Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007261.1 Kokia drynarioides strain JFW-HI SEQ_121877, 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: 11740
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:806 original size:3 final size:3
Alignment explanation
Indices: 798--845 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
788 ACTGTTGATG
798 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
844 TA
1 TA
846 AATTGTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2677 original size:48 final size:48
Alignment explanation
Indices: 2606--2759 Score: 211
Period size: 48 Copynumber: 3.2 Consensus size: 48
2596 GGGGAGGATC
* *
2606 AACGACCGTATTTGGGTCATCAGCACCGACAGGAGAAGGAGCAAGAGA
1 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
*
2654 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGC
1 AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
* * * * * *
2702 AACGACCGTATTCGGACGAGCAGCACCGACATGAGGAAGG-GCACGATA
1 AACGACCGTATTTGGGCCATCAGCACCGACAGGA-GAAGGAGCACGAGA
2750 AACGACCGTA
1 AACGACCGTA
2760 AGTGAGCTAC
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
48 90 0.95
49 5 0.05
ACGTcount: A:0.34, C:0.25, G:0.31, T:0.11
Consensus pattern (48 bp):
AACGACCGTATTTGGGCCATCAGCACCGACAGGAGAAGGAGCACGAGA
Found at i:4856 original size:187 final size:183
Alignment explanation
Indices: 4521--4888 Score: 666
Period size: 187 Copynumber: 2.0 Consensus size: 183
4511 TTTTCATGAG
4521 CTAAGTAGAATTGTAGAAATACATATGAACCATATATCGACTACGTGAAAGCAAAAGGTTCCCAA
1 CTAAGTAGAATTGTAGAAATACATATGAACCATATATCGACTACGTGAAAGCAAAAGGTTCCCAA
4586 CCTCTTTTTTTTGTTCACTAAAGGAATAATTAAATGTTTAATTTTAATTGAACCTCGTGTGTTAG
66 CCTCTTTTTTTTGTTCACTAAAGGAATAATTAAATGTTTAATTTTAATTGAACCTCGTGTGTTAG
*
4651 CATGATGGTTAAAGGTGTTCTTTATCTCAGGTGTGGTTCGAATTCGAGTCGAA
131 CATGATGGTTAAAGGTGTTCTTTATCTCAGATGTGGTTCGAATTCGAGTCGAA
4704 CTAAGTAGAATTGTAGAAATACATATGAACCATATATCGACTACGTGAAAGCAAAAGGTTCCCAA
1 CTAAGTAGAATTGTAGAAATACATATGAACCATATATCGACTACGTGAAAGCAAAAGGTTCCCAA
4769 CCTCTTTTTTTTTTTTGTTCACTAAAGGAATAATTAAATGTTTAATTTTAATTGAACC-CTGTGT
66 CCTC----TTTTTTTTGTTCACTAAAGGAATAATTAAATGTTTAATTTTAATTGAACCTC-GTGT
*
4833 GTTAGCCTGATGGTTAAAGGTGTTCTTTATCTCAGATGTGGTTCGAATTCGAGTCG
126 GTTAGCATGATGGTTAAAGGTGTTCTTTATCTCAGATGTGGTTCGAATTCGAGTCG
4889 TCTCAATCGT
Statistics
Matches: 178, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
183 69 0.39
186 1 0.01
187 108 0.61
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (183 bp):
CTAAGTAGAATTGTAGAAATACATATGAACCATATATCGACTACGTGAAAGCAAAAGGTTCCCAA
CCTCTTTTTTTTGTTCACTAAAGGAATAATTAAATGTTTAATTTTAATTGAACCTCGTGTGTTAG
CATGATGGTTAAAGGTGTTCTTTATCTCAGATGTGGTTCGAATTCGAGTCGAA
Found at i:6046 original size:29 final size:29
Alignment explanation
Indices: 6014--6147 Score: 69
Period size: 29 Copynumber: 4.6 Consensus size: 29
6004 TGGATGCCCG
6014 GGGGTAAAATGGTAATTTTCAAAAATTTT
1 GGGGTAAAATGGTAATTTTCAAAAATTTT
* *** * *
6043 GGGGTCAAAAAT-GAAATTTTTTCACA-TTC
1 GGGGT--AAAATGGTAATTTTCAAAAATTTT
* **
6072 GAGGGTAAAATTGTAATTTT-GGAAATTTT
1 G-GGGTAAAATGGTAATTTTCAAAAATTTT
* * *
6101 AGGGTTAAAAATGG-AATTTTCAAACATTTA
1 -GGGGT-AAAATGGTAATTTTCAAAAATTTT
* *
6131 GTGATAAAATGGTAATT
1 GGGGTAAAATGGTAATT
6148 CTTGGAAAGT
Statistics
Matches: 77, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
28 14 0.18
29 33 0.43
30 25 0.32
31 5 0.06
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTCAAAAATTTT
Found at i:6078 original size:59 final size:58
Alignment explanation
Indices: 6015--6333 Score: 259
Period size: 59 Copynumber: 5.4 Consensus size: 58
6005 GGATGCCCGG
* **
6015 GGGTAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAATGAAATTTTTTCACATTCGA
1 GGGTAAAATGGTAATTTT-GAAAATTTTGGGGTCAAAAATGAAATTTTTGGACATTCGA
* * * * * *** *
6074 GGGTAAAATTGTAATTTTGGAAATTTTAGGGTTAAAAATGGAATTTTCAAACATT-TA
1 GGGTAAAATGGTAATTTTGAAAATTTTGGGGTCAAAAATGAAATTTTTGGACATTCGA
* * * * *
6131 GTGATAAAATGGTAATTCTTGGAAAGTTTCGGGTCAAAAATGAAATTTTTGGACATTCAA
1 G-GGTAAAATGGTAATT-TTGAAAATTTTGGGGTCAAAAATGAAATTTTTGGACATTCGA
* * * * *
6191 GGGTAAAATGGTAATTGTTGGAAAA-TTCGAGGTCAAAAAT-AGAATTTTCGGATATTCGG
1 GGGTAAAATGGTAATT-TT-GAAAATTTTGGGGTCAAAAATGA-AATTTTTGGACATTCGA
* * * * * * * *
6250 GGGTAAAGTGGTAATTTTTGGAAAGTTTGAGGTTAAAAATGGAATTTTTGGAAATT-TA
1 GGGTAAAATGGTAA-TTTTGAAAATTTTGGGGTCAAAAATGAAATTTTTGGACATTCGA
*
6308 GGGGTAAAATGGTAATTTTAAAAATT
1 -GGGTAAAATGGTAATTTTGAAAATT
6334 CCTGGTAAAA
Statistics
Matches: 208, Mismatches: 43, Indels: 19
0.77 0.16 0.07
Matches are distributed among these distances:
57 2 0.01
58 55 0.26
59 143 0.69
60 8 0.04
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGAAAATTTTGGGGTCAAAAATGAAATTTTTGGACATTCGA
Found at i:6206 original size:29 final size:29
Alignment explanation
Indices: 6068--6326 Score: 135
Period size: 30 Copynumber: 8.8 Consensus size: 29
6058 ATTTTTTCAC
*
6068 ATTCGAGGGTAAAATTGTAA-TTTTGGAA
1 ATTCGAGGGTAAAATGGTAATTTTTGGAA
** **
6096 ATTTTAGGGTTAAAAATGG-AA-TTTTCAAA
1 ATTCGAGGG-T-AAAATGGTAATTTTTGGAA
* * *
6125 CATT-TAGTGATAAAATGGTAATTCTTGGAA
1 -ATTCGAG-GGTAAAATGGTAATTTTTGGAA
* *
6155 AGTTTC--GGGTCAAAAAT-GAAATTTTTGGAC
1 A--TTCGAGGGT--AAAATGGTAATTTTTGGAA
* *
6185 ATTCAAGGGTAAAATGGTAATTGTTGGAAA
1 ATTCGAGGGTAAAATGGTAATTTTTGG-AA
* * *
6215 ATTCGA-GGTCAAAAATAG-AATTTTCGGAT
1 ATTCGAGGGT--AAAATGGTAATTTTTGGAA
* *
6244 ATTCGGGGGTAAAGTGGTAATTTTTGGAA
1 ATTCGAGGGTAAAATGGTAATTTTTGGAA
* *
6273 AGTTTGAGGTTAAAAATGG-AATTTTTGGAA
1 A-TTCGAGGGT-AAAATGGTAATTTTTGGAA
*
6303 ATT-TAGGGGTAAAATGGTAATTTT
1 ATTCGA-GGGTAAAATGGTAATTTT
6327 AAAAATTCCT
Statistics
Matches: 176, Mismatches: 32, Indels: 45
0.70 0.13 0.18
Matches are distributed among these distances:
28 35 0.20
29 57 0.32
30 65 0.37
31 19 0.11
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (29 bp):
ATTCGAGGGTAAAATGGTAATTTTTGGAA
Found at i:6288 original size:118 final size:116
Alignment explanation
Indices: 6012--6374 Score: 370
Period size: 118 Copynumber: 3.1 Consensus size: 116
6002 TTTGGATGCC
*** * ** *
6012 CGGGGGTAAAATGGTAATTTTCAAAAATTTTGGGGTCAAAAATGAAATTTTTTCACATTCGAGGG
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTTT-GGGTCAAAAATGAAATTTTTGGACATTCAAGGG
* ** * * *
6077 TAAAATTGTAATTTTGG-AAATTTTAGGGTTAAAAATGGAATTTTCAAACATT
65 TAAAATGGTAATTTTGGAAAATTCCA-GGTAAAAAATGGAATTTTCAGATATT
** * * *
6129 TAGTGATAAAATGGTAATTCTTGGAAAGTTTCGGGTCAAAAATGAAATTTTTGGACATTCAAGGG
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTTT-GGGTCAAAAATGAAATTTTTGGACATTCAAGGG
* * * *
6194 TAAAATGGTAATTGTTGGAAAATTCGAGGTCAAAAATAGAATTTTCGGATATT
65 TAAAATGGTAATT-TTGGAAAATTCCAGGTAAAAAATGGAATTTTCAGATATT
* * * * * *
6247 CGGGGGTAAAGTGGTAATTTTTGGAAAGTTTGAGGTTAAAAATGGAATTTTTGGAAATTTAGGGG
1 CGGGGGTAAAATGGTAATTTTTGGAAAGTTTG-GGTCAAAAATGAAATTTTTGGACATTCAAGGG
* * * *
6312 TAAAATGGTAATTTT-AAAAATTCCTGGTAAAAAATGGAATTTTTAGATGTT
65 TAAAATGGTAATTTTGGAAAATTCCAGGTAAAAAATGGAATTTTCAGATATT
*
6363 CGGGGGAAAAAT
1 CGGGGGTAAAAT
6375 ATGATTTTTG
Statistics
Matches: 201, Mismatches: 42, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
116 38 0.19
117 67 0.33
118 90 0.45
119 6 0.03
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.34
Consensus pattern (116 bp):
CGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGTCAAAAATGAAATTTTTGGACATTCAAGGGT
AAAATGGTAATTTTGGAAAATTCCAGGTAAAAAATGGAATTTTCAGATATT
Found at i:7980 original size:6 final size:6
Alignment explanation
Indices: 7969--8053 Score: 65
Period size: 6 Copynumber: 14.8 Consensus size: 6
7959 TTGGATATTA
*
7969 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT CTAAA-- TAGATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT -TAAATT TAAATT
* * * *
8015 TAAACT T-AATA TAAACT TAAATT TAAA-A TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAAT
8054 CTTGTTGGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
4 5 0.08
5 9 0.15
6 41 0.67
7 6 0.10
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:7996 original size:23 final size:23
Alignment explanation
Indices: 7968--8053 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 23
7958 TTTGGATATT
7968 ATAAATTTAAATTTAAATTTATA
1 ATAAATTTAAATTTAAATTTATA
7991 ATAAATTTAAATTCTAAATAGATT-TAA
1 ATAAATTTAAATT-TAAAT---TTAT-A
* * * *
8018 ACTTAATATAAACTTAAATTTAAA
1 A-TAAATTTAAATTTAAATTTATA
8042 ATAAATTTAAAT
1 ATAAATTTAAAT
8054 CTTGTTGGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
23 21 0.43
24 9 0.18
26 1 0.02
27 9 0.18
28 9 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (23 bp):
ATAAATTTAAATTTAAATTTATA
Found at i:7997 original size:17 final size:16
Alignment explanation
Indices: 7975--8053 Score: 95
Period size: 17 Copynumber: 4.7 Consensus size: 16
7965 ATTATAAATT
7975 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
7992 TAAATTTAAATTCTAAA
1 TAAATTTAAATT-TAAA
* *
8009 TAGATTTAAACTTAATA
1 TAAATTTAAATTTAA-A
*
8026 TAAACTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
8043 TAAATTTAAAT
1 TAAATTTAAAT
8054 CTTGTTGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.06
17 46 0.87
18 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:10398 original size:30 final size:30
Alignment explanation
Indices: 10364--10428 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
10354 TAACTTAATA
* *
10364 AACAAATGCCTCTAAAATAGTAACAAAATT
1 AACAAATGCCGCTAAAATAATAACAAAATT
*
10394 AACAAGTGCCGCTAAAATAATAACAAAATT
1 AACAAATGCCGCTAAAATAATAACAAAATT
10424 AACAA
1 AACAA
10429 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.20
Consensus pattern (30 bp):
AACAAATGCCGCTAAAATAATAACAAAATT
Done.