Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006112.1 Kokia drynarioides strain JFW-HI SEQ_120622, 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: 2050
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Found at i:156 original size:18 final size:19
Alignment explanation
Indices: 122--163 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
112 AAAACGTTTC
*
122 AATAACTTTTATTAATATT
1 AATAACTGTTATTAATATT
141 AATAACTGTT-TTAATATT
1 AATAACTGTTATTAATATT
159 AATAA
1 AATAA
164 TAATACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (19 bp):
AATAACTGTTATTAATATT
Found at i:262 original size:7 final size:7
Alignment explanation
Indices: 240--278 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
230 TTGATATTAA
240 TAATAA-
1 TAATAAT
246 TAAT-AT
1 TAATAAT
252 TAATAAT
1 TAATAAT
259 TAATAAT
1 TAATAAT
266 TAATAAT
1 TAATAAT
273 TAATAA
1 TAATAA
279 AAAAAACACG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.26
7 22 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATAAT
Found at i:1416 original size:30 final size:30
Alignment explanation
Indices: 1382--1722 Score: 285
Period size: 30 Copynumber: 11.4 Consensus size: 30
1372 AAGGTCCTTA
1382 AACTCTCCAAAAATTACCA-TTTTACCCCCG
1 AACT-TCCAAAAATTACCATTTTTACCCCCG
* *
1412 AACTCCCAAAAA-T-CTCATTTTTTGA-CCCTG
1 AACTTCCAAAAATTAC-CA-TTTTT-ACCCCCG
*
1442 AACTTTCCAAAAATTACCA-TTTTACCCCCA
1 AAC-TTCCAAAAATTACCATTTTTACCCCCG
* * * *
1472 AACATCCAAAAA-TCCCATTTTTAACCCCA
1 AACTTCCAAAAATTACCATTTTTACCCCCG
* *
1501 AACTTTTCAAAAATTACCA-TTTTACCCCCT
1 AAC-TTCCAAAAATTACCATTTTTACCCCCG
* * *
1531 AACTTCCAAAAA-TCCCATTTTTAACCTCG
1 AACTTCCAAAAATTACCATTTTTACCCCCG
**
1560 AACTCTCCAAAAATTACCA-TTTTACCCCTA
1 AACT-TCCAAAAATTACCATTTTTACCCCCG
* * *
1590 AACTTCCAAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTACCATTTTT-ACCCCCG
*
1620 AATCTTCTAAAAATTACCATTTTTACCCCCG
1 AA-CTTCCAAAAATTACCATTTTTACCCCCG
* * *
1651 TACTTCTAAAAA-TCCCATTTTTTA-CCCCG
1 AACTTCCAAAAATTACCA-TTTTTACCCCCG
* *
1680 AACTTCTCGAAAATTACCA-TTTTACCCTCG
1 AACTTC-CAAAAATTACCATTTTTACCCCCG
1710 AACTTCCAAAAAT
1 AACTTCCAAAAAT
1723 CCAATTTTTG
Statistics
Matches: 249, Mismatches: 40, Indels: 45
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 11 0.04
29 86 0.35
30 102 0.41
31 45 0.18
32 3 0.01
33 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.31
Consensus pattern (30 bp):
AACTTCCAAAAATTACCATTTTTACCCCCG
Found at i:1741 original size:59 final size:59
Alignment explanation
Indices: 1389--1733 Score: 435
Period size: 59 Copynumber: 5.8 Consensus size: 59
1379 TTAAACTCTC
* * *
1389 CAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTTGACCCTGAACTT-T
1 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCCGAACTTCT
* * * * *
1448 CCAAAAATTACCATTTTACCCCCAAACATCCAAAAATCCCATTTTTAACCCCAAACTTTT
1 -CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCT
* * *
1508 CAAAAATTACCATTTTACCCCCTAACTTCCAAAAATCCCATTTTTAACCTCGAAC-TCT
1 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCT
** *
1566 CCAAAAATTACCATTTTACCCCTAAACTTCCAAAAAATCCCATTTTTGACCTCGAATCTTCT
1 -CAAAAATTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCCCGAA-CTTCT
* * *
1628 -AAAAATTACCATTTTTACCCCCGTACTTCTAAAAATCCCATTTTTTACCCCGAACTTCT
1 CAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCT
* * *
1687 CGAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCAATTTTTGA
1 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1734 TTTCGAACCT
Statistics
Matches: 251, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
58 2 0.01
59 128 0.51
60 103 0.41
61 15 0.06
62 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTCT
Done.