Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009365.1 Kokia drynarioides strain JFW-HI SEQ_124072, 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: 9852
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:667 original size:20 final size:21
Alignment explanation
Indices: 644--682 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
634 TAAATTTAAC
644 TTTAACC-TAAAATATTTATT
1 TTTAACCATAAAATATTTATT
* *
664 TTTACCCATAAATTATTTA
1 TTTAACCATAAAATATTTA
683 AAACCATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAACCATAAAATATTTATT
Found at i:3288 original size:41 final size:41
Alignment explanation
Indices: 3226--3526 Score: 386
Period size: 41 Copynumber: 7.3 Consensus size: 41
3216 ACTTGATGTA
*
3226 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* *
3268 TAAAGGAAGACTCGTGTCTCGAGATGAACATGATATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * *
3309 TAAAGCAAGACTCGTGACTCGAAATGAGCATGAAATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * * *
3350 AAAAGGAGGACTCGTGACTCGAAATCAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* *
3391 TAAAGGAAGACTCGTGTCTCGGGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * * *
3432 TAAAGGAATACTCATGTCTCGGGGTAAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * *
3473 TAAAGGAAGACTTGTGACTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATA-T
3515 TAAAGGAAGACT
1 TAAAGGAAGACT
3527 TATAACTCGG
Statistics
Matches: 229, Mismatches: 29, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
41 212 0.93
42 17 0.07
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
Found at i:3543 original size:123 final size:122
Alignment explanation
Indices: 3226--3564 Score: 369
Period size: 123 Copynumber: 2.7 Consensus size: 122
3216 ACTTGATGTA
* *
3226 TAAATGGAAGACTCATGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGAG
1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCG-G
* * * * * *
3291 -ATGAACATGATATTATATTAAAGCAAGACTCGTGACTCGAAATGAGCATGAAATTATAT
64 TA-GAGCATGAGATTATATTAAAGGAATACTCATGACTCGAAATAAGCATGAAATTATAT
* * * *
3350 AAAAGGAGGACTCGTGACTCGAAATCAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGGGG
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTC--GG
* *** *
3415 T-GAGCATGAGATTATATTAAAGGAATACTCATGTCTCGGGGTAAGCATGAGATTATAT
64 TAGAGCATGAGATTATATTAAAGGAATACTCATGACTCGAAATAAGCATGAAATTATAT
* * ** **
3473 TAAAGGAAGACTTGTGACTCGGGATGAGCATGAGATTATATTTAAAGGAAGACTTATAACTCGGT
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACTCGTGTCTCGGT
* *
3538 AGAGCATAAGATTGT-TTAAAAGGAATA
65 AGAGCATGAGATTATATT-AAAGGAATA
3565 TCTACGAGTC
Statistics
Matches: 180, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
122 5 0.03
123 153 0.85
124 21 0.12
125 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (122 bp):
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGGTA
GAGCATGAGATTATATTAAAGGAATACTCATGACTCGAAATAAGCATGAAATTATAT
Found at i:5713 original size:52 final size:52
Alignment explanation
Indices: 5632--5810 Score: 245
Period size: 52 Copynumber: 3.5 Consensus size: 52
5622 TTCGATGACT
*
5632 ATGACTATGTGTCATCGTGAGTATCTGAATCCTTTACAGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCG
* * *
5684 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAAAATATGAGGTCTG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCG
* * ** **
5736 ATG-CTTATGTGTCATCGTGAGTATATAAATCC-TAATGGATTAAAAGGTCCG
1 ATGAC-TATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCG
5787 ATGACTATGTGTCATCGTGAGTAT
1 ATGACTATGTGTCATCGTGAGTAT
5811 TAAATGAAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
51 34 0.30
52 78 0.70
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCG
Found at i:6555 original size:21 final size:21
Alignment explanation
Indices: 6514--6587 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
6504 GGAGTTTTTG
* **
6514 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAACTATCACTT
*
6535 GTAAT-GGTAGAACTGTCACTT
1 GT-ATCGGTAGAACTATCACTT
*
6556 GTATCGGTAGAACTATTACTT
1 GTATCGGTAGAACTATCACTT
6577 GTATCGGTAGA
1 GTATCGGTAGA
6588 GGTCTGCACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:6783 original size:13 final size:13
Alignment explanation
Indices: 6751--6775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6741 AAATTATATG
6751 AATAAAAAATAAA
1 AATAAAAAATAAA
6764 AATAAAAAATAA
1 AATAAAAAATAA
6776 TTATAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:9782 original size:16 final size:17
Alignment explanation
Indices: 9761--9793 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9751 GACCAAATTG
9761 TATG-TTTTTTTAGCTA
1 TATGTTTTTTTTAGCTA
9777 TATGTTTTTTTTAGCTA
1 TATGTTTTTTTTAGCTA
9794 AGTGACCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.64
Consensus pattern (17 bp):
TATGTTTTTTTTAGCTA
Done.