Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013878.1 Kokia drynarioides strain JFW-HI SEQ_128906, 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: 323362
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 33 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:305847 original size:36 final size:36
Alignment explanation
Indices: 305789--305974 Score: 219
Period size: 36 Copynumber: 5.2 Consensus size: 36
305779 TTAGCACAAT
* * * * *
305789 ATATTCACTATCACATGACATGAATAATATACCTAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
305825 ATATTTATTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * *
305861 ATATTTACTATGACATGGTATAAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * * *
305897 ATATTTATTGTTACATGACATGAATAACATACTCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
305933 ATATTTACTGTCACATGGCTTGAATAATATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
305969 ATATTT
1 ATATTT
305975 TTTTGCACAA
Statistics
Matches: 124, Mismatches: 26, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:305906 original size:72 final size:72
Alignment explanation
Indices: 305789--305974 Score: 241
Period size: 72 Copynumber: 2.6 Consensus size: 72
305779 TTAGCACAAT
* * * * * *
305789 ATATTCACTATCACATGACATGAATAATATACCTACATATTTATTGTCT-CATGGCATGAATAAC
1 ATATTTACTATCACATGGCTTAAATAATATACCCACATATTTATTGT-TACATGACATGAATAAC
305853 ATACCCAC
65 ATACCCAC
* *
305861 ATATTTACTATGACATGG-TATAAATAACATACCCACATATTTATTGTTACATGACATGAATAAC
1 ATATTTACTATCACATGGCT-TAAATAATATACCCACATATTTATTGTTACATGACATGAATAAC
*
305925 ATACTCAC
65 ATACCCAC
* *
305933 ATATTTACTGTCACATGGCTTGAATAATATACCCACATATTT
1 ATATTTACTATCACATGGCTTAAATAATATACCCACATATTT
305975 TTTTGCACAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
71 1 0.01
72 96 0.98
73 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (72 bp):
ATATTTACTATCACATGGCTTAAATAATATACCCACATATTTATTGTTACATGACATGAATAACA
TACCCAC
Found at i:307315 original size:41 final size:41
Alignment explanation
Indices: 307270--307352 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
307260 ACCAGAAAGC
307270 TAGTGAGTTGGGTATACGAATTTTGCAGTATGTAGAATCAT
1 TAGTGAGTTGGGTATACGAATTTTGCAGTATGTAGAATCAT
307311 TAGTGAGTTGGGTATACGAATTTTGCAGTATGTAGAATCAT
1 TAGTGAGTTGGGTATACGAATTTTGCAGTATGTAGAATCAT
307352 T
1 T
307353 CACAATAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (41 bp):
TAGTGAGTTGGGTATACGAATTTTGCAGTATGTAGAATCAT
Found at i:312030 original size:13 final size:13
Alignment explanation
Indices: 312012--312036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312002 AGTTGAAACC
312012 GATAAGAAAGAAA
1 GATAAGAAAGAAA
312025 GATAAGAAAGAA
1 GATAAGAAAGAA
312037 GGTGCGAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (13 bp):
GATAAGAAAGAAA
Found at i:319153 original size:64 final size:64
Alignment explanation
Indices: 319075--319202 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
319065 ACAAACAAGC
319075 ATATTTAGTCATATATACATATAATCACAATCAAACACAATTTATGATAATTTGGCCGTTGAGA
1 ATATTTAGTCATATATACATATAATCACAATCAAACACAATTTATGATAATTTGGCCGTTGAGA
319139 ATATTTAGTCATATATACATATAATCACAATCAAACACAATTTATGATAATTTGGCCGTTGAGA
1 ATATTTAGTCATATATACATATAATCACAATCAAACACAATTTATGATAATTTGGCCGTTGAGA
319203 CTATGAAACA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (64 bp):
ATATTTAGTCATATATACATATAATCACAATCAAACACAATTTATGATAATTTGGCCGTTGAGA
Found at i:319705 original size:23 final size:23
Alignment explanation
Indices: 319670--320136 Score: 596
Period size: 23 Copynumber: 20.4 Consensus size: 23
319660 ATCTTAATTT
319670 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
319693 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
319716 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
319739 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
319762 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
319785 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
319808 TTTGAGTACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
319831 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
319854 TTTAAACACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
319877 TTTAAGCATAATTTA-ATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
319899 TTTGAGCACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
319922 TTTAAGTATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
319945 TTTGAGCACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
319968 TTTAAGAATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
319991 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
320014 TTTAAGTATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
320037 TTTGAGCACAAAT-ATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
320059 TTTAAGCATAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
*
320082 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
320105 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
320128 TTTAAGCAC
1 TTTAAGCAC
320137 GAATATAAGA
Statistics
Matches: 382, Mismatches: 60, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
22 38 0.10
23 344 0.90
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:319949 original size:137 final size:138
Alignment explanation
Indices: 319674--320136 Score: 689
Period size: 137 Copynumber: 3.4 Consensus size: 138
319664 TAATTTTTTA
* * *
319674 AGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCATAAATCATATTAATA
1 AGCACAAATCACATTAATATTTAATCATAAATCACATTAATATTTAAGCACAAATCACATTAATA
* * * *
319739 TTTGAGCACAAATCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCACAAATCACATT
66 TTTAAGCATAAATCACATTAATATTTGAGCACAAATTATATTAATATTTAAGCATAAATCACATT
319804 AATATTTG
131 AATATTTG
* * * *
319812 AGTACAAATCATATTAATATTTAAGT-ACAAATCACATTAATATTTAAACACAAATCACATTAAT
1 AGCACAAATCACATTAATATTTAA-TCATAAATCACATTAATATTTAAGCACAAATCACATTAAT
* * *
319876 ATTTAAGCATAATTTA-ATTAATATTTGAGCACAAATTATATTAATATTTAAGTATAAATCACAT
65 ATTTAAGCATAAATCACATTAATATTTGAGCACAAATTATATTAATATTTAAGCATAAATCACAT
319940 TAATATTTG
130 TAATATTTG
* * **
319949 AGCACAAATTATATTAATATTTAAGAATAAATCACATTAATATTTAAGCACAAATCACATTAATA
1 AGCACAAATCACATTAATATTTAATCATAAATCACATTAATATTTAAGCACAAATCACATTAATA
*
320014 TTTAAGTATAAATCACATTAATATTTGAGCACAAA-TATATTAATATTTAAGCATAAATCACATT
66 TTTAAGCATAAATCACATTAATATTTGAGCACAAATTATATTAATATTTAAGCATAAATCACATT
* * *
320078 ACTACTTA
131 AATATTTG
*
320086 AGCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCAC
1 AGCACAAATCACATTAATATTTAATCATAAATCACATTAATATTTAAGCAC
320137 GAATATAAGA
Statistics
Matches: 291, Mismatches: 31, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
137 204 0.70
138 86 0.30
139 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.36
Consensus pattern (138 bp):
AGCACAAATCACATTAATATTTAATCATAAATCACATTAATATTTAAGCACAAATCACATTAATA
TTTAAGCATAAATCACATTAATATTTGAGCACAAATTATATTAATATTTAAGCATAAATCACATT
AATATTTG
Found at i:322989 original size:6 final size:6
Alignment explanation
Indices: 322978--323003 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
322968 CACACACCTC
322978 TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TC
323004 TTCCTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Done.