Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008091.1 Kokia drynarioides strain JFW-HI SEQ_122749, 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: 49231
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:10379 original size:6 final size:7
Alignment explanation
Indices: 10354--10378 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
10344 CCCCAATACA
10354 AAAAATT
1 AAAAATT
10361 AAAAATT
1 AAAAATT
10368 AAAAATT
1 AAAAATT
10375 AAAA
1 AAAA
10379 TAATCTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:21779 original size:55 final size:55
Alignment explanation
Indices: 21719--21829 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
21709 GTCGAAATAG
21719 TGTGTTTTAATGTTGATAAGCATTACAAATCATGGGATGATATATTAATCAGCCA
1 TGTGTTTTAATGTTGATAAGCATTACAAATCATGGGATGATATATTAATCAGCCA
21774 TGTGTTTTAATGTTGATAAGCATTACAAATCATGGGATGATATATTAATCAGCCA
1 TGTGTTTTAATGTTGATAAGCATTACAAATCATGGGATGATATATTAATCAGCCA
21829 T
1 T
21830 TACCAACAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (55 bp):
TGTGTTTTAATGTTGATAAGCATTACAAATCATGGGATGATATATTAATCAGCCA
Found at i:23160 original size:105 final size:105
Alignment explanation
Indices: 22734--23279 Score: 587
Period size: 105 Copynumber: 5.2 Consensus size: 105
22724 GATATCAAGT
* * * *
22734 TCAATGCCTTGCTTTCTCATCGTGTCGACAATAAT-TTCAGCTTTAGAAACCA-ACCCTTTCTTG
1 TCAATGCCTTGCTTTCTCATTGTGCCAACAAT-ATCTTCAGCTTTAGAAACCATTCCC-TTCTTG
* * * *
22797 CAAAGCGCATCAATCAATGTATTATACGTGACAACGTTTGGC
64 CAAAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
* * * * * * *
22839 TCGATCCCTTGCTTTCCCATCGTGTCAACAATAAT-GTCAGCTTTAGAAACCA-TCCCGTCCTTG
1 TCAATGCCTTGCTTTCTCATTGTGCCAACAAT-ATCTTCAGCTTTAGAAACCATTCCC-TTCTTG
* * * *
22902 CAAAGCACATCAATTAATGTATTATACGTGACAACATTAGGC
64 CAAAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
* * * * ** *
22944 TCAATGCCTAGCTTTGTCATTCTGCCAACAATAGCTTTGGCTTTAGAAATCATTCCCTTCTTGCA
1 TCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGAAACCATTCCCTTCTTGCA
* * * * * *
23009 AAGAGCATCGATGAATATACTATATGTGACAACATCAAGC
66 AAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
* * * *
23049 TTAATGCCTTGCTTTGTCATTGTGCCAACGATATCTTCAGCTTTAGAAACCATTCGCTTCTTGCA
1 TCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGAAACCATTCCCTTCTTGCA
* *
23114 AAACGCGTCAATCAATGTACTATATGTGACAACATTAGGC
66 AAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
* * * * *
23154 TCAATGCTTTGCTTTTTCATTGTACCAACGATATCTTCGGCTTTAGAAACCATTCCCTTCTTGCA
1 TCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGAAACCATTCCCTTCTTGCA
* * * * *
23219 AAGTGCATCGATCAATATACTATATGTAACGACATTAGGC
66 AAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
*
23259 TTAATGCCTTGCTTTCTCATT
1 TCAATGCCTTGCTTTCTCATT
23280 TCGTAGAAGA
Statistics
Matches: 371, Mismatches: 68, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
104 1 0.00
105 366 0.99
106 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (105 bp):
TCAATGCCTTGCTTTCTCATTGTGCCAACAATATCTTCAGCTTTAGAAACCATTCCCTTCTTGCA
AAGCGCATCAATCAATGTACTATATGTGACAACATTAGGC
Found at i:35180 original size:15 final size:15
Alignment explanation
Indices: 35160--35189 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35150 ATCCCTTCAG
35160 CTCCAAAGCCAATAT
1 CTCCAAAGCCAATAT
35175 CTCCAAAGCCAATAT
1 CTCCAAAGCCAATAT
35190 TAAGCCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (15 bp):
CTCCAAAGCCAATAT
Found at i:43032 original size:15 final size:15
Alignment explanation
Indices: 43011--43052 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
43001 TAAGCACATC
43011 AATCAAGAATTAATA
1 AATCAAGAATTAATA
* *
43026 TATCAAGAA-TACTA
1 AATCAAGAATTAATA
43040 AATCAAGAATTAA
1 AATCAAGAATTAA
43053 GCACACATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (15 bp):
AATCAAGAATTAATA
Found at i:43448 original size:25 final size:23
Alignment explanation
Indices: 43420--43465 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
43410 GTTGGATCCA
43420 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
43445 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
43466 CCCTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:46396 original size:3 final size:3
Alignment explanation
Indices: 46388--46422 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
46378 TAATTGGTTC
* *
46388 TGT TGT TGT TGA TAT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
46423 CAGGATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (3 bp):
TGT
Found at i:48403 original size:21 final size:21
Alignment explanation
Indices: 48379--48453 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
48369 TATTTAAATA
48379 TAAATATTTAATAATTATATT
1 TAAATATTTAATAATTATATT
48400 TAAATATTTAA-AA-TATAGTT
1 TAAATATTTAATAATTATA-TT
*
48420 TATATAATTTAATTAATT-T-TT
1 TAAAT-ATTTAA-TAATTATATT
*
48441 TAAATAATTAATA
1 TAAATATTTAATA
48454 TTAATTACTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 6 0.13
20 13 0.28
21 23 0.50
23 3 0.07
24 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TAAATATTTAATAATTATATT
Found at i:48465 original size:22 final size:21
Alignment explanation
Indices: 48423--48466 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
48413 TATAGTTTAT
* **
48423 ATAATTTAATTAATTTTTTAA
1 ATAATTAAATTAATTACTTAA
48444 ATAATTAATATTAATTACTTAA
1 ATAATTAA-ATTAATTACTTAA
48466 A
1 A
48467 AATATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTAAATTAATTACTTAA
Done.