Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012927.1 Kokia drynarioides strain JFW-HI SEQ_127944, 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: 113586
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 152 characters in sequence are not A, C, G, or T
Found at i:4687 original size:18 final size:18
Alignment explanation
Indices: 4664--4703 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
4654 TAAAAGTTTT
4664 ACTTGTGACATATATCGG
1 ACTTGTGACATATATCGG
*
4682 ACTTGTGACATCTATCGG
1 ACTTGTGACATATATCGG
4700 ACTT
1 ACTT
4704 CTACCGATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (18 bp):
ACTTGTGACATATATCGG
Found at i:5532 original size:48 final size:48
Alignment explanation
Indices: 5479--5640 Score: 207
Period size: 48 Copynumber: 3.3 Consensus size: 48
5469 TACACAACAA
* * * *
5479 CTTATAAACGTTTATGCTCATCATCTTGCACACGTTTACGCTTGTCAG
1 CTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTTGTCAG
5527 CTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTCGTCTCGTCAG
1 CTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACG--C-T-T-GTCAG
* * * *
5580 CTTATATACATTTACGCTCGTTAGCTTGCACACATTTACGCTCGTCAG
1 CTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTTGTCAG
5628 CTTATATACGTTT
1 CTTATATACGTTT
5641 TAAATTACTC
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
48 53 0.53
50 2 0.02
51 2 0.02
52 1 0.01
53 42 0.42
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (48 bp):
CTTATATACGTTTACGCTCGTCAGCTTGCACACGTTTACGCTTGTCAG
Found at i:5537 original size:24 final size:24
Alignment explanation
Indices: 5510--5640 Score: 127
Period size: 24 Copynumber: 5.2 Consensus size: 24
5500 CATCTTGCAC
*
5510 ACGTTTACGCTTGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTATAT
** *
5534 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATAT
5558 ACGTTTACGCTCGTCTCGTCAGCTTATAT
1 ACGTTTA----CG-CTCGTCAGCTTATAT
* * ** *
5587 ACATTTACGCTCGTTAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATAT
*
5611 ACATTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTATAT
5635 ACGTTT
1 ACGTTT
5641 TAAATTACTC
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
24 63 0.74
25 2 0.02
28 2 0.02
29 18 0.21
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTATAT
Found at i:5576 original size:29 final size:29
Alignment explanation
Indices: 5543--5625 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
5533 TACGTTTACG
*
5543 CTCGTCAGCTTGCACACGTTTACGCTCGT
1 CTCGTCAGCTTGCACACATTTACGCTCGT
** *
5572 CTCGTCAGCTTATATACATTTACGCTCG-
1 CTCGTCAGCTTGCACACATTTACGCTCGT
5600 -T--T-AGCTTGCACACATTTACGCTCGT
1 CTCGTCAGCTTGCACACATTTACGCTCGT
5625 C
1 C
5626 AGCTTATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
24 19 0.42
25 1 0.02
27 1 0.02
29 24 0.53
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (29 bp):
CTCGTCAGCTTGCACACATTTACGCTCGT
Found at i:6195 original size:19 final size:19
Alignment explanation
Indices: 6136--6196 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
6126 TTGGGTTTTC
*
6136 TTTTCTTCTCTTTCTTTACTCT
1 TTTTCTTCT-TTTCTTT--TAT
* ***
6158 TTTTATTCTTTTAAATTAT
1 TTTTCTTCTTTTCTTTTAT
6177 TTTTCTTCTTTTCTTTTAT
1 TTTTCTTCTTTTCTTTTAT
6196 T
1 T
6197 ATTAAATTAT
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
19 18 0.60
21 4 0.13
22 8 0.27
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTCTTCTTTTCTTTTAT
Found at i:10171 original size:40 final size:40
Alignment explanation
Indices: 10109--10185 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
10099 TTTAATATAA
* * *
10109 ATTTGAAAATTTTTATTAAAATAAATTAACTTATATAAAT
1 ATTTGAAAATTTTCAGTAAAATAAATTAAATTATATAAAT
10149 ATTTGAAAATTTTACAGT-AAATAAATTAAATTATATA
1 ATTTGAAAATTTT-CAGTAAAATAAATTAAATTATATA
10186 CATTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (40 bp):
ATTTGAAAATTTTCAGTAAAATAAATTAAATTATATAAAT
Found at i:10279 original size:185 final size:185
Alignment explanation
Indices: 10066--10523 Score: 826
Period size: 185 Copynumber: 2.5 Consensus size: 185
10056 CTAATTAATT
10066 TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAAATTTGAAAATTTTTATTAAAAT
1 TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAAATTTGAAAATTTTTATTAAAAT
10131 AAATTAACTTATATAAATATTTGAAAATTTTACAGTAAATAAATTAAATTATATACATTAAATTA
66 AAATTAACTTATATAAATATTTGAAAATTTTACAGTAAATAAATTAAATTATATACATTAAATTA
*
10196 AATTAATTAACTTATAAAAATATTTGAAACTTCTAATTTAAATTAAAGGGACAAA
131 AATTAATGAACTTATAAAAATATTTGAAACTTCTAATTTAAATTAAAGGGACAAA
10251 TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAAATTTGAAAATTTTTATTAAAAT
1 TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAAATTTGAAAATTTTTATTAAAAT
10316 AAATTAACTTATATAAATATTTGAAAATTTTACAGTAAATAAATTAAATTATATACATTAAATTA
66 AAATTAACTTATATAAATATTTGAAAATTTTACAGTAAATAAATTAAATTATATACATTAAATTA
10381 AATTAATGAACTTATAAAAATATTTGAAACTTCTAATTTAAATTAAAGGGACAAA
131 AATTAATGAACTTATAAAAATATTTGAAACTTCTAATTTAAATTAAAGGGACAAA
* * * ** * *
10436 TTTTAATATAAAATATTTTTTCCATTGAATTTATTTAATTTAAGTTTTGAAAAAGTTAATTTAAA
1 TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAA-ATTTGAAAATTTTTATTAAAA
*
10501 TAAATTAAATTATATAAATATTT
65 TAAATTAACTTATATAAATATTT
10524 TATCTAATAT
Statistics
Matches: 263, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
185 225 0.86
186 38 0.14
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (185 bp):
TTTTAATATAAAATATTTTATCCATTGAATTTATTTAATATAAATTTGAAAATTTTTATTAAAAT
AAATTAACTTATATAAATATTTGAAAATTTTACAGTAAATAAATTAAATTATATACATTAAATTA
AATTAATGAACTTATAAAAATATTTGAAACTTCTAATTTAAATTAAAGGGACAAA
Found at i:10356 original size:40 final size:40
Alignment explanation
Indices: 10294--10370 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
10284 TTTAATATAA
* * *
10294 ATTTGAAAATTTTTATTAAAATAAATTAACTTATATAAAT
1 ATTTGAAAATTTTCAGTAAAATAAATTAAATTATATAAAT
10334 ATTTGAAAATTTTACAGT-AAATAAATTAAATTATATA
1 ATTTGAAAATTTT-CAGTAAAATAAATTAAATTATATA
10371 CATTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (40 bp):
ATTTGAAAATTTTCAGTAAAATAAATTAAATTATATAAAT
Found at i:10797 original size:5 final size:5
Alignment explanation
Indices: 10787--10811 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10777 TGTTAGATTC
10787 ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT
10812 GAGTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:18763 original size:23 final size:24
Alignment explanation
Indices: 18733--18781 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
18723 TAAAATTAAC
* *
18733 AACATAAA-TATCAATATATACTA
1 AACATAAATTATCAACATATAATA
18756 AACATAAATTATCAACATATAATA
1 AACATAAATTATCAACATATAATA
18780 AA
1 AA
18782 TTTAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (24 bp):
AACATAAATTATCAACATATAATA
Found at i:20199 original size:2 final size:2
Alignment explanation
Indices: 20192--20217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20182 TAAGACATTG
20192 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
20218 GTCAAATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20928 original size:26 final size:28
Alignment explanation
Indices: 20899--20957 Score: 86
Period size: 26 Copynumber: 2.1 Consensus size: 28
20889 TGATATCTAA
20899 ATTTAAACTTTTTTTT-CT-AATTTGAT
1 ATTTAAACTTTTTTTTACTCAATTTGAT
*
20925 ATTTAAAGTTTTTTTTAGCTCAATTTGAT
1 ATTTAAACTTTTTTTTA-CTCAATTTGAT
20954 ATTT
1 ATTT
20958 GAATTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 15 0.52
28 2 0.07
29 12 0.41
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (28 bp):
ATTTAAACTTTTTTTTACTCAATTTGAT
Found at i:20985 original size:35 final size:36
Alignment explanation
Indices: 20918--20986 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
20908 TTTTTTTCTA
* *
20918 ATTTGATATTTAAAGTTTTTTTTAGCTCAATTTGAT
1 ATTTGATATTTAAAGTTTTTTTTACCTAAATTTGAT
** *
20954 ATTTGA-ATTTAATTTTTTTTTTCCCTAAATTTG
1 ATTTGATATTTAAAGTTTTTTTTACCTAAATTTG
20987 GTATCTAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 22 0.79
36 6 0.21
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (36 bp):
ATTTGATATTTAAAGTTTTTTTTACCTAAATTTGAT
Found at i:30213 original size:24 final size:25
Alignment explanation
Indices: 30184--30230 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30174 TGTTGTTTAA
*
30184 TTTTATGT-AATTTTTTAAACATAT
1 TTTTATGTAAAGTTTTTAAACATAT
*
30208 TTTTATTTAAAGTTTTTAAACAT
1 TTTTATGTAAAGTTTTTAAACAT
30231 GATTATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTATGTAAAGTTTTTAAACATAT
Found at i:30576 original size:18 final size:18
Alignment explanation
Indices: 30553--30590 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30543 TAATATAGTT
30553 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
*
30571 TTATTCGAGTTGTTCGAA
1 TTATTCGAGTTATTCGAA
30589 TT
1 TT
30591 CAAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:30668 original size:23 final size:23
Alignment explanation
Indices: 30624--30669 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
30614 AAAAAGAATT
* **
30624 TAACTTGATTCGTTTAACTCGAA
1 TAACTCGATTCGAATAACTCGAA
*
30647 TAACTCGATTCGAATAATTCGAA
1 TAACTCGATTCGAATAACTCGAA
30670 ATTCAAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTCGAA
Found at i:30778 original size:21 final size:23
Alignment explanation
Indices: 30748--30794 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
30738 GAAGGAGAGT
*
30748 AAAAGTTTTGAGG-AAAAA-GTA
1 AAAAGGTTTGAGGTAAAAATGTA
*
30769 AAAAGGTTTGGGGTAAAAATGTA
1 AAAAGGTTTGAGGTAAAAATGTA
30792 AAA
1 AAA
30795 TATTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (23 bp):
AAAAGGTTTGAGGTAAAAATGTA
Found at i:31419 original size:73 final size:73
Alignment explanation
Indices: 31331--31478 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
31321 CGAGGGCACC
31331 TGGGATTTGTATTTGAAGCTATGACATATAATAAGCAACCAGGGCATGCAGCTGCGAACATTCTT
1 TGGGATTTGTATTTGAAGCTATGACATATAATAAGCAACCAGGGCATGCAGCTGCGAACATTCTT
31396 GGTGTTGA
66 GGTGTTGA
31404 TGGGATTTGTATTTGAAGCTATGACATATAATAAGCAACCAGGGCATGCAGCTGCGAACATTCTT
1 TGGGATTTGTATTTGAAGCTATGACATATAATAAGCAACCAGGGCATGCAGCTGCGAACATTCTT
31469 GGTGTTGA
66 GGTGTTGA
31477 TG
1 TG
31479 AAGGCGACGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (73 bp):
TGGGATTTGTATTTGAAGCTATGACATATAATAAGCAACCAGGGCATGCAGCTGCGAACATTCTT
GGTGTTGA
Found at i:35662 original size:20 final size:20
Alignment explanation
Indices: 35637--35688 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
35627 CTAGTGAAAC
* * *
35637 TTCTACCGGTAGAACTTCAT
1 TTCTACCGATACAACTTCAG
*
35657 TTCTACCGATACAACTTTAG
1 TTCTACCGATACAACTTCAG
35677 TTCTACCGATAC
1 TTCTACCGATAC
35689 CTTGCAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (20 bp):
TTCTACCGATACAACTTCAG
Found at i:38763 original size:20 final size:20
Alignment explanation
Indices: 38738--38791 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
38728 CTCTAGTGAA
*
38738 ACTTCTACCGATAGAACTTT
1 ACTTCTACCGATACAACTTT
*
38758 ACTTCTACTGATACAACTTT
1 ACTTCTACCGATACAACTTT
* *
38778 AGTTTTACCGATAC
1 ACTTCTACCGATAC
38792 CTTGCCAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTT
Found at i:39208 original size:20 final size:20
Alignment explanation
Indices: 39183--39236 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
39173 CTCTAGTGAA
* *
39183 ACTTCTACTGGTAGAACTTT
1 ACTTCTACTGATACAACTTT
39203 ACTTCTACTGATACAACTTT
1 ACTTCTACTGATACAACTTT
* *
39223 AGTTCTACCGATAC
1 ACTTCTACTGATAC
39237 CTTGCCAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
ACTTCTACTGATACAACTTT
Found at i:39274 original size:445 final size:446
Alignment explanation
Indices: 38444--39334 Score: 1613
Period size: 445 Copynumber: 2.0 Consensus size: 446
38434 ATGGTTGATT
38444 GCTTATATTAGTGACCAATTTTTCAAAGAAAAATGAATGTCAAATTTGAACTTATTGAAAATTTA
1 GCTTATATTAGTGACCAATTTTTCAAAGAAAAATGAATGTCAAATTTGAACTTATTGAAAATTTA
38509 TGCTCCAAACCTGTATGTCTTAAATTGAAAATGATTTTTAGATAAGGGGAGCTTGAATCAAAAAT
66 TGCTCCAAACCTGTATGTCTTAAATTGAAAATGATTTTTAGATAAGGGGAGCTTGAATCAAAAAT
38574 GACTTTTATTAAGGGGGAGATATCTATTCAAAAACAAATTTAAAAAATGTTTTGTTATATCAAAA
131 GACTTTTATTAAGGGGGAGATATCTATTCAAAAACAAATTTAAAAAATGTTTTGTTATATCAAAA
*
38639 AGGGGGAGATTGTTAAATTAAGTCTTATTGGATAATATATTTTGATATAACAAATTAAAGTATTT
196 AGGGAGAGATTGTTAAATTAAGTCTTATTGGATAATATATTTTGATATAACAAATTAAAGTATTT
38704 TTGAGGAAAGCTAACTAGAAAAGACTCTAGTGAAACTTCTACCGATAGAACTTTACTTCTACTGA
261 TTGAGGAAAGCTAACTAGAAAAGACTCTAGTGAAACTTCTACCGATAGAACTTTACTTCTACTGA
*
38769 TACAACTTTAGTTTTACCGATACCTTGCCAACTTTTACCAAAACAAGTCAAGTCAGTAGCCAAAA
326 TACAACTTTAGTTCTACCGATACCTTGCCAACTTTTACCAAAACAAGTCAAGTCAGTAGCCAAAA
* * * *
38834 TTTAGGATCCCTTGTACTTCTACCGATACTCTGATGGGATTTACCTATACCAAATG
391 TTCAAGATCCCTTGTACTGCTACCGATACTCTGATGGGATTTACCGATACCAAATG
38890 GCTTATATTAGTGACCAATTTTTCAAAGAAAAATGAATGTCAAATTTGAACTTATTGAAAATTTA
1 GCTTATATTAGTGACCAATTTTTCAAAGAAAAATGAATGTCAAATTTGAACTTATTGAAAATTTA
** **
38955 TGCTCCAAACCTGTATGTCTTAAATTGAAAATGATTTTTATTTAAGGGGAGCTTGAATTGAAAAT
66 TGCTCCAAACCTGTATGTCTTAAATTGAAAATGATTTTTAGATAAGGGGAGCTTGAATCAAAAAT
*
39020 GACTTTTATTAA-GGGGAGATATCTATTCAGAAACAAATTTAAAAAATGTTTTGTTATATCAAAA
131 GACTTTTATTAAGGGGGAGATATCTATTCAAAAACAAATTTAAAAAATGTTTTGTTATATCAAAA
*
39084 AGGGAGAGATTGTTAAATTAAGTCTTATTGGATACTATATTTTGATATAACAAATTAAAGTATTT
196 AGGGAGAGATTGTTAAATTAAGTCTTATTGGATAATATATTTTGATATAACAAATTAAAGTATTT
* * *
39149 TTGAGGAAAGCTAAGTAGAAAAGACTCTAGTGAAACTTCTACTGGTAGAACTTTACTTCTACTGA
261 TTGAGGAAAGCTAACTAGAAAAGACTCTAGTGAAACTTCTACCGATAGAACTTTACTTCTACTGA
*
39214 TACAACTTTAGTTCTACCGATACCTTGCCAACTTTTACCGAAACAAGTCAAGTCAGTAGCCAAAA
326 TACAACTTTAGTTCTACCGATACCTTGCCAACTTTTACCAAAACAAGTCAAGTCAGTAGCCAAAA
* *
39279 TTCAAGATCCCTTGTACTGCTACTGATACTCTGATGGGTTTTACCGATACCAAATG
391 TTCAAGATCCCTTGTACTGCTACCGATACTCTGATGGGATTTACCGATACCAAATG
39335 AAACCCTCAA
Statistics
Matches: 427, Mismatches: 18, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
445 289 0.68
446 138 0.32
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.34
Consensus pattern (446 bp):
GCTTATATTAGTGACCAATTTTTCAAAGAAAAATGAATGTCAAATTTGAACTTATTGAAAATTTA
TGCTCCAAACCTGTATGTCTTAAATTGAAAATGATTTTTAGATAAGGGGAGCTTGAATCAAAAAT
GACTTTTATTAAGGGGGAGATATCTATTCAAAAACAAATTTAAAAAATGTTTTGTTATATCAAAA
AGGGAGAGATTGTTAAATTAAGTCTTATTGGATAATATATTTTGATATAACAAATTAAAGTATTT
TTGAGGAAAGCTAACTAGAAAAGACTCTAGTGAAACTTCTACCGATAGAACTTTACTTCTACTGA
TACAACTTTAGTTCTACCGATACCTTGCCAACTTTTACCAAAACAAGTCAAGTCAGTAGCCAAAA
TTCAAGATCCCTTGTACTGCTACCGATACTCTGATGGGATTTACCGATACCAAATG
Found at i:40557 original size:16 final size:17
Alignment explanation
Indices: 40538--40582 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
40528 ATTAAAAATA
*
40538 TATAAAATATTATA-TT
1 TATAAAATATTACATTT
*
40554 TATAAAATATCACATTT
1 TATAAAATATTACATTT
40571 TATAAATATATT
1 TATAAA-ATATT
40583 TGTACAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAAAATATTACATTT
Found at i:41039 original size:2 final size:2
Alignment explanation
Indices: 41027--41059 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
41017 TCTCTTTGTG
*
41027 AT AT CT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41060 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43084 original size:19 final size:19
Alignment explanation
Indices: 43060--43102 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
43050 AAACATAAAT
43060 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
43079 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
43098 TAAAT
1 TAAAT
43103 CTTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:44644 original size:14 final size:15
Alignment explanation
Indices: 44621--44653 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
44611 ATAAATAAAT
*
44621 AAATAGAAAAA-TAA
1 AAATAAAAAAATTAA
44635 AAATAAAAAAATTAA
1 AAATAAAAAAATTAA
44650 AAAT
1 AAAT
44654 TGGGTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (15 bp):
AAATAAAAAAATTAA
Found at i:48308 original size:21 final size:21
Alignment explanation
Indices: 48266--48309 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
48256 CCACAATTTT
**
48266 CTTTTGAAAATCTATAGTTTG
1 CTTTTGAAAATCTATAAATTG
48287 CTTTTGAAAATCTATAAATTG
1 CTTTTGAAAATCTATAAATTG
48308 CT
1 CT
48310 GCTTAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (21 bp):
CTTTTGAAAATCTATAAATTG
Found at i:50694 original size:19 final size:19
Alignment explanation
Indices: 50670--50712 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
50660 AAACATAAAT
50670 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
50689 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
50708 TAAAT
1 TAAAT
50713 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:54654 original size:29 final size:30
Alignment explanation
Indices: 54605--54661 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
54595 GCTAAGTATT
* * *
54605 GTTCTAGAAAAAGTAATTTTGAGAAGATCG
1 GTTCTAAAAAAACTAATTTTGACAAGATCG
54635 GTTCTAAAAAAACT-ATTTTGACAAGAT
1 GTTCTAAAAAAACTAATTTTGACAAGAT
54662 GGATTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
GTTCTAAAAAAACTAATTTTGACAAGATCG
Found at i:54803 original size:27 final size:28
Alignment explanation
Indices: 54750--54803 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
54740 TTTTTGTACT
* * *
54750 GATGATTCTGAAAAAGTAAATTTGGGAA
1 GATGATTCTGAAAAAATAAACTCGGGAA
*
54778 GATGGTTCTGAAAAAAT-AACTCGGGA
1 GATGATTCTGAAAAAATAAACTCGGGA
54804 TTCCTGGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.41, C:0.07, G:0.26, T:0.26
Consensus pattern (28 bp):
GATGATTCTGAAAAAATAAACTCGGGAA
Found at i:60644 original size:61 final size:62
Alignment explanation
Indices: 60579--60715 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 62
60569 TTGGTTCTCA
** *
60579 ATTAAATGAAACAAGAAGCCAAAAATAATGTGTTGAAAA-TATTTAAAAGAACTTCTATTTC
1 ATTAAATGAAACAAGAAGCCAAAAATAATGTGTACAAAAGTATTCAAAAGAACTTCTATTTC
* * * * * * *
60640 ATTAAATGATATAATATGCCAAAACTAATGTGTACAAAAGTATTCAAATGAACTTCTATTTT
1 ATTAAATGAAACAAGAAGCCAAAAATAATGTGTACAAAAGTATTCAAAAGAACTTCTATTTC
60702 ATTAAATGAAACAA
1 ATTAAATGAAACAA
60716 TATAAAAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 32 0.51
62 31 0.49
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (62 bp):
ATTAAATGAAACAAGAAGCCAAAAATAATGTGTACAAAAGTATTCAAAAGAACTTCTATTTC
Found at i:60718 original size:62 final size:61
Alignment explanation
Indices: 60579--60718 Score: 181
Period size: 62 Copynumber: 2.3 Consensus size: 61
60569 TTGGTTCTCA
* * ** *
60579 ATTAAATGAAACAAGAAGCCAAAAATAATGTGTTGAAAATATTTAAAAGAACTTCTATTTC
1 ATTAAATGAAACAATATGCCAAAAATAATGTGTACAAAATATTCAAAAGAACTTCTATTTC
* * * * *
60640 ATTAAATGATATAATATGCCAAAACTAATGTGTACAAAAGTATTCAAATGAACTTCTATTTT
1 ATTAAATGAAACAATATGCCAAAAATAATGTGTACAAAA-TATTCAAAAGAACTTCTATTTC
60702 ATTAAATGAAACAATAT
1 ATTAAATGAAACAATAT
60719 AAAAATAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
61 32 0.48
62 34 0.52
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (61 bp):
ATTAAATGAAACAATATGCCAAAAATAATGTGTACAAAATATTCAAAAGAACTTCTATTTC
Found at i:66718 original size:15 final size:15
Alignment explanation
Indices: 66700--66729 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66690 ATTGTGAAAG
66700 ATGAAAAAGAAATGA
1 ATGAAAAAGAAATGA
*
66715 ATGAAAAAGATATGA
1 ATGAAAAAGAAATGA
66730 GGCTCTGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
ATGAAAAAGAAATGA
Found at i:68695 original size:18 final size:18
Alignment explanation
Indices: 68654--68708 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
68644 AATCCCATAA
*
68654 GACGATGGGAATTGAGGT
1 GACGATGGGAATTGAGAT
* * *
68672 GGCGATGAGAATTGATAT
1 GACGATGGGAATTGAGAT
*
68690 GACGATGGGAATTGTGAT
1 GACGATGGGAATTGAGAT
68708 G
1 G
68709 GGGATTGAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.05, G:0.40, T:0.25
Consensus pattern (18 bp):
GACGATGGGAATTGAGAT
Found at i:69835 original size:12 final size:12
Alignment explanation
Indices: 69818--69862 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
69808 GGTTGCGTCG
69818 CCCGATACATCT
1 CCCGATACATCT
69830 CCCGATACATCT
1 CCCGATACATCT
69842 CCCGATACATCT
1 CCCGATACATCT
69854 CCCGATACA
1 CCCGATACA
69863 ATGTTGCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.27, C:0.42, G:0.09, T:0.22
Consensus pattern (12 bp):
CCCGATACATCT
Found at i:70507 original size:31 final size:31
Alignment explanation
Indices: 70439--70507 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
70429 GACTATTCAC
* *
70439 ATAAAAAT-TATAAAAAATATTAATTAAATT
1 ATAAAAATCAATAAAAAATATTAAATAAATT
* *
70469 ATTAAAATCAATAAATAATATTAAATAATATT
1 ATAAAAATCAATAAAAAATATTAAATAA-ATT
70501 A-AAAAAT
1 ATAAAAAT
70508 AAGATTAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
30 7 0.22
31 21 0.66
32 4 0.12
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (31 bp):
ATAAAAATCAATAAAAAATATTAAATAAATT
Found at i:81889 original size:29 final size:30
Alignment explanation
Indices: 81852--81925 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
81842 TCAACAATGT
* * * * *
81852 CACAGATTAGGGC-ATACACATTCGACTTA
1 CACATATTAGGACAATACACAATCAACTAA
81881 CACATATTAGGACATATACACAATCAACTAA
1 CACATATTAGGACA-ATACACAATCAACTAA
81912 CACATATTAGGACA
1 CACATATTAGGACA
81926 CTTAAGCATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 11 0.29
31 27 0.71
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (30 bp):
CACATATTAGGACAATACACAATCAACTAA
Found at i:81900 original size:31 final size:31
Alignment explanation
Indices: 81865--81925 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
81855 AGATTAGGGC
* * *
81865 ATACACATTCGACTTACACATATTAGGACAT
1 ATACACAATCAACTAACACATATTAGGACAT
81896 ATACACAATCAACTAACACATATTAGGACA
1 ATACACAATCAACTAACACATATTAGGACA
81926 CTTAAGCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (31 bp):
ATACACAATCAACTAACACATATTAGGACAT
Found at i:85763 original size:29 final size:29
Alignment explanation
Indices: 85690--85769 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
85680 GATTAAATCA
*
85690 AAATTAAAGTTTCAAGTATATATTTGAACC
1 AAATTAAA-TTTCAAGTATATAATTGAACC
* **
85720 ACAATTAGAATTTCACGTATATAATTGCCCC
1 A-AATTA-AATTTCAAGTATATAATTGAACC
* *
85751 AAATTAAAATTCATGTATA
1 AAATTAAATTTCAAGTATA
85770 CAAATGCACA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
29 11 0.26
30 6 0.14
31 23 0.55
32 2 0.05
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (29 bp):
AAATTAAATTTCAAGTATATAATTGAACC
Found at i:87210 original size:51 final size:51
Alignment explanation
Indices: 87095--87332 Score: 282
Period size: 51 Copynumber: 4.6 Consensus size: 51
87085 TTTCATTTAA
* ** * * *
87095 TACTCACAATGACA-TATAGTCATCGGACCCCTTGTTTTGTATAGGAATTCATC
1 TACTCACGATGACACT-TAGTCATCGGA-CCCTTAATTCGTAAAGG-ATTCATT
* * * * *
87148 TACTCACGATGACACTGAGTCATCAGACCCTTAATTCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATTCGTAAAGGATTCATT
* *
87199 TACTCACGATGATACTTAGTCATCGGACCTTTAA-TCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATTC-GTAAAGGATTCATT
* * *
87250 TACTCACGATGACACTTAGTCATTGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCCTTAATTCGTAAAGGATTCATT
87301 TACTCACGATGACACTTAGTCATCGGACCCTT
1 TACTCACGATGACACTTAGTCATCGGACCCTT
87333 TCATTTATAG
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.01
51 123 0.77
52 11 0.07
53 22 0.14
54 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCCTTAATTCGTAAAGGATTCATT
Found at i:96467 original size:46 final size:43
Alignment explanation
Indices: 96381--96472 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 43
96371 TACAACATCT
96381 ATTTATTCAACCAAACACAAGAATACTATTACAGCTCTATTTC
1 ATTTATTCAACCAAACACAAGAATACTATTACAGCTCTATTTC
* *
96424 ATTTCATTCAACCAAACA-ATTGAATTACTGATTACAGTTCTATTTC
1 ATTT-ATTCAACCAAACACA-AGAA-TACT-ATTACAGCTCTATTTC
96470 ATT
1 ATT
96473 ACTAACACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 5 0.12
44 16 0.37
45 4 0.09
46 18 0.42
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (43 bp):
ATTTATTCAACCAAACACAAGAATACTATTACAGCTCTATTTC
Found at i:98242 original size:17 final size:17
Alignment explanation
Indices: 98211--98252 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
98201 GGAAAAAGTA
*
98211 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
98229 GTTAAAGAAGATGAAAG
1 GTTAAAGAAGATGAAAG
*
98246 TTTAAAG
1 GTTAAAG
98253 GTTAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.24
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:111038 original size:102 final size:102
Alignment explanation
Indices: 110862--111068 Score: 405
Period size: 102 Copynumber: 2.0 Consensus size: 102
110852 TGTCTTATGA
110862 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
1 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
110927 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
66 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
*
110964 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGTTGTGTTTT
1 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
111029 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
66 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
111066 CAT
1 CAT
111069 CAAGTTAAAT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (102 bp):
CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
Done.