Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003906.1 Kokia drynarioides strain JFW-HI SEQ_116968, 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: 12579
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:1588 original size:42 final size:42
Alignment explanation
Indices: 1522--1986 Score: 498
Period size: 39 Copynumber: 11.5 Consensus size: 42
1512 ATTTTAAAGA
** * **
1522 TAAGAGATTGG-T-ATGTCTTCAATCTGTCTCATGATCAAGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* *
1562 TAAGAGATTGGATGATGTCTTTAATCTACCCCATGATCGGGA
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
*
1604 TAAGAGATTGGATGA---CTTCAATCTACCCCATGATCGAGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* *
1643 TAAGAGATTAGATGATGTCTTCAATCTACCCCATGATTGGGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
** * *
1685 TAAGAGATTGGATG--G-CTTCAATCTGTCCTATGATCGGGA
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* ** * *
1724 TAAAAGATTAAATGATGTCTTCAATTTACCCCATGATCAGGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* ** * *
1766 TAAGAGATTGGACGA---CTTCAATCTGTCTCATGATCGAGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* * *
1805 TAAGAGATTGGAT-ATGTCTTCAATTTGCCCTATGATCGGGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* * *
1846 TAAGAGATTGGAT-A--ACTTCAATCTTCCCCATGATCGAGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
*
1885 TAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATCGGGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
1924 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
1 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
* * *
1966 TAAAAGATTAGATGATATCTT
1 TAAGAGATTGGATGATGTCTT
1987 TGCTTTGCTC
Statistics
Matches: 354, Mismatches: 55, Indels: 30
0.81 0.13 0.07
Matches are distributed among these distances:
38 1 0.00
39 164 0.46
40 12 0.03
41 36 0.10
42 141 0.40
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGG
Found at i:1644 original size:81 final size:81
Alignment explanation
Indices: 1522--1986 Score: 571
Period size: 81 Copynumber: 5.7 Consensus size: 81
1512 ATTTTAAAGA
* * * * * *
1522 TAAGAGATTGGTATGTCTTCAATCTGTCTCATGATCAAGGTAAGAGATTGGATGATGTCTTTAAT
1 TAAGAGATTGG-ATGACTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAAT
*
1587 CTACCCCATGATCGGGA
65 CTACCCCATGATCGGGG
*
1604 TAAGAGATTGGATGACTTCAATCTACCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAATC
1 TAAGAGATTGGATGACTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAATC
*
1669 TACCCCATGATTGGGG
66 TACCCCATGATCGGGG
* * * * *
1685 TAAGAGATTGGATGGCTTCAATCTGTCCTATGATCG-GGATAAAAGATTAAATGATGTCTTCAAT
1 TAAGAGATTGGATGACTTCAATCTGCCCCATGATCGAGG-TAAGAGATTAGATGATGTCTTCAAT
* *
1749 TTACCCCATGATCAGGG
65 CTACCCCATGATCGGGG
* * * * *
1766 TAAGAGATTGGACGACTTCAATCTGTCTCATGATCGAGGTAAGAGATTGGAT-ATGTCTTCAATT
1 TAAGAGATTGGATGACTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAATC
* *
1830 TGCCCTATGATCGGGG
66 TACCCCATGATCGGGG
* * *
1846 TAAGAGATTGGATAACTTCAATCTTCCCCATGATCGAGGTAAGAGATT-G--GATGGCTTCAATC
1 TAAGAGATTGGATGACTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAATC
*
1908 TGCCCCATGATCGGGG
66 TACCCCATGATCGGGG
* * * *
1924 TAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAAAGATTAGATGATATCTT
1 TAAGAGATTGGATGA---CTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTT
1987 TGCTTTGCTC
Statistics
Matches: 332, Mismatches: 42, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
78 39 0.12
79 1 0.00
80 70 0.21
81 202 0.61
82 14 0.04
84 6 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (81 bp):
TAAGAGATTGGATGACTTCAATCTGCCCCATGATCGAGGTAAGAGATTAGATGATGTCTTCAATC
TACCCCATGATCGGGG
Found at i:2472 original size:99 final size:99
Alignment explanation
Indices: 2303--2733 Score: 331
Period size: 99 Copynumber: 4.4 Consensus size: 99
2293 ACGCCTCTAA
* ** * *
2303 GGTACCAGATTTG-CTGTTGCGGCCTCAATCATTCCCATCGTATCTTCTAAGGTACAAGGTTC-A
1 GGTACCAGATTCGTC-GTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCGC
2366 CTATTGCAACCTCAACCTTTCCCTTTAAATCTTCAT
65 CT-TTGCAACCTCAACCTTTCCCTTTAAATCTTCAT
* * * * * *
2402 GGTACCAGATTTGTCATTGCGGGCTCAATCCTTCCTATCACATCTTCTAAGGTACAGGGTTCGTC
1 GGTACCAGATTCGTCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCGCC
* * ** * *
2467 TTTGCAGCCTTAATATTTCCC-TT-CATTTTCAT
66 TTTGCAACCTCAACCTTTCCCTTTAAATCTTCAT
* *** * * * * * ** * *
2499 GATGTTAGATCCGTCGTTGTGGTCTCGATCTTTCCCATCATGTCTTCCAAGGTATAGGGTTCGCC
1 GGTACCAGATTCGTCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCGCC
* ** * * * * *
2564 GTTGCGGCCTCAACTTTTCTCTTCATATCTTTAT
66 TTTGCAACCTCAACCTTTCCCTTTAAATCTTCAT
* * * *
2598 GGTATCGGATTCATCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCACC
1 GGTACCAGATTCGTCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCGCC
2663 ATTATG--ACCTCAACCTTTCCCTTT--A-CTTCCAT
66 -TT-TGCAACCTCAACCTTTCCCTTTAAATCTT-CAT
* * * * *
2695 GGTACTAGATTCGCCGTTGCAGCTTCAATCTTTCCCATC
1 GGTACCAGATTCGTCGTTGCGGCCTCAATCATTCCCATC
2734 CTTGTTCTAC
Statistics
Matches: 255, Mismatches: 70, Indels: 16
0.75 0.21 0.05
Matches are distributed among these distances:
96 3 0.01
97 104 0.41
98 3 0.01
99 139 0.55
100 4 0.02
101 2 0.01
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (99 bp):
GGTACCAGATTCGTCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAGGTACAGGGTTCGCC
TTTGCAACCTCAACCTTTCCCTTTAAATCTTCAT
Found at i:3419 original size:112 final size:112
Alignment explanation
Indices: 3222--3437 Score: 353
Period size: 112 Copynumber: 1.9 Consensus size: 112
3212 ATCGTTAAAC
* *
3222 CACTAACCGTTATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGGTGGATGAAATTGAATTTG
1 CACTAACCGTCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGGTGGATCAAATTGAATTTG
* *
3287 ATTTGAGGCAAAGCTCGCATGATTGAAAAGATTAAAAATCATTAGTT
66 ATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTAGTT
* *
3334 CACTAACCGTCATTTCAATGCAAGAATGCTTGAATAGGGTTGTAAGGTGGA-CAAATTTGAATTT
1 CACTAACCGTCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGGTGGATCAAA-TTGAATTT
*
3398 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
65 GATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAAT
3438 GGCAAACATT
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
111 3 0.03
112 93 0.97
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (112 bp):
CACTAACCGTCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGGTGGATCAAATTGAATTTG
ATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTAGTT
Found at i:4595 original size:16 final size:16
Alignment explanation
Indices: 4574--4615 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
4564 TCATCTTTAC
4574 TTTCTTTTCTTTTT-CT
1 TTTCTTTT-TTTTTCCT
4590 TTTCTTCTTTTTTTCCT
1 TTTCTT-TTTTTTTCCT
4607 TTT-TTTTTT
1 TTTCTTTTTT
4616 GAAAAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTTTTTCCT
Found at i:9853 original size:7 final size:8
Alignment explanation
Indices: 9836--9863 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
9826 AAAAGAAATA
9836 TTTTTATT
1 TTTTTATT
9844 TTTTTATT
1 TTTTTATT
9852 TTTTTATT
1 TTTTTATT
9860 TTTT
1 TTTT
9864 CTTAAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:9896 original size:23 final size:21
Alignment explanation
Indices: 9852--9907 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
9842 TTTTTTTATT
*
9852 TTTTTATTTTTTCTTAAAATC
1 TTTTTATCTTTTCTTAAAATC
* **
9873 TATTTTTATCTTTTGTTATTATC
1 --TTTTTATCTTTTCTTAAAATC
9896 TTTTTATCTTTT
1 TTTTTATCTTTT
9908 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTTATCTTTTCTTAAAATC
Done.