Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013664.1 Kokia drynarioides strain JFW-HI SEQ_128692, 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: 76198
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:4712 original size:31 final size:31
Alignment explanation
Indices: 4677--4750 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
4667 GTTATAAAAT
* **
4677 AGTCATTAAATTATTTGAAAATTTTCATTGA
1 AGTCATTGAATTACATGAAAATTTTCATTGA
* * * *
4708 AGTCATTGAACTACATGAAAGTTTTTATTTA
1 AGTCATTGAATTACATGAAAATTTTCATTGA
4739 AGTCATTGAATT
1 AGTCATTGAATT
4751 GTTAAGGGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.43
Consensus pattern (31 bp):
AGTCATTGAATTACATGAAAATTTTCATTGA
Found at i:9751 original size:3 final size:3
Alignment explanation
Indices: 9743--9769 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9733 ATTACCCACA
9743 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
9770 TGTGTCGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25037 original size:18 final size:17
Alignment explanation
Indices: 25014--25048 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
25004 GAATAAATCT
25014 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
25032 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
25049 CCTTAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:25224 original size:15 final size:14
Alignment explanation
Indices: 25206--25261 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
25196 TAATGGGAAG
25206 AAGATATTCGAATCA
1 AAGATATT-GAATCA
25221 AAGATA-TGAGA--A
1 AAGATATTGA-ATCA
25233 GAAGATATTGGAATCA
1 -AAGATATT-GAATCA
25249 AAGATATTGAATC
1 AAGATATTGAATC
25262 TTTTGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
12 1 0.03
13 8 0.23
14 9 0.26
15 16 0.46
16 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (14 bp):
AAGATATTGAATCA
Found at i:25241 original size:28 final size:28
Alignment explanation
Indices: 25202--25255 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
25192 AACTTAATGG
25202 GAAGAAGATATTCGAATCAAAGATATGA
1 GAAGAAGATATTCGAATCAAAGATATGA
*
25230 GAAGAAGATATTGGAATCAAAGATAT
1 GAAGAAGATATTCGAATCAAAGATAT
25256 TGAATCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (28 bp):
GAAGAAGATATTCGAATCAAAGATATGA
Found at i:25632 original size:31 final size:29
Alignment explanation
Indices: 25563--25636 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
25553 ACAAAATACT
**
25563 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
*
25592 AACATAAGTGACTAAAATGTAACCTGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
25623 AACAAAAGTGACTA
1 AACATAAGTGACTA
25637 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:42119 original size:18 final size:17
Alignment explanation
Indices: 42096--42129 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42086 CATTGGATAT
42096 GACACTTCAATATTTTAC
1 GACACTTCAAT-TTTTAC
42114 GACACTTCAATTTTTA
1 GACACTTCAATTTTTA
42130 AGTGATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (17 bp):
GACACTTCAATTTTTAC
Found at i:51623 original size:16 final size:17
Alignment explanation
Indices: 51592--51624 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
51582 TTGAAATTAT
51592 TAAAATTATTTTAAAATA
1 TAAAATTA-TTTAAAATA
51610 TAAAATTA-TTAAAAT
1 TAAAATTATTTAAAAT
51625 CATCATCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTATTTAAAATA
Found at i:51682 original size:6 final size:6
Alignment explanation
Indices: 51671--51700 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
51661 TTACCCTCCT
*
51671 CCCTTC CCCTTC CCCTTC CCCTTT CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
51701 TTCTTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCCTTC
Found at i:54691 original size:30 final size:26
Alignment explanation
Indices: 54646--54731 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 26
54636 TTTTGCTGTC
54646 ATTTTATTATTATATTACTAT-TGTTTT
1 ATTTTATTATTATATTA-TATAT-TTTT
54673 ATTTTATTATTGGGATATTATATAATTTTT
1 ATTTTATTATT---ATATTATAT-ATTTTT
*
54703 ATTTTATTATTA-ATT-T-TATTATT
1 ATTTTATTATTATATTATATATTTTT
54726 ATTTTA
1 ATTTTA
54732 GAGGTTGCTT
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
23 11 0.21
24 1 0.02
25 1 0.02
26 3 0.06
27 12 0.23
29 3 0.06
30 21 0.40
31 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (26 bp):
ATTTTATTATTATATTATATATTTTT
Found at i:54718 original size:18 final size:19
Alignment explanation
Indices: 54688--54728 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
54678 ATTATTGGGA
54688 TATTATATAATTTTTATT-T
1 TATTATATAA-TTTTATTAT
54707 TATTAT-TAATTTTATTAT
1 TATTATATAATTTTATTAT
54725 TATT
1 TATT
54729 TTAGAGGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTATATAATTTTATTAT
Found at i:54720 original size:12 final size:11
Alignment explanation
Indices: 54646--54731 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
54636 TTTTGCTGTC
54646 ATTTTATTATT
1 ATTTTATTATT
* *
54657 ATATTACTATT
1 ATTTTATTATT
*
54668 GTTTTATT-TT
1 ATTTTATTATT
54678 ATTATTGGGA-TATT
1 ATT-TT---ATTATT
* * *
54692 ATATAATTTTT
1 ATTTTATTATT
54703 ATTTTATTATT
1 ATTTTATTATT
54714 AATTTTATTATT
1 -ATTTTATTATT
54726 ATTTTA
1 ATTTTA
54732 GAGGTTGCTT
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
10 5 0.09
11 33 0.59
12 11 0.20
13 2 0.04
14 5 0.09
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:60825 original size:30 final size:32
Alignment explanation
Indices: 60769--60834 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 32
60759 TCTTTGCATA
60769 CCCTTAAAAATTTAGAAAACTATTA-TTAAG-
1 CCCTTAAAAATTTAGAAAACTATTATTTAAGT
* * *
60799 CCCTTAAAACTTTTTGAAAA-TTTTATTTAAGT
1 CCCTTAAAA-ATTTAGAAAACTATTATTTAAGT
60831 CCCT
1 CCCT
60835 CATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 13 0.43
31 13 0.43
32 4 0.13
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (32 bp):
CCCTTAAAAATTTAGAAAACTATTATTTAAGT
Found at i:73387 original size:2 final size:2
Alignment explanation
Indices: 73380--73409 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73370 ATGTACAGTT
73380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73410 AAATGAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74152 original size:20 final size:20
Alignment explanation
Indices: 74107--74145 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
74097 AAAAATTTAA
*
74107 AAAAATAATTTTTAGAACTT
1 AAAAATAATTTTTAGAAATT
74127 AAAAAT-ATTTTTAGAAATT
1 AAAAATAATTTTTAGAAATT
74146 CCAAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
AAAAATAATTTTTAGAAATT
Done.