Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007534.1 Kokia drynarioides strain JFW-HI SEQ_122159, 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: 6205
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:1317 original size:32 final size:34
Alignment explanation
Indices: 1268--1330 Score: 112
Period size: 32 Copynumber: 1.9 Consensus size: 34
1258 CAAACGAAAA
1268 TTTGTGGAAAAAGGACACATAATAAAATATAATT
1 TTTGTGGAAAAAGGACACATAATAAAATATAATT
1302 TTTGTGG-AAAA-GACACATAATAAAATATA
1 TTTGTGGAAAAAGGACACATAATAAAATATA
1331 GTTTATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 18 0.62
33 4 0.14
34 7 0.24
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (34 bp):
TTTGTGGAAAAAGGACACATAATAAAATATAATT
Found at i:3907 original size:17 final size:17
Alignment explanation
Indices: 3887--3960 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 17
3877 TTAAAATCTT
* *
3887 AATTCATTTTAATTTTA
1 AATTTATTTTAAATTTA
*
3904 AATTTATTGTAAATTTA
1 AATTTATTTTAAATTTA
** ** *
3921 ACCTTATTTGGAGTTTA
1 AATTTATTTTAAATTTA
3938 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
3955 AATTTA
1 AATTTA
3961 AAAGTTTAAT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:4210 original size:17 final size:18
Alignment explanation
Indices: 4177--4212 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4167 ATGAAGATCT
4177 GCAAAAGATAAAACAGAG
1 GCAAAAGATAAAACAGAG
*
4195 GCAAAAGA-ACAACAGAG
1 GCAAAAGATAAAACAGAG
4212 G
1 G
4213 AGGAAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.14, G:0.25, T:0.03
Consensus pattern (18 bp):
GCAAAAGATAAAACAGAG
Found at i:5393 original size:30 final size:28
Alignment explanation
Indices: 5317--5573 Score: 160
Period size: 30 Copynumber: 8.6 Consensus size: 28
5307 AAAAGGTCCT
* *
5317 TAAACTTTTTTAAAATTACATTTTAACCAC
1 TAAA-TTTTCTAAAATTATATTTTAACC-C
*
5347 -ATATTTTTCTAAAATTATATTTTAACCTC
1 TA-AATTTTCTAAAATTATATTTTAACC-C
*
5376 TAAATTTCTCAAAAATTATATTTTTAACCC
1 TAAATTT-TCTAAAATTATA-TTTTAACCC
* *
5406 TAAAACTTTTCCAAAATTATATTTTGACCC
1 T-AAA-TTTTCTAAAATTATATTTTAACCC
* * *
5436 TTAAAGTCTTCCAAAATTACATTTTAACCC
1 -TAAA-TTTTCTAAAATTATATTTTAACCC
* *
5466 TTGAACTTTTCTAAAATTATATTTTGACCCC
1 -T-AAATTTTCTAAAATTATATTTT-AACCC
* * *
5497 TAAATATTT-TCGAAATCACATTTTAACCC
1 TAAAT-TTTCT-AAAATTATATTTTAACCC
* * *
5526 TCAAACTTTTCTAAAATCATATCTTGACCC
1 T-AAA-TTTTCTAAAATTATATTTTAACCC
5556 TCAAACTTCTT-TAAAATT
1 T-AAA-TT-TTCTAAAATT
5574 TCATTTCCAT
Statistics
Matches: 185, Mismatches: 27, Indels: 30
0.76 0.11 0.12
Matches are distributed among these distances:
29 36 0.19
30 113 0.61
31 33 0.18
32 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTTTCTAAAATTATATTTTAACCC
Found at i:5532 original size:120 final size:120
Alignment explanation
Indices: 5328--5556 Score: 302
Period size: 120 Copynumber: 1.9 Consensus size: 120
5318 AAACTTTTTT
* * *
5328 AAAATTACATTTTAACCACATATTTTTCTAAAATTATATTTTAACCTCTAAATTTCTCAAAAATT
1 AAAATTACATTTTAACCACATACTTTTCTAAAATTATATTTTAACCCCTAAATTTCTCAAAAATC
* * *
5393 ATATTTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCTTAAAGTCTTCC
66 ACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCTTAAAGTCTTCC
* * * *
5448 AAAATTACATTTTAACC-CTTGAACTTTTCTAAAATTATATTTTGACCCCTAAATATTTTC-GAA
1 AAAATTACATTTTAACCACAT--ACTTTTCTAAAATTATATTTTAACCCCTAAAT-TTCTCAAAA
* *
5511 ATCACA-TTTTAACCCTCAAACTTTTCTAAAATCATATCTTGACCCT
63 ATCACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCT
5557 CAAACTTCTT
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
119 2 0.02
120 53 0.56
121 35 0.37
122 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (120 bp):
AAAATTACATTTTAACCACATACTTTTCTAAAATTATATTTTAACCCCTAAATTTCTCAAAAATC
ACATTTTTAACCCTAAAACTTTTCCAAAATCATATCTTGACCCTTAAAGTCTTCC
Found at i:5579 original size:60 final size:60
Alignment explanation
Indices: 5325--5579 Score: 252
Period size: 60 Copynumber: 4.2 Consensus size: 60
5315 CTTAAACTTT
* * * *
5325 TTTAAAATTACATTTTAA-CCACATATTTTTCTAAAATTATATTTT-AACCTCTAAATTTC
1 TTTAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAA-TTC
** * * * *
5384 TCAAAAATTATATTTTTAACCCTAAAACTTTTCCAAAATTATATTTTGACCCT-TAAAGTC
1 TTTAAAATTACA-TTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAATTC
* **
5444 TTCCAAAATTACATTTTAACCCTTGAACTTTTCTAAAATTATATTTTGACCC-CTAAATAT-
1 TT-TAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAAT-TC
* * * *
5504 TTTCGAAATCACATTTTAACCCTCAAACTTTTCTAAAATCATATCTTGACCCTC-AAACTTC
1 TTT-AAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAA-TTC
*
5565 TTTAAAATTTCATTT
1 TTTAAAATTACATTT
5580 CCATCCCAAG
Statistics
Matches: 159, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
59 9 0.06
60 106 0.67
61 40 0.25
62 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (60 bp):
TTTAAAATTACATTTTAACCCTCAAACTTTTCTAAAATTATATTTTGACCCTCTAAATTC
Done.