Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002623.1 Kokia drynarioides strain JFW-HI SEQ_114847, 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: 8610
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:649 original size:48 final size:48
Alignment explanation
Indices: 577--688 Score: 181
Period size: 48 Copynumber: 2.4 Consensus size: 48
567 TTAATGCAAG
* *
577 GCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAACAAAGAT
1 GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT
* *
625 GCATTTAACAAACAAAACACTTAATGATGCAAATTATTAAACAAAGAT
1 GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT
673 GCATTTAACAAA-AAAA
1 GCATTTAACAAACAAAA
689 GAAAATTTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 4 0.07
48 56 0.93
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.23
Consensus pattern (48 bp):
GCATTTAACAAACAAAACACTTAATAATGCAAATTACTAAACAAAGAT
Found at i:6636 original size:80 final size:80
Alignment explanation
Indices: 6492--6641 Score: 230
Period size: 80 Copynumber: 1.9 Consensus size: 80
6482 ACTAATTTCA
* * *
6492 TTTTAACTCTTGTAGAGAAGCTAATGAGTCATGTCTCTTCATTCGGATCTGACGTGGTTAAAAAG
1 TTTTAACTCTTGTAGAGAAGCCAATGAGTCATGTCTCTTCATTCGGATCTGACGTAGCTAAAAAG
6557 ACATGGCAATTTCGT
66 ACATGGCAATTTCGT
* *
6572 TTTTAACTCTTGTAG-GAAAGCCAATGAGTCATGTCTCTTCATTCGGATCTGATGTAGCTGAAAA
1 TTTTAACTCTTGTAGAG-AAGCCAATGAGTCATGTCTCTTCATTCGGATCTGACGTAGCTAAAAA
*
6636 GGCATG
65 GACATG
6642 ACATTTCTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.02
80 62 0.98
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (80 bp):
TTTTAACTCTTGTAGAGAAGCCAATGAGTCATGTCTCTTCATTCGGATCTGACGTAGCTAAAAAG
ACATGGCAATTTCGT
Found at i:7128 original size:48 final size:46
Alignment explanation
Indices: 7076--7220 Score: 168
Period size: 48 Copynumber: 3.0 Consensus size: 46
7066 GCTAATGCAT
* *
7076 TAATGCAAGGCATTTAGCAAAGATGCATTTAACAAACAAAACAGTTAA
1 TAATGC-AGG-ATTTAACAAAGATGCATTTAACAAACAAAACACTTAA
7124 TAATGCA-GATTACTAAACAAAGATGCATTTAACAAACAAAACACTTAA
1 TAATGCAGGATT--T-AACAAAGATGCATTTAACAAACAAAACACTTAA
* *
7172 TGATGCA-GATTATTAAACAAAGATGCATTTAACAAAAAAAACACTTAA
1 TAATGCAGGA-T-TT-AACAAAGATGCATTTAACAAACAAAACACTTAA
7220 T
1 T
7221 GAAACATAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
45 3 0.03
46 1 0.01
47 2 0.02
48 80 0.91
49 1 0.01
50 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.24
Consensus pattern (46 bp):
TAATGCAGGATTTAACAAAGATGCATTTAACAAACAAAACACTTAA
Found at i:7221 original size:48 final size:48
Alignment explanation
Indices: 7093--7222 Score: 224
Period size: 48 Copynumber: 2.7 Consensus size: 48
7083 AGGCATTTAG
* *
7093 CAAAGATGCATTTAACAAACAAAACAGTTAATAATGCAGATTACTAAA
1 CAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAA
*
7141 CAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTATTAAA
1 CAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAA
*
7189 CAAAGATGCATTTAACAAAAAAAACACTTAATGA
1 CAAAGATGCATTTAACAAACAAAACACTTAATGA
7223 AACATAAATA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 78 1.00
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (48 bp):
CAAAGATGCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAA
Found at i:8054 original size:214 final size:214
Alignment explanation
Indices: 7585--8064 Score: 558
Period size: 215 Copynumber: 2.2 Consensus size: 214
7575 ATTTCCCGAG
* *
7585 AAAATTGCTCGAAGGAA-TGCATCATCTTGAATACTTTAAGGAA-CAGAAGTTATAAAAGAACTA
1 AAAATTGCTCGAAGGAATTG-ATCGTCTTGAATACTTTAAGGAACCA-AAGTTATAAAAGAACCA
* * *
7648 GTAAAAGTTTAAAAAGTTCGGAAGTTCGTCCCAGAACCAATAGAGAATCAATTCTCATGTAAAAT
64 GTAAAAGTTTAAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAATCAATTCTCACGTAAAAT
* * * *
7713 GTGTTTAATTTAAAGACCAAATCCTGTTTACAAAGTGACAAACTATTTAGACCAAATGATTCGAT
129 GTGTTTAATTCAAAAACCAAAT-CTGTTTACAAAATGACAAACTATTTAGACCAAATGATTCAAT
* *
7778 TACCCAAGCATGGAATGTTCAA
193 TACACAAGAATGGAATGTTCAA
* * * *
7800 AAAATTGCTTGAAAGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAGGAACCAGT
1 AAAATTGCTCGAAGGAATTGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAGT
* ** * * *
7865 AAAAGTTTGACCAGTTCGGAATTTTGTCCAAGAACCAAGAGAGAAAT-AATTGTCACGTAATAA-
66 AAAAGTTTAAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAG-AATCAATTCTCACGTAA-AAT
* * *
7928 GTTTTTAATTCAAAAACACAAAT-TTTTTACAAAATGACAAACTATTTAGACCAAATGGTGT-AA
129 GTGTTTAATTCAAAAAC-CAAATCTGTTTACAAAATGACAAACTATTTAGACCAAATGAT-TCAA
** ** **
7991 TTTTATGAGAATGGAATGTTTGA
192 TTACACAAGAATGGAATGTTCAA
* * *
8014 AAAATTGCTCGAAGGAATTGATCGTCTTGATTAGTTTAAGGTACCAAAGTT
1 AAAATTGCTCGAAGGAATTGATCGTCTTGAATACTTTAAGGAACCAAAGTT
8065 GATACGAGTC
Statistics
Matches: 223, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
214 94 0.42
215 116 0.52
216 13 0.06
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (214 bp):
AAAATTGCTCGAAGGAATTGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACCAGT
AAAAGTTTAAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAATCAATTCTCACGTAAAATGT
GTTTAATTCAAAAACCAAATCTGTTTACAAAATGACAAACTATTTAGACCAAATGATTCAATTAC
ACAAGAATGGAATGTTCAA
Done.