Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003322.1 Kokia drynarioides strain JFW-HI SEQ_116017, 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: 77459
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:376 original size:4 final size:4
Alignment explanation
Indices: 353--435 Score: 89
Period size: 4 Copynumber: 20.2 Consensus size: 4
343 AACACATTAC
* * *
353 CTTT CTTT AC-TT CTTT -TTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
401 CTTT CCTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
436 CCGTTTATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
3 4 0.06
4 51 0.76
5 12 0.18
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:406 original size:17 final size:17
Alignment explanation
Indices: 386--435 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
376 CCTCTCCTTC
386 TTCCTTTCTTTCTTTCT
1 TTCCTTTCTTTCTTTCT
403 TTCCTTTCTTTCTTTCT
1 TTCCTTTCTTTCTTTCT
420 TTCCTTTCTTTCTTTC
1 TTCCTTTCTTTCTTTC
436 CCGTTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCCTTTCTTTCTTTCT
Found at i:2213 original size:19 final size:18
Alignment explanation
Indices: 2170--2223 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
2160 AAGTTTAACA
*
2170 CAAAAAAATATAAAAA-T
1 CAAAAATATATAAAAATT
*
2187 GAAAAATATATAAAAATT
1 CAAAAATATATAAAAATT
2205 CAGAAAATATATATAAAAT
1 CA-AAAATATATA-AAAAT
2224 CTAGAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 10 0.32
20 5 0.16
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (18 bp):
CAAAAATATATAAAAATT
Found at i:3611 original size:12 final size:12
Alignment explanation
Indices: 3596--3630 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
3586 TTTCTCAATA
*
3596 CACACACACGCG
1 CACACACACACG
3608 CACACACACACG
1 CACACACACACG
3620 CACACACACAC
1 CACACACACAC
3631 ACTGTCTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.40, C:0.51, G:0.09, T:0.00
Consensus pattern (12 bp):
CACACACACACG
Found at i:3614 original size:14 final size:14
Alignment explanation
Indices: 3595--3632 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3585 TTTTCTCAAT
*
3595 ACACACACACGCGC
1 ACACACACACGCAC
3609 ACACACACACGCAC
1 ACACACACACGCAC
3623 ACACACACAC
1 ACACACACAC
3633 TGTCTGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.42, C:0.50, G:0.08, T:0.00
Consensus pattern (14 bp):
ACACACACACGCAC
Found at i:14041 original size:58 final size:58
Alignment explanation
Indices: 13977--14090 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
13967 AAGGAAAGAT
13977 GTAATTAAAGGACTTCAATAACTAAGGCACTGTTTAATATGATTTACACACAAGGATG
1 GTAATTAAAGGACTTCAATAACTAAGGCACTGTTTAATATGATTTACACACAAGGATG
*
14035 GTAATTAAAGGACTTGAATAACTAAGGCACTGTTTAATATGATTTACACACAAGGA
1 GTAATTAAAGGACTTCAATAACTAAGGCACTGTTTAATATGATTTACACACAAGGA
14091 AAACTGCAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (58 bp):
GTAATTAAAGGACTTCAATAACTAAGGCACTGTTTAATATGATTTACACACAAGGATG
Found at i:17489 original size:3 final size:3
Alignment explanation
Indices: 17481--17518 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17471 TTTATAGAAA
17481 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
17519 AATATTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:30714 original size:4 final size:4
Alignment explanation
Indices: 30705--30731 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30695 ATTTGATTTC
30705 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
30732 AAAACCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:36159 original size:21 final size:20
Alignment explanation
Indices: 36133--36171 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
36123 TTGAGAATAA
*
36133 AAATTAATTTTATATTGTATT
1 AAATTAAATTT-TATTGTATT
36154 AAATTAAATTTTATTGTA
1 AAATTAAATTTTATTGTA
36172 GGGATAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
AAATTAAATTTTATTGTATT
Found at i:48775 original size:20 final size:20
Alignment explanation
Indices: 48747--48785 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
48737 ATTTAAAATT
48747 TTACCTAAA-AAGTTTTTAAA
1 TTACCTAAATAA-TTTTTAAA
*
48767 TTACTTAAATAATTTTTAA
1 TTACCTAAATAATTTTTAA
48786 CTGTCCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (20 bp):
TTACCTAAATAATTTTTAAA
Found at i:52810 original size:30 final size:30
Alignment explanation
Indices: 52774--52830 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52764 GATAGTTTAT
52774 ATTTTTATAATTTTTAAAGT-ATTAAATAAA
1 ATTTTTATAA-TTTTAAAGTGATTAAATAAA
* *
52804 ATTTTTATCATTTTCAAGTGATTAAAT
1 ATTTTTATAATTTTAAAGTGATTAAAT
52831 GACCTTCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (30 bp):
ATTTTTATAATTTTAAAGTGATTAAATAAA
Found at i:53731 original size:5 final size:5
Alignment explanation
Indices: 53721--53745 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53711 GAATGATTTG
53721 GAATT GAATT GAATT GAATT GAATT
1 GAATT GAATT GAATT GAATT GAATT
53746 AGAACGAGAA
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:0.20, T:0.40
Consensus pattern (5 bp):
GAATT
Found at i:68673 original size:6 final size:6
Alignment explanation
Indices: 68662--68687 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
68652 AATCAAAAGG
68662 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
68688 AGAGAGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:68761 original size:14 final size:14
Alignment explanation
Indices: 68744--68774 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
68734 AAGGTTTAAA
68744 AAATTTAATTAATT
1 AAATTTAATTAATT
*
68758 AAATTTATTTAATT
1 AAATTTAATTAATT
68772 AAA
1 AAA
68775 GATTTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:69668 original size:130 final size:131
Alignment explanation
Indices: 69524--70101 Score: 591
Period size: 130 Copynumber: 4.5 Consensus size: 131
69514 ATGTAATCAC
* *
69524 TTTTTAGTAAATTTATCAATCACTTGACTT-AGGTTGCCTCAAATTTACGCAA-CTAGATTTTAA
1 TTTTTAGTAAATTTATCAATCACTCGA-TTCAGGTTGCCTCAAATTTACGCAATC-AAATTTTAA
* * * * ** * *
69587 CCTTATGTTACTTTAATTGAAAAAGTATTCAGATTCTCCGAGGATTTAAAATGAACACGTAGAT-
64 TCTCAGGTTACTTTAATTGAAAAAATATTCAGATTCTCTTAGAATTTAATATGAACACGTAGATC
69651 ATT
129 ATT
* * * * * *
69654 TTTTTAATAAATTTATCAATCACTTGATTCAGGTTACCTCAAACTTATGTAATCAAATTTTAATC
1 TTTTTAGTAAATTTATCAATCACTCGATTCAGGTTGCCTCAAATTTACGCAATCAAATTTTAATC
* * *
69719 TCAGGTTATTTTAATTAAAAAAATATTTAGATTCTCTTAGAATTTAATATGAACACGTAG-TCAT
66 TCAGGTTACTTTAATTGAAAAAATATTCAGATTCTCTTAGAATTTAATATGAACACGTAGATCAT
69783 T
131 T
** * * *
69784 TTGCTAGTAAATTTATCAATCACTCGATTCAAGTTGCCTCAAATTTGCACAATCAAATTTTAATC
1 TTTTTAGTAAATTTATCAATCACTCGATTCAGGTTGCCTCAAATTTACGCAATCAAATTTTAATC
** * * * *
69849 TCAGGTTACTTTAATTGAAAATTTATTCAAATCCTCTTAGTATTTAATATGAACACGTA-ATCAC
66 TCAGGTTACTTTAATTGAAAAAATATTCAGATTCTCTTAGAATTTAATATGAACACGTAGATCAT
69913 T
131 T
* * ** * *
69914 CTTTTAGTAAATTTATCCATCACTCG-TTTGGAGTTGCTTCAAATTTACGCAATCAAATTATAAT
1 TTTTTAGTAAATTTATCAATCACTCGATTCAG-GTTGCCTCAAATTTACGCAATCAAATTTTAAT
* * * * * * * **
69978 -TATAGGTTAATTTAATTGGAAAAGTGTT-TGAATTCTCTTAAAATTTGGTATGAACACGTA-AT
65 CT-CAGGTTACTTTAATTGAAAAAATATTCAG-ATTCTCTTAGAATTTAATATGAACACGTAGAT
**
70040 CCCT
128 CATT
* * *
70044 CTTTTAGT-AATTTATCAACCACTCGATTCAAGTTGCCTCAAATTTACGCAATCAAATT
1 TTTTTAGTAAATTTATCAATCACTCGATTCAGGTTGCCTCAAATTTACGCAATCAAATT
70102 CAAATTCTCC
Statistics
Matches: 372, Mismatches: 68, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
129 47 0.13
130 324 0.87
131 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (131 bp):
TTTTTAGTAAATTTATCAATCACTCGATTCAGGTTGCCTCAAATTTACGCAATCAAATTTTAATC
TCAGGTTACTTTAATTGAAAAAATATTCAGATTCTCTTAGAATTTAATATGAACACGTAGATCAT
T
Found at i:70683 original size:78 final size:78
Alignment explanation
Indices: 70554--70708 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 78
70544 GCATCAATAT
* * * *
70554 AACATTATGGCACGTTGGCTATTAGTTTTGTTACAACTTAAACACAGCGTATTTAGAA-TGATTG
1 AACATTATGGCACGTTGGCTATTAATTTTGTTACAACTCAAACACACCGTATTTA-AAGTGATTA
70618 CAAACATAACATAG
65 CAAACATAACATAG
70632 AACATTATGGCACGTTGGCTATTAATTTTGTTACAACTCAAACACACCGTATTTAAAGTGATTAC
1 AACATTATGGCACGTTGGCTATTAATTTTGTTACAACTCAAACACACCGTATTTAAAGTGATTAC
70697 AAACATAACATA
66 AAACATAACATA
70709 TATGTATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
77 2 0.03
78 70 0.97
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (78 bp):
AACATTATGGCACGTTGGCTATTAATTTTGTTACAACTCAAACACACCGTATTTAAAGTGATTAC
AAACATAACATAG
Found at i:77128 original size:21 final size:21
Alignment explanation
Indices: 77083--77128 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
77073 TTTTGTACAT
* *
77083 AAATTATGATAATTTACCATT
1 AAATTATGATAATTTACAATA
77104 AAATTATTGATAATTTA-AATA
1 AAATTA-TGATAATTTACAATA
77125 AAAT
1 AAAT
77129 ATATCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATTATGATAATTTACAATA
Done.