Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015100.1 Kokia drynarioides strain JFW-HI SEQ_130144, 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: 28198
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Warning! 118 characters in sequence are not A, C, G, or T
Found at i:7261 original size:3 final size:3
Alignment explanation
Indices: 7253--7282 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
7243 TGAATGCGTC
7253 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
7283 AACTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:13008 original size:40 final size:38
Alignment explanation
Indices: 12963--13042 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 38
12953 TGTTTTTATT
*
12963 TTTAATATAATATTTT-TATTAACATTTTAAATATAAATAA
1 TTTAATATAAT-TTTTATATTAACATTAT-AATAT-AATAA
*
13003 TTTAATATAATTTTTAATATTTACATTATAATATAATAA
1 TTTAATATAATTTTT-ATATTAACATTATAATATAATAA
13042 T
1 T
13043 ATTATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
39 10 0.28
40 16 0.44
41 10 0.28
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (38 bp):
TTTAATATAATTTTTATATTAACATTATAATATAATAA
Found at i:13020 original size:12 final size:13
Alignment explanation
Indices: 12960--13022 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 13
12950 ATTTGTTTTT
12960 ATTTTTAATATAA
1 ATTTTTAATATAA
12973 TATTTTT-AT-TAA
1 -ATTTTTAATATAA
*
12985 CATTTTAAATATAA
1 -ATTTTTAATATAA
*
12999 ATAATTTAATAT-A
1 AT-TTTTAATATAA
13012 ATTTTTAATAT
1 ATTTTTAATAT
13023 TTACATTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 16 0.39
13 9 0.22
14 16 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTAATATAA
Found at i:14101 original size:29 final size:29
Alignment explanation
Indices: 14046--14107 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
14036 ATCAAATATA
*
14046 TAATGTTATACATCAAATTTGATTTTATG
1 TAATGTTATACATCAAATTTGATTTTATC
* * *
14075 TAATTTTATACATACATATTTTA-TTTATC
1 TAATGTTATACAT-CAAATTTGATTTTATC
14104 TAAT
1 TAAT
14108 ATATAAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (29 bp):
TAATGTTATACATCAAATTTGATTTTATC
Found at i:17691 original size:125 final size:123
Alignment explanation
Indices: 17458--17710 Score: 328
Period size: 125 Copynumber: 2.0 Consensus size: 123
17448 ACATCATCCC
* *
17458 CGTTAATTTTTTTAATAATACTTTCATCAAATCTATCAAAAAAAGTTTGAAAAAAAAAACAGAGA
1 CGTTAATTTTTTTAACAATACTTTCATCAAATCTATCAAAAAAAGTTTGAAAAAAAAAACAAAGA
* * * * * *
17523 TTGATGGCTAAAATATCTAAAAAAATACAATTAAAACCATTTTGACGAAATATGTAAA
66 CTGATGCCAAAAAAATCTAAAAAAATACAATTAAAACCATTTTGACAAAATATATAAA
** * * * *
17581 CGTTAATTTTTTTAACGGTACTTTCATTAAATTTGTTAAAAAAAGTTTGAAAAAAAAAAAACAAA
1 CGTTAATTTTTTTAACAATACTTTCATCAAATCTATCAAAAAAAGTTTG--AAAAAAAAAACAAA
* *
17646 GGCTGATTGCCAAAAAAATCT-AAAAAATACAATTAATACCATTTTGACAAAATATATAAA
64 GACTGA-TGCCAAAAAAATCTAAAAAAATACAATTAAAACCATTTTGACAAAATATATAAA
17706 CGTTA
1 CGTTA
17711 GTGACCAAAT
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
123 42 0.38
125 58 0.52
126 11 0.10
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (123 bp):
CGTTAATTTTTTTAACAATACTTTCATCAAATCTATCAAAAAAAGTTTGAAAAAAAAAACAAAGA
CTGATGCCAAAAAAATCTAAAAAAATACAATTAAAACCATTTTGACAAAATATATAAA
Found at i:18404 original size:231 final size:231
Alignment explanation
Indices: 18001--18464 Score: 883
Period size: 231 Copynumber: 2.0 Consensus size: 231
17991 ATTTAAAAAC
* *
18001 AATAAAATTACCACGTATTCTTATCCATACCCAATGAGTGATTAAAGTGAATGTCAATCAACCAC
1 AATAAAATTACCACATATTCTTATCCATACCCAATGAGCGATTAAAGTGAATGTCAATCAACCAC
18066 ATTCTATGTATTTAAGGGTTTAACGAGGTTAATTACGAAATTAAAACTCGAATCTAAATTCAAAT
66 ATTCTATGTATTTAAGGGTTTAACGAGGTTAATTACGAAATTAAAACTCGAATCTAAATTCAAAT
*
18131 CGTGGAATTTCAACAACATATCTCGAAAAAGTGAATAGACAAGCCTTCCTATTTTCTTAATTTAG
131 CGTGAAATTTCAACAACATATCTCGAAAAAGTGAATAGACAAGCCTTCCTATTTTCTTAATTTAG
18196 CTCTGAGTTTAGGTTACCTCGAGACAAGAAATAGAG
196 CTCTGAGTTTAGGTTACCTCGAGACAAGAAATAGAG
*
18232 AATAAAATTACCACATATTCTTATCCATACTCAATGAGCGATTAAAGTGAATGTCAATCAACCAC
1 AATAAAATTACCACATATTCTTATCCATACCCAATGAGCGATTAAAGTGAATGTCAATCAACCAC
18297 ATTCTATGTATTTAAGGGTTTAACGAGGTTAATTACGAAATTAAAACTCGAATCTAAATTCAAAT
66 ATTCTATGTATTTAAGGGTTTAACGAGGTTAATTACGAAATTAAAACTCGAATCTAAATTCAAAT
*
18362 CGTGAAATTTCAACAACGTATCTCGAAAAAGTGAATAGACAAGCCTTCCTATTTTCTTAATTTAG
131 CGTGAAATTTCAACAACATATCTCGAAAAAGTGAATAGACAAGCCTTCCTATTTTCTTAATTTAG
18427 CTCTGAGTTTAGGTTACCTCGAGACAAGAAATAGAG
196 CTCTGAGTTTAGGTTACCTCGAGACAAGAAATAGAG
18463 AA
1 AA
18465 AAGCTATTTT
Statistics
Matches: 228, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 228 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (231 bp):
AATAAAATTACCACATATTCTTATCCATACCCAATGAGCGATTAAAGTGAATGTCAATCAACCAC
ATTCTATGTATTTAAGGGTTTAACGAGGTTAATTACGAAATTAAAACTCGAATCTAAATTCAAAT
CGTGAAATTTCAACAACATATCTCGAAAAAGTGAATAGACAAGCCTTCCTATTTTCTTAATTTAG
CTCTGAGTTTAGGTTACCTCGAGACAAGAAATAGAG
Found at i:18734 original size:48 final size:50
Alignment explanation
Indices: 18672--18773 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 50
18662 ATAATCACAT
* *
18672 ACCTCCCAAACATGACACTCAAGGGCTCAT-A-AACTTTTATTCAATTGC
1 ACCTCCCAAACATGACAATCAAGGCCTCATAACAACTTTTATTCAATTGC
* *
18720 ACCTCCCGACCATGACAATCAAGGCCTCATGACATCAACTTTTATTCAATTGC
1 ACCTCCCAAACATGACAATCAAGGCCTCAT-A-A-CAACTTTTATTCAATTGC
18773 A
1 A
18774 AGGCAGGCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
48 26 0.58
51 1 0.02
53 18 0.40
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.26
Consensus pattern (50 bp):
ACCTCCCAAACATGACAATCAAGGCCTCATAACAACTTTTATTCAATTGC
Found at i:19074 original size:42 final size:43
Alignment explanation
Indices: 19022--19103 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
19012 TAGATAACAT
* *
19022 CACAAATGATAAAT-AAAATTGTTTAAAAT-AATATAAATTGAA
1 CACAAATGATAAATAAAAATT-TTCAAAATAAAAATAAATTGAA
*
19064 CACAAGTGATAAATAAAAATTTTCAAAATAAAAATAAATT
1 CACAAATGATAAATAAAAATTTTCAAAATAAAAATAAATT
19104 TACGACAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 20 0.57
43 15 0.43
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (43 bp):
CACAAATGATAAATAAAAATTTTCAAAATAAAAATAAATTGAA
Found at i:19416 original size:28 final size:28
Alignment explanation
Indices: 19385--19440 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
19375 AACAAAAGTG
19385 AAATTAT-ATTTTAATTCTTAAAAAATTA
1 AAATTATGA-TTTAATTCTTAAAAAATTA
* * *
19413 AAATTTTGATTTAATTTTTTAAAAATTA
1 AAATTATGATTTAATTCTTAAAAAATTA
19441 TAAAGATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
AAATTATGATTTAATTCTTAAAAAATTA
Found at i:20505 original size:22 final size:22
Alignment explanation
Indices: 20480--20539 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
20470 TAAAAATGAT
* * *
20480 AAAATTTTAATTTAATTTTTTA
1 AAAATTATAATTTAATATTGTA
*
20502 AAAATTATATTTTTAATATTGTA
1 AAAATTATA-ATTTAATATTGTA
*
20525 AAAATTACAATTTAA
1 AAAATTATAATTTAA
20540 CTTCGGCCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAAATTATAATTTAATATTGTA
Found at i:22146 original size:29 final size:29
Alignment explanation
Indices: 22112--22167 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
22102 TTTGATTCTT
* *
22112 TTTAATAGTATAAGGACTAAATTGATCCA
1 TTTAATAATAGAAGGACTAAATTGATCCA
* *
22141 TTTAATAATAGAGGGACTAATTTGATC
1 TTTAATAATAGAAGGACTAAATTGATC
22168 TAGTACCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (29 bp):
TTTAATAATAGAAGGACTAAATTGATCCA
Found at i:26097 original size:35 final size:35
Alignment explanation
Indices: 26048--26115 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
26038 GACTTAGCAC
** * *
26048 TTATGTGTTCTTTGGTTGTATTTGGATGGATGTAT
1 TTATGTGTAATTTGGTTGTATTCGGAGGGATGTAT
*
26083 TTATGTGTAATTTGGTTGTGTTCGGAGGGATGT
1 TTATGTGTAATTTGGTTGTATTCGGAGGGATGT
26116 GATATGATGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.15, C:0.03, G:0.32, T:0.50
Consensus pattern (35 bp):
TTATGTGTAATTTGGTTGTATTCGGAGGGATGTAT
Done.