Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010848.1 Kokia drynarioides strain JFW-HI SEQ_125815, 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: 30445
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:63 original size:2 final size:2
Alignment explanation
Indices: 56--88 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46 TTACTAATTA
56 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89 AGATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7720 original size:17 final size:18
Alignment explanation
Indices: 7698--7733 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7688 TAAATAAATT
7698 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
7715 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
7733 A
1 A
7734 TAGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:8150 original size:37 final size:38
Alignment explanation
Indices: 8083--8161 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
8073 GTGTCATTAT
* **
8083 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
* **
8121 TTTACTTCGGCTAGA-CCGATGAGACACTGGGTGTCAC
1 TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
8158 TTTA
1 TTTA
8162 TTGCTTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 21 0.60
38 14 0.40
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (38 bp):
TTTACTTCGGATAGATCCGATGAGACACTGGGTACCAC
Found at i:9063 original size:29 final size:29
Alignment explanation
Indices: 9027--9210 Score: 198
Period size: 29 Copynumber: 6.3 Consensus size: 29
9017 CCCTGTTTTA
* *
9027 TTCC-AAAATTATATTTTTACCCTCAAAC
1 TTCCTAAAATCATATTTTGACCCTCAAAC
* *
9055 TTCCTAAAATTATATTTTTACCCTCAAAC
1 TTCCTAAAATCATATTTTGACCCTCAAAC
* *
9084 TTCCTAAAATCACATTTTGACCC-CTAAAT
1 TTCCTAAAATCATATTTTGACCCTC-AAAC
* *
9113 TCTCCTAAAATCACATTTTGACCCTTAAAC
1 T-TCCTAAAATCATATTTTGACCCTCAAAC
9143 TCTCCTAAAATCATATTTTGACCCT-AAACC
1 T-TCCTAAAATCATATTTTGACCCTCAAA-C
*
9173 TTTCC-AAAATCATATTTTAACCC-CAAAC
1 -TTCCTAAAATCATATTTTGACCCTCAAAC
9201 TTTCCTAAAA
1 -TTCCTAAAA
9211 ATACATTTTG
Statistics
Matches: 140, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
28 11 0.08
29 75 0.54
30 53 0.38
31 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
TTCCTAAAATCATATTTTGACCCTCAAAC
Found at i:9121 original size:30 final size:30
Alignment explanation
Indices: 9085--9267 Score: 168
Period size: 30 Copynumber: 6.3 Consensus size: 30
9075 CCCTCAAACT
9085 TCCTAAAATCACATTTTGACCCCTAAATTC
1 TCCTAAAATCACATTTTGACCCCTAAATTC
* *
9115 TCCTAAAATCACATTTTGACCCTTAAACTC
1 TCCTAAAATCACATTTTGACCCCTAAATTC
*
9145 TCCTAAAATCATATTTTGA-CCCTAAACCTT-
1 TCCTAAAATCACATTTTGACCCCTAAA--TTC
* *
9175 TCC-AAAATCATATTTTAACCCC-AAACTT-
1 TCCTAAAATCACATTTTGACCCCTAAA-TTC
* * * *
9203 TCCTAAAAAT-ACATTTTGTCCCCGAATTTT
1 TCCT-AAAATCACATTTTGACCCCTAAATTC
* *
9233 TCC-AAAATTACATTTTGA-CCTTAAATTC
1 TCCTAAAATCACATTTTGACCCCTAAATTC
9261 TCC-AAAA
1 TCCTAAAA
9268 CTTCATTTTT
Statistics
Matches: 130, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
28 24 0.18
29 43 0.33
30 62 0.48
31 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCTAAAATCACATTTTGACCCCTAAATTC
Found at i:9131 original size:59 final size:57
Alignment explanation
Indices: 9068--9248 Score: 188
Period size: 59 Copynumber: 3.1 Consensus size: 57
9058 CTAAAATTAT
*
9068 ATTTTTACCCTCAAACTTCCTAAAATCACATTTTGACCCCTAAATTCTCCTAAAATCAC
1 ATTTTAACCCTCAAACTTCCTAAAATCACATTTTGACCCCTAAATT-TCC-AAAATCAC
* * * *
9127 ATTTTGACCCTTAAACTCTCCTAAAATCATATTTTGA-CCCTAAACCTTTCCAAAATCAT
1 ATTTTAACCCTCAAACT-TCCTAAAATCACATTTTGACCCCTAAA--TTTCCAAAATCAC
* * * *
9186 ATTTTAACCC-CAAACTTTCCTAAAAAT-ACATTTTGTCCCCGAATTTTTCCAAAATTAC
1 ATTTTAACCCTCAAAC-TTCCT-AAAATCACATTTTGACCCCTAA-ATTTCCAAAATCAC
9244 ATTTT
1 ATTTT
9249 GACCTTAAAT
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
58 31 0.30
59 49 0.48
60 21 0.20
61 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (57 bp):
ATTTTAACCCTCAAACTTCCTAAAATCACATTTTGACCCCTAAATTTCCAAAATCAC
Found at i:9218 original size:29 final size:30
Alignment explanation
Indices: 9039--9252 Score: 196
Period size: 29 Copynumber: 7.3 Consensus size: 30
9029 CCAAAATTAT
* * *
9039 ATTTTTACCCTCAAAC-TTCCTAAAATTAT
1 ATTTTGACCCTCAAACTTTCCTAAAATCAC
*
9068 ATTTTTACCCTCAAAC-TTCCTAAAATCAC
1 ATTTTGACCCTCAAACTTTCCTAAAATCAC
9097 ATTTTGACCC-CTAAA-TTCTCCTAAAATCAC
1 ATTTTGACCCTC-AAACTT-TCCTAAAATCAC
* * *
9127 ATTTTGACCCTTAAACTCTCCTAAAATCAT
1 ATTTTGACCCTCAAACTTTCCTAAAATCAC
*
9157 ATTTTGACCCT-AAACCTTTCC-AAAATCAT
1 ATTTTGACCCTCAAA-CTTTCCTAAAATCAC
*
9186 ATTTTAACCC-CAAACTTTCCTAAAAAT-AC
1 ATTTTGACCCTCAAACTTTCCT-AAAATCAC
* ** *
9215 ATTTTGTCCC-CGAATTTTTCC-AAAATTAC
1 ATTTTGACCCTC-AAACTTTCCTAAAATCAC
9244 ATTTTGACC
1 ATTTTGACC
9253 TTAAATTCTC
Statistics
Matches: 160, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.08
29 83 0.52
30 64 0.40
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCTCAAACTTTCCTAAAATCAC
Found at i:11582 original size:29 final size:30
Alignment explanation
Indices: 11550--11608 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
11540 TATGGTTTAA
11550 TGTGTAATTATATATATG-AATGTTGATTT
1 TGTGTAATTATATATATGAAATGTTGATTT
* *
11579 TGTGTAATTTTATATATGAAATTTTGATTT
1 TGTGTAATTATATATATGAAATGTTGATTT
11609 GATTCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (30 bp):
TGTGTAATTATATATATGAAATGTTGATTT
Found at i:12477 original size:20 final size:20
Alignment explanation
Indices: 12431--12478 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
12421 ACATGACTAT
12431 ACAATGAAAAATTGAAAGAA
1 ACAATGAAAAATTGAAAGAA
* *
12451 ATAAATGAAAAATT-CAAGTAA
1 A-CAATGAAAAATTGAAAG-AA
12472 ACAATGA
1 ACAATGA
12479 CAACACAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (20 bp):
ACAATGAAAAATTGAAAGAA
Found at i:13423 original size:3 final size:3
Alignment explanation
Indices: 13415--13439 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13405 ACACTTAAAC
13415 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
13440 ACAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13577 original size:57 final size:58
Alignment explanation
Indices: 13478--13598 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
13468 AAAATGAGTT
** *
13478 GTTTATGAGTATTATTTAGGAATAAAATTATATTTTGATTTAAAAATATTTGAATTTA
1 GTTTATGAGTATTATTTAAAAATAAAATTATATTTGGATTTAAAAATATTTGAATTTA
* * * **
13536 GTTTATGAGT-TTTTTTAAAAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTATTATTTAAAAATAAAATTATATTTGGATTTAAAAATATTTGAATTTA
13593 GTTTAT
1 GTTTAT
13599 TGATGGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 45 0.82
58 10 0.18
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.50
Consensus pattern (58 bp):
GTTTATGAGTATTATTTAAAAATAAAATTATATTTGGATTTAAAAATATTTGAATTTA
Found at i:14230 original size:29 final size:29
Alignment explanation
Indices: 14186--14305 Score: 104
Period size: 29 Copynumber: 4.1 Consensus size: 29
14176 AAATAATTTT
* *
14186 TTTTTTTTTTAGTTTTT-AAGAGGTTTAAA
1 TTTTTTTTTTAATTTTTAAAGA-GTTAAAA
14215 TTTTTTTTTTAATTTTTAAAGAGTTAAAA
1 TTTTTTTTTTAATTTTTAAAGAGTTAAAA
* * * *
14244 -TTTTTTTTTACCGACTTATAAATAGTTTAAA
1 TTTTTTTTTTA---ATTTTTAAAGAGTTAAAA
*
14275 -TTTTTTTTAAATTTTTAAAGA-TTCAAAA
1 TTTTTTTTTTAATTTTTAAAGAGTT-AAAA
14303 TTT
1 TTT
14306 CAATTTTTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
27 2 0.03
28 21 0.28
29 24 0.32
30 4 0.05
31 23 0.31
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTTTTTTTTAATTTTTAAAGAGTTAAAA
Found at i:16830 original size:145 final size:146
Alignment explanation
Indices: 16555--16838 Score: 371
Period size: 145 Copynumber: 2.0 Consensus size: 146
16545 TTCTCATTGC
* * * *
16555 ATGAATATAAAAATTCACATTTCTCAAATGTCCATAGCTCCTAGAATGTAAACTCAAAAGTAAAC
1 ATGAATATAAAAATCCACATTTCTCAAACGTCCATAGCTCCTAGAATGTAAAATCAAAACTAAAC
* *
16620 AGTAATGTTTGATCAGCTAGCCACAAGACTTTAAGTTCAATATCCAAGAAATTTTCAATTCTCAG
66 AGTAATGTTTGAGCAGCTAGCCACAACACTTTAAGTTCAATATCCAAGAAATTTTCAATTCTCAG
*
16685 ATGAGTTTCATATTCT
131 ATAAGTTTCATATTCT
* * * * *
16701 ATGAATAT-AAAATCCATATCTT-TCAAACGTCCTTTGCTCCTTGAATGTAAATATC-AAACTTA
1 ATGAATATAAAAATCCACAT-TTCTCAAACGTCCATAGCTCCTAGAATGTAAA-ATCAAAACTAA
* *
16763 ACAGTGAA-GTTTGAGCAGCTAGCCACCAACAC-TTAAGTTCAATATCCCAGAAATTTTCAATTT
64 ACAGT-AATGTTTGAGCAGCTAGCCA-CAACACTTTAAGTTCAATATCCAAGAAATTTTCAATTC
16826 TCAGATAAGTTTC
127 TCAGATAAGTTTC
16839 TATGTTTACA
Statistics
Matches: 120, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
145 101 0.84
146 19 0.16
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (146 bp):
ATGAATATAAAAATCCACATTTCTCAAACGTCCATAGCTCCTAGAATGTAAAATCAAAACTAAAC
AGTAATGTTTGAGCAGCTAGCCACAACACTTTAAGTTCAATATCCAAGAAATTTTCAATTCTCAG
ATAAGTTTCATATTCT
Found at i:19322 original size:26 final size:25
Alignment explanation
Indices: 19260--19330 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 25
19250 AAAAATTAAA
19260 TTATAATTTTTACTAAAAATTATAATT
1 TTATAATTTTT--TAAAAATTATAATT
* * *
19287 TTCTCA--TTTTAATAAATTATATTT
1 TTATAATTTTTTAA-AAATTATAATT
19311 TTATAATTTTTTAAAAATTA
1 TTATAATTTTTTAAAAATTA
19331 AATCAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
23 3 0.08
24 14 0.39
25 9 0.25
26 6 0.17
27 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
TTATAATTTTTTAAAAATTATAATT
Found at i:19369 original size:29 final size:29
Alignment explanation
Indices: 19299--19372 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
19289 CTCATTTTAA
*
19299 TAAATTATATTTTTATAATTTTTTAAAAAT
1 TAAA-TATAATTTTATAATTTTTTAAAAAT
*
19329 TAAATCAAAATTTTAT-A-TTTTTAAAAGATT
1 TAAAT-ATAATTTTATAATTTTTTAAAA-A-T
19359 TAAATATAATTTTA
1 TAAATATAATTTTA
19373 CTAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 9 0.24
29 11 0.29
30 18 0.47
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TAAATATAATTTTATAATTTTTTAAAAAT
Found at i:24189 original size:18 final size:18
Alignment explanation
Indices: 24144--24190 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
24134 TCATGATCAA
24144 ATGCAGTCACATACTCAG
1 ATGCAGTCACATACTCAG
* * *
24162 ATGTAATCACATGCTC-G
1 ATGCAGTCACATACTCAG
24179 TATGCAGTCACA
1 -ATGCAGTCACA
24191 GTAGTCTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (18 bp):
ATGCAGTCACATACTCAG
Done.