Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002015.1 Kokia drynarioides strain JFW-HI SEQ_113885, 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: 2165
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Found at i:25 original size:15 final size:15
Alignment explanation
Indices: 5--50 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1 TTTG
5 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
20 ATATTAATAATTATT
1 ATATTAATAATAATA
35 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
50 A
1 A
51 AAAAACGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:37 original size:7 final size:7
Alignment explanation
Indices: 12--50 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2 TTGATATTAA
12 TAATAA-
1 TAATAAT
18 TAAT-AT
1 TAATAAT
24 TAATAAT
1 TAATAAT
*
31 TATTAAT
1 TAATAAT
38 TAATAAT
1 TAATAAT
45 TAATAA
1 TAATAA
51 AAAAACGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:1249 original size:59 final size:59
Alignment explanation
Indices: 1157--1762 Score: 757
Period size: 59 Copynumber: 10.4 Consensus size: 59
1147 GGAGGTCCTT
* *
1157 GAACTTTCCAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1216 GAACTTTCCAAAAATTATCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
*
1275 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * *
1333 GATCTTCCCAAAAATTACCATTTTATCCTCGAACATCCAAAAATCTCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
1392 GAACCTTCTAAAAATTACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1451 GAACTTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1510 AAACCTTCTAAAAATTACCA-TTTATCCC-CAAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * *
1568 GAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCA---TTAACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * * *
1624 GGA-TCTTCTAAAAATTACCATTTTACCCTCGAACTTCAAAAAAACCCATATTT-ACCTC
1 GAACT-TTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * **
1682 GGA-TCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTT-ATTCC
1 GAACT-TTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
1740 GAACATTCC-AAAACTACCATTTT
1 GAACTTTCCAAAAATTACCATTTT
1763 GCCACTTTGT
Statistics
Matches: 485, Mismatches: 53, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.00
56 46 0.09
57 13 0.03
58 167 0.34
59 258 0.53
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
GAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:1458 original size:176 final size:176
Alignment explanation
Indices: 1162--1762 Score: 815
Period size: 176 Copynumber: 3.4 Consensus size: 176
1152 TCCTTGAACT
*
1162 TTCCAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
* *
1227 AAATTATCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCCAAAAATTA
66 AAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCTAAAAATTA
1292 CCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTC-GATC
131 CCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTCAGATC
* * * * * *
1337 TTCCCAAAAATTACCATTTTATCCTCGAACATCCAAAAATCTCATTTTTGACCCCGAACCTTCTA
1 TT-CCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCA
* * *
1402 AAAATTACCATTTTACCCTCGAATTTCCAAAAATCCCATTTTTGACCCCGAACTTTCTAAAAATT
65 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCTAAAAATT
* * * *
1467 ACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCAAACC
130 ACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCTCAGATC
* * *
1515 TTCTAAAAATTACCA-TTTATCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
* * *
1579 AAATTACCATTTTACCCCCGAACTTCCAAAAATCTCA---TTAACCTCGGA-TCTTCTAAAAATT
66 AAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACT-TTCTAAAAATT
* * *
1640 ACCATTTTACCCTCGAACTTCAAAAAAACCCATATTT-ACCTCGGATC
130 ACCATTTTACCCTCGAACTTCCAAAAATCCCAT-TTTGACCTCAGATC
* * * ** *
1687 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTT-ATTCCGAACATTCC-A
1 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
*
1750 AAACTACCATTTT
66 AAATTACCATTTT
1763 GCCACTTTGT
Statistics
Matches: 376, Mismatches: 44, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
171 13 0.03
172 35 0.09
173 78 0.21
175 2 0.01
176 222 0.59
177 22 0.06
178 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (176 bp):
TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACTTTCCAA
AAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACTTTCTAAAAATTA
CCATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCTCAGATC
Found at i:1762 original size:28 final size:28
Alignment explanation
Indices: 1157--1762 Score: 456
Period size: 29 Copynumber: 20.8 Consensus size: 28
1147 GGAGGTCCTT
*
1157 GAACTTTCCAAAAATCACCATTTTACCCCC
1 GAAC-TTCCAAAAAT-ACCATTTTACCCTC
*
1187 GAACTTCCAAAAATCCCATTTTTGACCC-C
1 GAACTTCCAAAAATACCA-TTTT-ACCCTC
*
1216 GAACTTTCCAAAAATTATCATTTTACCCTC
1 GAAC-TTCCAAAAA-TACCATTTTACCCTC
1246 GAACTTCCAAAAAT-CTCATTTTTGA-CCTC
1 GAACTTCCAAAAATAC-CA-TTTT-ACCCTC
1275 GAACTTTCCAAAAATTACCATTTTACCCTC
1 GAAC-TTCCAAAAA-TACCATTTTACCCTC
*
1305 GAACTTCCAAAAATCCCATTTTGA-CCTC
1 GAACTTCCAAAAATACCATTTT-ACCCTC
* *
1333 GATCTTCCCAAAAATTACCATTTTATCCTC
1 GAACTT-CCAAAAA-TACCATTTTACCCTC
*
1363 GAACATCCAAAAAT-CTCATTTTTGACCC-C
1 GAACTTCCAAAAATAC-CA-TTTT-ACCCTC
*
1392 GAACCTTCTAAAAATTACCATTTTACCCTC
1 GAA-CTTCCAAAAA-TACCATTTTACCCTC
* *
1422 GAATTTCCAAAAATCCCATTTTTGACCC-C
1 GAACTTCCAAAAATACCA-TTTT-ACCCTC
* *
1451 GAACTTTCTAAAAATTACCATTTTACCCCC
1 GAAC-TTCCAAAAA-TACCATTTTACCCTC
* *
1481 AAACTTCCAAAAATCCCATTTTTGA-CCTC
1 GAACTTCCAAAAATACCA-TTTT-ACCCTC
* *
1510 AAACCTTCTAAAAATTACCA-TTTATCCC-C
1 GAA-CTTCCAAAAA-TACCATTTTA-CCCTC
* *
1539 AAACTTCCAAAAATCCCATTTTTGACCC-C
1 GAACTTCCAAAAATACCA-TTTT-ACCCTC
*
1568 GAACTTTCCAAAAATTACCATTTTACCCCC
1 GAAC-TTCCAAAAA-TACCATTTTACCCTC
*
1598 GAACTTCCAAAAAT-CTCA--TTAACCTC
1 GAACTTCCAAAAATAC-CATTTTACCCTC
* *
1624 GGATCTTCTAAAAATTACCATTTTACCCTC
1 -GAACTTCCAAAAA-TACCATTTTACCCTC
*
1654 GAACTT-CAAAAAAACCCATATTTA-CCTC
1 GAACTTCCAAAAATA-CCAT-TTTACCCTC
* *
1682 GGATCTTCTAAAAATTACCATTTTACCCTC
1 -GAACTTCCAAAAA-TACCATTTTACCCTC
**
1712 GAACTTCCAAAAAT-CCTATTTTTATTC-C
1 GAACTTCCAAAAATACC-A-TTTTACCCTC
*
1740 GAACATTCCAAAACTACCATTTT
1 GAAC-TTCCAAAAATACCATTTT
1763 GCCACTTTGT
Statistics
Matches: 476, Mismatches: 44, Indels: 114
0.75 0.07 0.18
Matches are distributed among these distances:
26 6 0.01
27 20 0.04
28 74 0.16
29 196 0.41
30 156 0.33
31 22 0.05
32 2 0.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (28 bp):
GAACTTCCAAAAATACCATTTTACCCTC
Done.