Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011037.1 Kokia drynarioides strain JFW-HI SEQ_126008, 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: 4150
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Found at i:3240 original size:29 final size:29
Alignment explanation
Indices: 3194--3506 Score: 267
Period size: 30 Copynumber: 10.8 Consensus size: 29
3184 AAGGTCCCTA
* *
3194 AACTTCCAAAATTTCCATTTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
***
3223 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* *
3253 AACTTCCAAAAATTCCA-TTTTAACCCCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* **
3281 AACATCCAAAAAT-CCATTTTTTGACCCCAA
1 AACTTCCAAAAATCCCA-TTTTT-ACCCCCG
* **
3311 AACTTCCAAAAATCTCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* * *
3341 AACTTCTAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
** * *
3370 AACTTCCAAAAATTACATTTTTACTCTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* *
3399 AATTTCCAAAAATCCAATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* * *
3428 AAACTTCCAAAAATTCCGTTTTTA-CCTCG
1 -AACTTCCAAAAATCCCATTTTTACCCCCG
* * * *
3457 AACTTCTAAAAATCTCATTTTTA-GCCTG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
*
3485 AACTTCCAAAAATCTCATTTTT
1 AACTTCCAAAAATCCCATTTTT
3507 GACCTCAAAA
Statistics
Matches: 233, Mismatches: 44, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
27 3 0.01
28 57 0.24
29 84 0.36
30 87 0.37
31 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCCG
Found at i:3281 original size:58 final size:57
Alignment explanation
Indices: 3189--3505 Score: 302
Period size: 58 Copynumber: 5.5 Consensus size: 57
3179 CCCTAAAGGT
* *
3189 CCCTAAACTTCCAAAATTTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAACTTCCAAAAATTCCA-TTTTAACCCCGAACTTCCAAAAATCCCATTTTTGA
*
3247 CCCTAAAACTTCCAAAAATTCCATTTTAACCCCGAACATCCAAAAAT-CCATTTTTTGA
1 CCCT-AAACTTCCAAAAATTCCATTTTAACCCCGAACTTCCAAAAATCCCA-TTTTTGA
* * * * *
3305 CCCCAAAACTTCCAAAAA-TCTCATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTT-A
1 -CCCTAAACTTCCAAAAATTC-CA-TTTTAACCCC-GAACTTCCAAAAATCCCATTTTTGA
* * * * * *
3364 CCCTCGAACTTCCAAAAATTACATTTTTACTCTCGAATTTCCAAAAATCCAATTTTTGA
1 CCCT-AAACTTCCAAAAATTCCATTTTAAC-CCCGAACTTCCAAAAATCCCATTTTTGA
* * * * * *
3423 CCCCGAAACTTCCAAAAATTCCGTTTTTACCTCGAACTTCTAAAAATCTCATTTTT-A
1 -CCCTAAACTTCCAAAAATTCCATTTTAACCCCGAACTTCCAAAAATCCCATTTTTGA
* *
3480 GCCTGAACTTCCAAAAA-TCTCATTTT
1 CCCTAAACTTCCAAAAATTC-CATTTT
3506 TGACCTCAAA
Statistics
Matches: 216, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
55 2 0.01
56 19 0.09
57 6 0.03
58 97 0.45
59 69 0.32
60 20 0.09
61 3 0.01
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTCCATTTTAACCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:3346 original size:88 final size:85
Alignment explanation
Indices: 3198--3592 Score: 395
Period size: 88 Copynumber: 4.5 Consensus size: 85
3188 TCCCTAAACT
* * *
3198 TCCAAAATTTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAAA
1 TCCAAAA-ATCCATTTTTA-CCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAAA
3263 AATTCCATTTTAACCCCGAACA
64 AATTCCATTTTAACCCCGAACA
* *
3285 TCCAAAAATCCATTTTTTGACCCCAAAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTCTAA
1 TCCAAAAATCCA-TTTTT-ACCCC-GAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAA
* *
3350 AAATTCCATTTTTACCCTCGAACT
63 AAATTCCATTTTAACCC-CGAACA
* * * *
3374 TCCAAAAATTACATTTTTACTCTCGAATTTCCAAAAATC-CAATTTTTGACCCCGAAACTTCCAA
1 TCCAAAAA-TCCATTTTTAC-CCCGAACTTCCAAAAATCTC-ATTTTTGACCCCAAAACTTCCAA
* * * *
3438 AAATTCCGTTTTTACCTCGAACT
63 AAATTCCATTTTAACCCCGAACA
* * * *
3461 TCTAAAAATCTCATTTTTAGCCTGAACTTCCAAAAATCTCATTTTTGACCTCAAAACATT-CAAA
1 TCCAAAAATC-CATTTTTACCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAAAC-TTCCAAA
* *
3525 AATTACCATTTCACCCCCGAGA-A
64 AATT-CCATTTTAACCCCGA-ACA
* * *
3548 TCCAAAATTACCA-TTTTACCCCGGA-TATCCGAAAAGTCTCATTTT
1 TCCAAAAAT-CCATTTTTACCCCGAACT-TCC-AAAAATCTCATTTT
3593 GAACTCCGAT
Statistics
Matches: 258, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
85 1 0.00
86 55 0.21
87 73 0.28
88 106 0.41
89 20 0.08
90 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.32
Consensus pattern (85 bp):
TCCAAAAATCCATTTTTACCCCGAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTCCAAAAA
TTCCATTTTAACCCCGAACA
Found at i:3577 original size:27 final size:29
Alignment explanation
Indices: 3523--3582 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
3513 AAAACATTCA
3523 AAAATTACCATTTCACCCCCGAGAATCC-
1 AAAATTACCATTTCACCCCCGAGAATCCG
*
3551 AAAATTACCATTTTA-CCCCG-GATATCCG
1 AAAATTACCATTTCACCCCCGAGA-ATCCG
3579 AAAA
1 AAAA
3583 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 9 0.31
28 18 0.62
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAATTACCATTTCACCCCCGAGAATCCG
Done.