Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013857.1 Kokia drynarioides strain JFW-HI SEQ_128885, 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: 22074
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7060 original size:18 final size:18
Alignment explanation
Indices: 6975--7074 Score: 79
Period size: 18 Copynumber: 5.7 Consensus size: 18
6965 AATTGTAAAA
6975 AAAATTATAAGA-AA-TAT
1 AAAATTATAA-ATAATTAT
*
6992 AAAAATTATTAAAT-ATTAA
1 -AAAATTA-TAAATAATTAT
*
7011 AAAAATA-AAATAGA-TAT
1 AAAATTATAAATA-ATTAT
*
7028 AAACTTATAAA-AATTATT
1 AAAATTATAAATAATTA-T
7046 AAAA-TATAAATAATTAT
1 AAAATTATAAATAATTAT
7063 AAAATTATAAAT
1 AAAATTATAAAT
7075 TTTTTATGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
16 5 0.08
17 21 0.32
18 35 0.53
19 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATTATAAATAATTAT
Found at i:7074 original size:7 final size:8
Alignment explanation
Indices: 6975--7073 Score: 51
Period size: 9 Copynumber: 11.4 Consensus size: 8
6965 AATTGTAAAA
6975 AAAATTAT
1 AAAATTAT
*
6983 AAGAAATAT
1 AA-AATTAT
6992 AAAAATTATT
1 -AAAATTA-T
7002 AAATATTA-
1 AAA-ATTAT
*
7010 AAAA-AAT
1 AAAATTAT
7017 AAAATAGATAT
1 AAAAT---TAT
*
7028 AAACTTAT
1 AAAATTAT
7036 AAAAATTATT
1 -AAAATTA-T
7046 AAAA-TAT
1 AAAATTAT
7053 AAATAATTAT
1 -AA-AATTAT
7063 AAAATTAT
1 AAAATTAT
7071 AAA
1 AAA
7074 TTTTTTATGA
Statistics
Matches: 71, Mismatches: 6, Indels: 28
0.68 0.06 0.27
Matches are distributed among these distances:
6 1 0.01
7 6 0.08
8 21 0.30
9 26 0.37
10 11 0.15
11 6 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (8 bp):
AAAATTAT
Found at i:7075 original size:15 final size:17
Alignment explanation
Indices: 7033--7073 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
7023 GATATAAACT
7033 TATAAAAATTATTAAAA
1 TATAAAAATTATTAAAA
7050 TATAAATAATTA-TAAAA
1 TATAAA-AATTATTAAAA
7067 TTATAAA
1 -TATAAA
7074 TTTTTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAAAATTATTAAAA
Found at i:7167 original size:28 final size:27
Alignment explanation
Indices: 7108--7191 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 27
7098 ATTTTTTATA
* * * *
7108 AAAAATATTAAAATTCTATAAAAATCAT
1 AAAAATATTAAAATTATAT-AAACTTAC
7136 AAAAATATTAAAATTAATATAAACTTAC
1 AAAAATATTAAAATT-ATATAAACTTAC
* *
7164 AAAAATAATAAAAATTCATAAAAACTTA
1 AAAAAT-ATTAAAATT-ATATAAACTTA
7192 AACTCGATCA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
28 26 0.55
29 21 0.45
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATATTAAAATTATATAAACTTAC
Found at i:7168 original size:29 final size:28
Alignment explanation
Indices: 7107--7191 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
7097 AATTTTTTAT
* **
7107 AAAAAATATTAAAATTCTATAAAAAT-C
1 AAAAAATATTAAAATTATATAAACTTAC
7134 ATAAAAATATTAAAATTAATATAAACTTAC
1 A-AAAAATATTAAAATT-ATATAAACTTAC
* *
7164 -AAAAATAATAAAAATTCATAAAAACTTA
1 AAAAAAT-ATTAAAATT-ATATAAACTTA
7192 AACTCGATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 21 0.44
29 25 0.52
30 1 0.02
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAATATTAAAATTATATAAACTTAC
Found at i:7186 original size:19 final size:18
Alignment explanation
Indices: 7103--7187 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 18
7093 ATTTAATTTT
* *
7103 TTATAAAAAATATTAAAAT
1 TTAT-AAAAATAATAAAAA
*
7122 TCTATAAAAATCATAAAAA
1 T-TATAAAAATAATAAAAA
* *
7141 -TATTAAAATTAATATAAAC
1 TTA-TAAAAATAATA-AAAA
*
7160 TTACAAAAATAATAAAAA
1 TTATAAAAATAATAAAAA
7178 TTCATAAAAA
1 TT-ATAAAAA
7188 CTTAAACTCG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 2 0.04
18 14 0.27
19 30 0.59
20 5 0.10
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTATAAAAATAATAAAAA
Found at i:9218 original size:16 final size:17
Alignment explanation
Indices: 9188--9230 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
9178 AAATAAAATT
*
9188 AATTAAAATTCATTTTA
1 AATTTAAATTCATTTTA
*
9205 AATTTAAATT-ATTTTG
1 AATTTAAATTCATTTTA
9221 AATTTAAATT
1 AATTTAAATT
9231 TTACAAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTTAAATTCATTTTA
Found at i:9298 original size:9 final size:9
Alignment explanation
Indices: 9282--9323 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
9272 GATAACTTAA
9282 AATTTAAAT
1 AATTTAAAT
*
9291 ATTTTAAATT
1 AATTTAAA-T
9301 AATTTAAAT
1 AATTTAAAT
*
9310 AA-ATAAAT
1 AATTTAAAT
9318 AATTTA
1 AATTTA
9324 GCTTAGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.26
9 12 0.44
10 8 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTTAAAT
Found at i:9895 original size:60 final size:58
Alignment explanation
Indices: 9804--10113 Score: 289
Period size: 60 Copynumber: 5.2 Consensus size: 58
9794 TGTGAAAAAA
* * *
9804 AAATTTATTGAGTGTTGGCCATGCAACGATCGACACCCTTTTTTAATCTGATAAAAAAATC
1 AAATTT-TTGGGTGTTGGCCATGCAATGACCGACACCCTTTTTT-ATCTGAT-AAAAAATC
* * * *
9865 AAATTTTTGGGTGTTGGCCATGTAATGATCGACACTCCTTTTTTGTCAGATAAAAAATAC
1 AAATTTTTGGGTGTTGGCCATGCAATGACCGACAC-CCTTTTTTATCTGATAAAAAAT-C
* ** * * * * *
9925 AATTTTTTTTGTGTTGGTCATACAATGGCCGACATCCCTTTTTAATTTGATAAAAAAAATC
1 AAATTTTTGGGTGTTGGCCATGCAATGACCGACA-CCCTTTTTTATCTGAT--AAAAAATC
* * *
9986 AAATTTTTGGGTGTTGGTCATGCAATGACCTACACCCTTTTTTTATCAGATAAAAAAT-
1 AAATTTTTGGGTGTTGGCCATGCAATGACCGACACCC-TTTTTTATCTGATAAAAAATC
**** * * *
10044 ATAATTTTTTTACGTTGGCCATACAATGGCCGACACCCTTATTTATCTGATAAAAAATC
1 A-AATTTTTGGGTGTTGGCCATGCAATGACCGACACCCTTTTTTATCTGATAAAAAATC
*
10103 ATATTTTTGGG
1 AAATTTTTGGG
10114 GGGTATCGGC
Statistics
Matches: 201, Mismatches: 40, Indels: 19
0.77 0.15 0.07
Matches are distributed among these distances:
58 25 0.12
59 43 0.21
60 72 0.36
61 54 0.27
62 7 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (58 bp):
AAATTTTTGGGTGTTGGCCATGCAATGACCGACACCCTTTTTTATCTGATAAAAAATC
Found at i:10028 original size:121 final size:118
Alignment explanation
Indices: 9834--10113 Score: 386
Period size: 121 Copynumber: 2.3 Consensus size: 118
9824 ATGCAACGAT
* *
9834 CGACACCCTTTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGTAATGATCGACA
1 CGACACCC-TTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGCAATGACCGACA
* ** *
9899 CTCCTTTTTTGTCAGATAAAAAATACAATTTTTTTTGTGTTGGTCATACAATGGC
65 CTCCTTTTTTATCAGATAAAAAATACAA-TTTTTTTACGTTGGCCATACAATGGC
* * *
9954 CGACATCCCTTTTTAATTTGATAAAAAAAATCAAATTTTTGGGTGTTGGTCATGCAATGACCTAC
1 CGACA-CCCTTTTTAATCTGAT-AAAAAAATCAAATTTTTGGGTGTTGGCCATGCAATGACCGAC
*
10019 AC-CCTTTTTTTATCAGATAAAAAATATAATTTTTTTACGTTGGCCATACAATGGC
64 ACTCC-TTTTTTATCAGATAAAAAATACAATTTTTTTACGTTGGCCATACAATGGC
*
10074 CGACACCCTTATTT-ATCTGAT-AAAAAATCATATTTTTGGG
1 CGACACCCTT-TTTAATCTGATAAAAAAATCAAATTTTTGGG
10114 GGGTATCGGC
Statistics
Matches: 144, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
117 18 0.12
119 11 0.08
120 50 0.35
121 65 0.45
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (118 bp):
CGACACCCTTTTTAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGCAATGACCGACAC
TCCTTTTTTATCAGATAAAAAATACAATTTTTTTACGTTGGCCATACAATGGC
Found at i:10241 original size:60 final size:59
Alignment explanation
Indices: 10119--10447 Score: 310
Period size: 60 Copynumber: 5.5 Consensus size: 59
10109 TTGGGGGGTA
** * *
10119 TCGGCCATTGCATTACCAACACACAAAAAAATTGAAATTTTTTTATCAGATAAATAGG-GGTG
1 TCGGCCATTGCATGGCCAACAC-C-AAAAAATTG-AA-TTTTTTATCTGATAAAAAGGAGGTG
*
10181 TCGGCCATTGTATGGCCAACACCAAAAAATTGAATTTTTTATCTGATAAAAAAGGAGGTG
1 TCGGCCATTGCATGGCCAACACCAAAAAATTGAATTTTTTATCTGAT-AAAAAGGAGGTG
* * * *
10241 TCGGCCATTGCATGGCCAACACCTAAAAATTTGATTTTTTTTAT-TAGATAAATAGGA-ATG
1 TCGGCCATTGCATGGCCAACACC-AAAAAATTGA-ATTTTTTATCT-GATAAAAAGGAGGTG
* * * * * * *
10301 TCGACCATTGTATGACCAACACAAAAAAATTGTATTTTTTATCTGACAAAAA-AAGAGTG
1 TCGGCCATTGCATGGCCAACACCAAAAAATTGAATTTTTTATCTGATAAAAAGGAG-GTG
* *
10360 TCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAT-ATTAAAAAGG-GATG
1 TCGGCCATTGCATGGCCAACACCAAAAAA-TTGAATTTTTTATC-TGA-TAAAAAGGAGGTG
** * *
10420 TCTACCATTGCATGGCAAACACCTAAAA
1 TCGGCCATTGCATGGCCAACACCAAAAA
10448 TTTTTTTTTT
Statistics
Matches: 221, Mismatches: 34, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
57 1 0.00
58 26 0.12
59 44 0.20
60 95 0.43
61 25 0.11
62 30 0.14
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (59 bp):
TCGGCCATTGCATGGCCAACACCAAAAAATTGAATTTTTTATCTGATAAAAAGGAGGTG
Found at i:10459 original size:119 final size:119
Alignment explanation
Indices: 10119--10447 Score: 435
Period size: 120 Copynumber: 2.7 Consensus size: 119
10109 TTGGGGGGTA
** * *
10119 TCGGCCATTGCATTACCAACACACAAAAAAATTGAAATTTTTTTATCAGATAAATAGGGGTGTCG
1 TCGGCCATTGCATGGCCAACAC-CAAAAAATTTG--ATTTTTTTATCAGATAAATAGGGATGTCG
* * * *
10184 GCCATTGTATGGCCAACACCAAAAAATTGAATTTTTTATCTGATAAAAAAGGAGGTG
63 ACCATTGTATGGCCAACACCAAAAAATTGTATTTTTTATCTGACAAAAAAAGAGGTG
* * *
10241 TCGGCCATTGCATGGCCAACACCTAAAAATTTGATTTTTTTTATTAGATAAATAGGAATGTCGAC
1 TCGGCCATTGCATGGCCAACACCAAAAAATTTGA-TTTTTTTATCAGATAAATAGGGATGTCGAC
* *
10306 CATTGTATGACCAACACAAAAAAATTGTATTTTTTATCTGACAAAAAAAGA-GTG
65 CATTGTATGGCCAACACCAAAAAATTGTATTTTTTATCTGACAAAAAAAGAGGTG
* * *
10360 TCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCATATTAAAAAGGGATGTCTAC
1 TCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAGA-TAAATAGGGATGTCGAC
* * *
10425 CATTGCATGGCAAACACCTAAAA
65 CATTGTATGGCCAACACCAAAAA
10448 TTTTTTTTTT
Statistics
Matches: 181, Mismatches: 24, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
118 11 0.06
119 69 0.38
120 72 0.40
121 9 0.05
122 20 0.11
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (119 bp):
TCGGCCATTGCATGGCCAACACCAAAAAATTTGATTTTTTTATCAGATAAATAGGGATGTCGACC
ATTGTATGGCCAACACCAAAAAATTGTATTTTTTATCTGACAAAAAAAGAGGTG
Found at i:11411 original size:4 final size:4
Alignment explanation
Indices: 11384--11425 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
11374 TGTAAATTAA
11384 TATT T-TT TATAT TATAT T-TT TATT TATT TATT TATT TATT TA
1 TATT TATT TAT-T TAT-T TATT TATT TATT TATT TATT TATT TA
11426 GTGAAAAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 5 0.14
4 23 0.66
5 7 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:14328 original size:20 final size:19
Alignment explanation
Indices: 14289--14337 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
14279 ATTTGATTTT
* *
14289 ATTATTTAA-ATTAAATTA
1 ATTATTTAATAATAAAATA
14307 ATCTATTTAATAATAAAATA
1 AT-TATTTAATAATAAAATA
14327 ATTAATTTAAT
1 ATT-ATTTAAT
14338 CTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 8 0.31
20 16 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATTTAATAATAAAATA
Found at i:14578 original size:19 final size:21
Alignment explanation
Indices: 14540--14579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
14530 TAATGTGAAT
*
14540 TTTTATGGATATATAAAATAA
1 TTTTATAGATATATAAAATAA
14561 TTTTATAGATA-A-AAAATAA
1 TTTTATAGATATATAAAATAA
14580 AGAGTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTATAGATATATAAAATAA
Found at i:16365 original size:43 final size:43
Alignment explanation
Indices: 16304--16389 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
16294 AATTTTTACC
*
16304 GCTCACACCAATCTTTCTCCTTTTATCCCCCAAATCCTAATTT
1 GCTCACACCAATCTTTCTCCTTTTATCCCCCAAACCCTAATTT
16347 GCTCACACCAATCTTTCTCCTTTTATCCCCCAAACCCTAATTT
1 GCTCACACCAATCTTTCTCCTTTTATCCCCCAAACCCTAATTT
16390 CTTACTTACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36
Consensus pattern (43 bp):
GCTCACACCAATCTTTCTCCTTTTATCCCCCAAACCCTAATTT
Found at i:20137 original size:13 final size:13
Alignment explanation
Indices: 20119--20154 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
20109 TACTTTATAT
20119 TATGTTATTTTTA
1 TATGTTATTTTTA
20132 TATGTTATTTTTA
1 TATGTTATTTTTA
*
20145 TATATTATTT
1 TATGTTATTT
20155 AATTTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (13 bp):
TATGTTATTTTTA
Done.