Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012126.1 Kokia drynarioides strain JFW-HI SEQ_127125, 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: 72632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 222 characters in sequence are not A, C, G, or T
Found at i:10786 original size:22 final size:22
Alignment explanation
Indices: 10751--10792 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10741 TAACGAAACG
*
10751 ATAACAAAACAACAACAAAATA
1 ATAACAAAACAACAAAAAAATA
* *
10773 ATAACAACATAACAAAAAAA
1 ATAACAAAACAACAAAAAAA
10793 AATTAAGCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.74, C:0.17, G:0.00, T:0.10
Consensus pattern (22 bp):
ATAACAAAACAACAAAAAAATA
Found at i:23453 original size:21 final size:20
Alignment explanation
Indices: 23429--23467 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23419 AAAAAATTGA
*
23429 ATTTATAAGTATAAAAAAACT
1 ATTTATAAG-AAAAAAAAACT
23450 ATTTATAAGAAAAAAAAA
1 ATTTATAAGAAAAAAAAA
23468 TCAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
ATTTATAAGAAAAAAAAACT
Found at i:46643 original size:18 final size:17
Alignment explanation
Indices: 46622--46661 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
46612 AAACATAACG
46622 AAAAAT-AAATTTAGAAA
1 AAAAATAAAATTTA-AAA
46639 AAAAATCAAAATTTAAAA
1 AAAAAT-AAAATTTAAAA
46657 AAAAA
1 AAAAA
46662 ATTTCAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 8 0.38
19 7 0.33
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAATAAAATTTAAAA
Found at i:48412 original size:11 final size:11
Alignment explanation
Indices: 48394--48444 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
48384 TTGTTTTTTT
48394 TATTATTTTAC
1 TATTATTTTAC
* **
48405 TATCATTTCGC
1 TATTATTTTAC
*
48416 TATTATATTAC
1 TATTATTTTAC
*
48427 TATTATTTTAT
1 TATTATTTTAC
48438 TATTATT
1 TATTATT
48445 ATTTAGATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (11 bp):
TATTATTTTAC
Found at i:48441 original size:22 final size:22
Alignment explanation
Indices: 48388--48443 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
48378 TTATCATTGT
* *
48388 TTTTTTTATTATTTTACTATCA
1 TTTTATTATTATATTACTATCA
*** *
48410 TTTCGCTATTATATTACTATTA
1 TTTTATTATTATATTACTATCA
48432 TTTTATTATTAT
1 TTTTATTATTAT
48444 TATTTAGATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTATTATTATATTACTATCA
Found at i:51477 original size:23 final size:23
Alignment explanation
Indices: 51458--51541 Score: 105
Period size: 23 Copynumber: 3.6 Consensus size: 23
51448 AACTTAATCA
*
51458 AACATGTTGACGAACATTAAACG
1 AACATGTTCACGAACATTAAACG
*
51481 AACATGTTCATGAACATTAAACG
1 AACATGTTCACGAACATTAAACG
* **
51504 AACATGTTCATGAACATATAATTG
1 AACATGTTCACGAACAT-TAAACG
*
51528 AACATGTTTACGAA
1 AACATGTTCACGAA
51542 TAATGTTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
23 38 0.70
24 16 0.30
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (23 bp):
AACATGTTCACGAACATTAAACG
Found at i:51508 original size:46 final size:47
Alignment explanation
Indices: 51432--51535 Score: 113
Period size: 46 Copynumber: 2.2 Consensus size: 47
51422 TTTAATATTC
* * * *
51432 ACGAATATGTTCATTTAACTTAATCAAACATGTTGACGAACAT-TAA
1 ACGAACATGTTCATTGAACTTAAACAAACATGTTCACGAACATATAA
* *
51478 ACGAACATGTTCA-TGAACATTAAACGAACATGTTCATGAACATATAA
1 ACGAACATGTTCATTGAAC-TTAAACAAACATGTTCACGAACATATAA
**
51525 TTGAACATGTT
1 ACGAACATGTT
51536 TACGAATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 4 0.08
46 32 0.67
47 12 0.25
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (47 bp):
ACGAACATGTTCATTGAACTTAAACAAACATGTTCACGAACATATAA
Found at i:52148 original size:12 final size:14
Alignment explanation
Indices: 52117--52154 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
52107 ATAATTAATA
52117 CTATT-AAATATTT
1 CTATTAAAATATTT
52130 CTATTAAAAT-TTT
1 CTATTAAAATATTT
52143 CT-TTAAAATATT
1 CTATTAAAATATT
52155 CATTCAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (14 bp):
CTATTAAAATATTT
Found at i:57919 original size:3 final size:3
Alignment explanation
Indices: 57911--57951 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
57901 GAAAAAGATA
57911 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
57952 AGAATCCACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:63807 original size:35 final size:35
Alignment explanation
Indices: 63761--63827 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
63751 AAAAGCGATT
63761 GTTAATATAAAGATCACAAGTTTCACCTGCACTTA
1 GTTAATATAAAGATCACAAGTTTCACCTGCACTTA
63796 GTTAATATAAAGATCACAAGTTTCACCTGCAC
1 GTTAATATAAAGATCACAAGTTTCACCTGCAC
63828 CTATAGTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (35 bp):
GTTAATATAAAGATCACAAGTTTCACCTGCACTTA
Found at i:64668 original size:85 final size:86
Alignment explanation
Indices: 64523--64692 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 86
64513 ACCTGGGTTT
* *
64523 TGATCAAGTTGCAATTATCCAAGTAAACAATTTGCAAGTTTCTCTTTTTCCCTAATTGGAGTTTC
1 TGATCAAGTTGCAATTATCCAAGTAAACAAGTTGCAAGTTTCTCTTTTTCCCTAATTGGAGTTTA
*
64588 TATTGTTTAGATTTGGATGAG
66 TATTATTTAGATTTGGATGAG
*
64609 TGATCAAGTTGCAATTATCCAAGTAAAC-AGTTGCAAGTTTCTCTTTTTCCCTATTTGGAGTTTA
1 TGATCAAGTTGCAATTATCCAAGTAAACAAGTTGCAAGTTTCTCTTTTTCCCTAATTGGAGTTTA
64673 TATTATTTAGATTTGGATGA
66 TATTATTTAGATTTGGATGA
64693 TAGGGGATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 52 0.65
86 28 0.35
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (86 bp):
TGATCAAGTTGCAATTATCCAAGTAAACAAGTTGCAAGTTTCTCTTTTTCCCTAATTGGAGTTTA
TATTATTTAGATTTGGATGAG
Done.