Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012798.1 Kokia drynarioides strain JFW-HI SEQ_127811, 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: 23805
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 131 characters in sequence are not A, C, G, or T
Found at i:3476 original size:25 final size:25
Alignment explanation
Indices: 3442--3519 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 25
3432 AAACTTTTTA
*
3442 TTTTGCTCCAATAATGAGCAGATGG
1 TTTTGCTCCAACAATGAGCAGATGG
3467 TTTTGCTCCAACAAT-----GATGG
1 TTTTGCTCCAACAATGAGCAGATGG
* *
3487 TTTTTCTCCAACAATGAGCAAAGTGG
1 TTTTGCTCCAACAATGAGCAGA-TGG
3513 TTTTGCT
1 TTTTGCT
3520 ATTTTGGAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 19 0.44
25 15 0.35
26 9 0.21
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (25 bp):
TTTTGCTCCAACAATGAGCAGATGG
Found at i:10795 original size:11 final size:11
Alignment explanation
Indices: 10761--10798 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
10751 TTATCATAAA
*
10761 ATGTGACTAA-
1 ATGTGATTAAT
10771 ATGTGATT-AT
1 ATGTGATTAAT
10781 ATGTGATTAAT
1 ATGTGATTAAT
10792 ATGTGAT
1 ATGTGAT
10799 GTGATAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 1 0.04
10 15 0.60
11 9 0.36
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (11 bp):
ATGTGATTAAT
Found at i:10825 original size:49 final size:49
Alignment explanation
Indices: 10771--11054 Score: 250
Period size: 59 Copynumber: 5.4 Consensus size: 49
10761 ATGTGACTAA
*
10771 ATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTAAAATATTC
1 ATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* *
10820 ATGTGATTAAATGTGACTGAATGTTATTAATTTGTGATGTGATAAATGTTGAAATATTC
1 ATGTGATT--A--T-A-TG--TG--ATTAATATGTGATGTGATAAATGCTGAAATATTC
*
10879 ATGTGATTAAATGTGACTAAAAGTGATTAATATGTGATGTGATAAACT-CTGAAACATTC
1 ATGTGATT--A--T-A-T----GTGATTAATATGTGATGTGATAAA-TGCTGAAATATTC
* *
10938 ATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* * * * * *
10987 ATGTGACTA-ATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTC
1 ATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
11035 ATGTGATT-TATGTGATTAAT
1 ATGTGATTATATGTGATTAAT
11055 GTGTAAAAGA
Statistics
Matches: 201, Mismatches: 17, Indels: 35
0.79 0.07 0.14
Matches are distributed among these distances:
48 53 0.26
49 49 0.24
51 1 0.00
53 2 0.01
54 2 0.01
55 2 0.01
57 3 0.01
59 85 0.42
60 1 0.00
61 2 0.01
63 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (49 bp):
ATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
Found at i:10834 original size:59 final size:59
Alignment explanation
Indices: 10761--11011 Score: 276
Period size: 59 Copynumber: 4.4 Consensus size: 59
10751 TTATCATAAA
* *
10761 ATGTGACTAAATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTAAAATATTC
1 ATGTGATTAAATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* * * *
10820 ATGTGATTAAATGTGACTGA-ATGTTATTAATTTGTGATGTGATAAATGTTGAAATATTC
1 ATGTGATTAAATGTGA-TTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* * * *
10879 ATGTGATTAAATGTGACTAAAAGTGATTAATATGTGATGTGATAAACT-CTGAAACATTC
1 ATGTGATTAAATGTGATTATATGTGATTAATATGTGATGTGATAAA-TGCTGAAATATTC
*
10938 A--TG------TG-G-TTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGATTAAATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
*
10987 ATGTGACT-AATGTGATTAATATGTG
1 ATGTGATTAAATGTGATT-ATATGTG
11012 TTGTGTTAAA
Statistics
Matches: 161, Mismatches: 17, Indels: 28
0.78 0.08 0.14
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 1 0.01
51 4 0.02
56 2 0.01
57 3 0.02
58 3 0.02
59 105 0.65
60 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (59 bp):
ATGTGATTAAATGTGATTATATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
Found at i:10835 original size:33 final size:32
Alignment explanation
Indices: 10797--10899 Score: 78
Period size: 33 Copynumber: 3.3 Consensus size: 32
10787 TTAATATGTG
10797 ATGTGA-TAAATGCTAAAATATTCATGTGATTAA
1 ATGTGACTAAATG-T-AAATATTCATGTGATTAA
* * * *
10830 ATGTGACTGAATGT---TATTAATTTG--T-G
1 ATGTGACTAAATGTAAATATTCATGTGATTAA
10856 ATGTGA-TAAATGTTGAAATATTCATGTGATTAA
1 ATGTGACTAAATG-T-AAATATTCATGTGATTAA
10889 ATGTGACTAAA
1 ATGTGACTAAA
10900 AGTGATTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 19
0.66 0.10 0.24
Matches are distributed among these distances:
25 5 0.10
26 7 0.13
27 1 0.02
29 8 0.15
30 8 0.15
32 1 0.02
33 13 0.25
34 9 0.17
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (32 bp):
ATGTGACTAAATGTAAATATTCATGTGATTAA
Found at i:11007 original size:24 final size:25
Alignment explanation
Indices: 10889--11010 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 25
10879 ATGTGATTAA
* *
10889 ATGTGACTAAAAGTGATTAATATGTG
1 ATGTGA-TAAATGTGATTAATATGTC
* *
10915 ATGTGATAAACTCTGA--AACAT-TC
1 ATGTGATAAA-TGTGATTAATATGTC
* *
10938 ATGTGGTTAAATGTGATTAATATGTG
1 ATGT-GATAAATGTGATTAATATGTC
10964 ATGTGATAAATGCTGA--AATAT-TC
1 ATGTGATAAATG-TGATTAATATGTC
10987 ATGTGACT-AATGTGATTAATATGT
1 ATGTGA-TAAATGTGATTAATATGT
11011 GTTGTGTTAA
Statistics
Matches: 76, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
22 3 0.04
23 20 0.26
24 20 0.26
25 16 0.21
26 17 0.22
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (25 bp):
ATGTGATAAATGTGATTAATATGTC
Found at i:11022 original size:48 final size:49
Alignment explanation
Indices: 10889--11054 Score: 203
Period size: 48 Copynumber: 3.4 Consensus size: 49
10879 ATGTGATTAA
* *
10889 ATGTGACTAAAAGTGATTAATATGTGATGTGATAAACT-CTGAAACATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAA-TGCTGAAATATTC
**
10938 ATGTGGTTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
* * * * *
10987 ATGTGACT-AATGTGATTAATATGTGTTGTGTTAAATGCTTAAGTACTC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
**
11035 ATGTGA-TTTATGTGATTAAT
1 ATGTGACTAAATGTGATTAAT
11055 GTGTAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 53 0.51
49 49 0.48
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (49 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
Found at i:12163 original size:60 final size:61
Alignment explanation
Indices: 11895--12164 Score: 235
Period size: 61 Copynumber: 4.5 Consensus size: 61
11885 AAAACATGAG
* * * * * * *
11895 TATAAAGGAATGCTTTTATGGAAAAACTCTAGACATGAAATCCTTTGTGACGAGTATTGAA
1 TATAAAGGAATGCCTTTATGGAAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAA
* * * * * * *
11956 TATAAAGGAACGCCTTTGTGGTAAAACTCTGGGCAAGAAAGCTTTTGTGGTAAGTACTGAA
1 TATAAAGGAATGCCTTTATGGAAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAA
* * * * *
12017 TATAAAGGAATGTCTTTATGGAAACACTTTGGACAGAAAAGCCTTTGTGGCAAGTACTAAA
1 TATAAAGGAATGCCTTTATGGAAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAA
* * * ** *
12078 TGA-AAATG-TTGCCTTTGTGGAAAAACAT-TGGACAGGAAAGCCTTTGTGGTGAGTATTGAA
1 T-ATAAAGGAATGCCTTTATGGAAAAAC-TCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAA
* *
12138 TGTAAAGGAA-G-CTTTCATGGGAAAACT
1 TATAAAGGAATGCCTTT-ATGGAAAAACT
12165 TTGAAAGGGT
Statistics
Matches: 164, Mismatches: 40, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
59 5 0.03
60 55 0.34
61 103 0.63
62 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (61 bp):
TATAAAGGAATGCCTTTATGGAAAAACTCTGGACAGGAAAGCCTTTGTGGCAAGTACTGAA
Found at i:14731 original size:17 final size:17
Alignment explanation
Indices: 14709--14741 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14699 TTTTTTTTCT
14709 TATAAAAGA-CATAAAAA
1 TATAAAA-ATCATAAAAA
14726 TATAAAAATCATAAAA
1 TATAAAAATCATAAAA
14742 TATTAGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (17 bp):
TATAAAAATCATAAAAA
Found at i:14771 original size:19 final size:20
Alignment explanation
Indices: 14749--14794 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
14739 AAATATTAGT
*
14749 AAAATTTTTAAAA-AAATTA
1 AAAATTTATAAAATAAATTA
* *
14768 AAAA-CTATAAAATATATTA
1 AAAATTTATAAAATAAATTA
14787 AAAATTTA
1 AAAATTTA
14795 GATAAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.29
19 13 0.62
20 2 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTTATAAAATAAATTA
Found at i:14802 original size:37 final size:38
Alignment explanation
Indices: 14721--14809 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 38
14711 TAAAAGACAT
*
14721 AAAAATATAAAAATCATAAAATATTAGTAAAATTTTTAA
1 AAAAAT-TAAAAATCATAAAATATTAGTAAAATATTTAA
*
14760 AAAAATTAAAAA-CTATAAAATA-TATTAAAA-ATTTAGA
1 AAAAATTAAAAATC-ATAAAATATTAGTAAAATATTTA-A
*
14797 TAAAATTATAAAA
1 AAAAATTA-AAAA
14810 AAAATTCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 4 0.09
37 16 0.36
38 18 0.41
39 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (38 bp):
AAAAATTAAAAATCATAAAATATTAGTAAAATATTTAA
Found at i:14909 original size:19 final size:19
Alignment explanation
Indices: 14869--14925 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
14859 AATTTAATGA
* *
14869 ATTCTAAAATATTA-AAAA
1 ATTCTAAAAAATTATAAAT
14887 ATTCTAAAAAATTATAAAT
1 ATTCTAAAAAATTATAAAT
* *
14906 ATTCTTAAAAATTGTAAAT
1 ATTCTAAAAAATTATAAAT
14925 A
1 A
14926 GTATAATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTCTAAAAAATTATAAAT
Found at i:14942 original size:28 final size:28
Alignment explanation
Indices: 14911--14976 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
14901 TAAATATTCT
* *
14911 TAAAAATTGTAA-ATAGTATAATAACTTA
1 TAAAAATTATAATAAAGTATAATAA-TTA
* * *
14939 TAAAAGTTATAATAAATTCTAATAATTA
1 TAAAAATTATAATAAAGTATAATAATTA
14967 TAAAAATTAT
1 TAAAAATTAT
14977 GAAATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 22 0.71
29 9 0.29
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (28 bp):
TAAAAATTATAATAAAGTATAATAATTA
Found at i:14950 original size:9 final size:9
Alignment explanation
Indices: 14719--15004 Score: 116
Period size: 9 Copynumber: 30.1 Consensus size: 9
14709 TATAAAAGAC
14719 ATAAAAA-T
1 ATAAAAATT
*
14727 ATAAAAATC
1 ATAAAAATT
14736 ATAAAATATT
1 ATAAAA-ATT
*
14746 AGTAAAATTT
1 A-TAAAAATT
* *
14756 TTAAAAA-A
1 ATAAAAATT
*
14764 ATTAAAAACT
1 A-TAAAAATT
14774 AT-AAAATAT
1 ATAAAAAT-T
14783 ATTAAAAATTT
1 A-TAAAAA-TT
*
14794 AGATAAAATT
1 ATA-AAAATT
14804 ATAAAAAAAATT
1 AT---AAAAATT
*
14816 CATAAACACTT
1 -ATAAA-AATT
* *
14827 ATGAATATT
1 ATAAAAATT
14836 ATAAAAACTT
1 ATAAAAA-TT
14846 ATAAAAA-T
1 ATAAAAATT
*
14854 AAAAAAATT
1 ATAAAAATT
*
14863 -TAATGAATT
1 ATAA-AAATT
*
14872 CTAAAATATT
1 ATAAAA-ATT
14882 A-AAAAATT
1 ATAAAAATT
*
14890 CTAAAAAATT
1 AT-AAAAATT
*
14900 ATAAATATT
1 ATAAAAATT
*
14909 CTTAAAAATT
1 -ATAAAAATT
* * *
14919 GTAAATAGT
1 ATAAAAATT
*
14928 ATAATAACTT
1 ATAA-AAATT
*
14938 ATAAAAGTT
1 ATAAAAATT
14947 ATAATAAATT
1 ATAA-AAATT
* *
14957 CTAATAATT
1 ATAAAAATT
14966 ATAAAAATT
1 ATAAAAATT
* *
14975 ATGAAATTT
1 ATAAAAATT
*
14984 TTAAAAATAT
1 ATAAAAAT-T
14994 ATAAAATATT
1 ATAAAA-ATT
15004 A
1 A
15005 ATACATGAAA
Statistics
Matches: 205, Mismatches: 46, Indels: 52
0.68 0.15 0.17
Matches are distributed among these distances:
8 23 0.11
9 83 0.40
10 69 0.34
11 20 0.10
12 7 0.03
13 3 0.01
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:14967 original size:19 final size:19
Alignment explanation
Indices: 14914--14999 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
14904 ATATTCTTAA
*
14914 AAATTGTAAATAG-TATAAT
1 AAATTATAAA-AGTTATAAT
*
14933 AACTTATAAAAGTTATAAT
1 AAATTATAAAAGTTATAAT
*
14952 AAATTCTAATAA-TTATAA-
1 AAATTATAA-AAGTTATAAT
* * *
14970 AAATTATGAAATTTTTAA-
1 AAATTATAAAAGTTATAAT
14988 AAATATATAAAA
1 AAAT-TATAAAA
15000 TATTAATACA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.04
18 18 0.33
19 33 0.60
20 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (19 bp):
AAATTATAAAAGTTATAAT
Found at i:19154 original size:6 final size:6
Alignment explanation
Indices: 19143--19238 Score: 147
Period size: 6 Copynumber: 16.0 Consensus size: 6
19133 TAAATAAATA
19143 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
* * * * *
19191 AATAAT AATAAT AATAAT AGTAAT AGTAAT AGTAAT AGTAAT AGTAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
19239 GTAAATATTG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (6 bp):
AATAAT
Done.