTACCGGGTTACCGT
Found at i:41691 original size:197 final size:197
Alignment explanation
Indices: 41334--41801 Score: 571
Period size: 197 Copynumber: 2.4 Consensus size: 197
41324 TGTCACTGCG
* * * *
41334 GCCTCACCTTTCCCT-TCATATCTTCATGGTACCGGATTTGCTGTTGCGGCCTCAATCCTTCCCT
1 GCCTCAACTTTTCCTATCACATCTTCATGGTACCGGATTTGCCGTTGCGGCCTCAATCCTTCCCT
* * * * * *
41398 TCACATCTTCTAAAGTATCGGGTTTGTCGTTGCAGCTTCGACCTTTCCTTTCATATGCTCATGGT
66 TCACATCTTCTAAAGTACCGGGTTAGTCATTGCAGCCTCAACCTTTCCTTTCATATCCTCATGGT
* * * * * * * *
41463 ACCGGGTTCACCGTTGTGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCGGGTTCGTCGTTG
131 ACCAGGTTCACCATCGCGGCCTCAACCTTTCCCATCATATCTTCATGATACCGGGTTCGCCGTTG
41528 CA
196 CA
* * *
41530 GCCTCAACTTTTCCTATCACATCTTCATGGTACCGGATTCGCCGTTACGGCCTCAATCCTTCCTT
1 GCCTCAACTTTTCCTATCACATCTTCATGGTACCGGATTTGCCGTTGCGGCCTCAATCCTTCCCT
*
41595 TCACTTCTTCTAAAGTACCGGGTTAGTCATTGCAGCCTCAACCTTTCCTTTCATATCCTCATGGT
66 TCACATCTTCTAAAGTACCGGGTTAGTCATTGCAGCCTCAACCTTTCCTTTCATATCCTCATGGT
* * * * *
41660 ACCAGGTTCGCTATCGCGGCCTTATCCTTTCCCATCATATCTTCATGATACTGGGTTCGCCGTTG
131 ACCAGGTTCACCATCGCGGCCTCAACCTTTCCCATCATATCTTCATGATACCGGGTTCGCCGTTG
**
41725 TG
196 CA
* * * * * * *
41727 GCATCAACCTTTCCCATCACATCTTTTAAGGTATCGGGTTTGCCGTTGCGGCCTCAA-CCTTTCC
1 GCCTCAACTTTTCCTATCACATC-TTCATGGTACCGGATTTGCCGTTGCGGCCTCAATCC-TTCC
*
41791 CTTCATATCTT
64 CTTCACATCTT
41802 AGTATTTTTT
Statistics
Matches: 228, Mismatches: 41, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
196 13 0.06
197 176 0.77
198 39 0.17
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (197 bp):
GCCTCAACTTTTCCTATCACATCTTCATGGTACCGGATTTGCCGTTGCGGCCTCAATCCTTCCCT
TCACATCTTCTAAAGTACCGGGTTAGTCATTGCAGCCTCAACCTTTCCTTTCATATCCTCATGGT
ACCAGGTTCACCATCGCGGCCTCAACCTTTCCCATCATATCTTCATGATACCGGGTTCGCCGTTG
CA
Found at i:42780 original size:18 final size:20
Alignment explanation
Indices: 42757--42803 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
42747 CAACCTCTCG
42757 TTTTCTTTTTCCTT-CT-TT
1 TTTTCTTTTTCCTTCCTCTT
42775 TTTTC-TTTTCCTTCCTCTT
1 TTTTCTTTTTCCTTCCTCTT
*
42794 TTTTATTTTT
1 TTTTCTTTTT
42804 ATTTTTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 6 0.24
20 4 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTTTTTCCTTCCTCTT
Found at i:42783 original size:17 final size:19
Alignment explanation
Indices: 42757--42802 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42747 CAACCTCTCG
42757 TTTTCTTTTTCCTT-CT-TT
1 TTTTC-TTTTCCTTCCTCTT
42775 TTTTCTTTTCCTTCCTCTT
1 TTTTCTTTTCCTTCCTCTT
*
42794 TTTTATTTT
1 TTTTCTTTT
42803 TATTTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTCCTTCCTCTT
Found at i:45462 original size:30 final size:29
Alignment explanation
Indices: 45381--45458 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
45371 AATTTCGAGG
* *
45381 AAAATGTAATTTTGGGAAATTTTAGGGGTT
1 AAAATGTAATTTT-AGAAAATTTAGGGGTT
*
45411 CAAATGTAATTTTAGAAAATTTAGGGGTT
1 AAAATGTAATTTTAGAAAATTTAGGGGTT
* *
45440 AAAATGTATTTTTTGAAAA
1 AAAATGTAATTTTAGAAAA
45459 ATTTTGAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAATTTAGGGGTT
Found at i:45474 original size:30 final size:29
Alignment explanation
Indices: 45350--45504 Score: 95
Period size: 30 Copynumber: 5.3 Consensus size: 29
45340 AAGAAAAAAG
* * *
45350 GGTCAAAATG-AAGTTTTTGAGAATTTCGA
1 GGTCAAAATGTAA-TTTTAGAAAATTTAGA
* * *
45379 GG--AAAATGTAATTTTGGGAAATTTTAGG
1 GGTCAAAATGTAATTTT-AGAAAATTTAGA
*
45407 GGTTC-AAATGTAATTTTAGAAAATTTAGG
1 GG-TCAAAATGTAATTTTAGAAAATTTAGA
* * * *
45436 GGTTAAAATGTATTTTTTGAAAAATTTTGA
1 GGTCAAAATGTAATTTTAG-AAAATTTAGA
* * *
45466 GGTCAAAATATGATTTTGGAAAAGTTTA-A
1 GGTCAAAATGTAATTTTAGAAAA-TTTAGA
45495 GAGTCAAAAT
1 G-GTCAAAAT
45505 ACAAGGGCCA
Statistics
Matches: 99, Mismatches: 18, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
27 10 0.10
28 12 0.12
29 32 0.32
30 45 0.45
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTAGAAAATTTAGA
Found at i:45556 original size:29 final size:30
Alignment explanation
Indices: 45514--45594 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
45504 TACAAGGGCC
45514 AAATGTGATTTT-GGAAAATCTAAGGGTCA
1 AAATGTGATTTTGGGAAAATCTAAGGGTCA
* * *
45543 AAATGTGATTTTGGGAAAGTTTGAGGGTCA
1 AAATGTGATTTTGGGAAAATCTAAGGGTCA
45573 AAATGTGATTTTTGGGTAAAAT
1 AAATGTGA-TTTTGGG-AAAAT
45595 AAAGGCTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 12 0.27
30 22 0.49
31 7 0.16
32 4 0.09
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
AAATGTGATTTTGGGAAAATCTAAGGGTCA
Done.