Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010445.1 Kokia drynarioides strain JFW-HI SEQ_125339, 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: 27861
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:557 original size:17 final size:17
Alignment explanation
Indices: 537--619 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
527 AAATAAATTT
537 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
* *
554 TAAACTTAAATTTCA-AC
1 TAAATTTAAATTT-ATAA
* *
571 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTATAA
* * *
588 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
605 TAAATTTAAGTTTAT
1 TAAATTTAAATTTAT
620 TGGGCCCAGG
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 1 0.02
17 50 0.96
18 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:578 original size:34 final size:34
Alignment explanation
Indices: 538--619 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
528 AATAAATTTT
* *
538 AAATTTAAATTTATAATAAACTTAAATTTCAACC
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
* * *
572 AAATTTAAATTTAGAATAAACTTAATTTTAAAAT
1 AAATTTAAATTTATAATAAACTTAAATTTAAAAC
*
606 AAATTTAAGTTTAT
1 AAATTTAAATTTAT
620 TGGGCCCAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (34 bp):
AAATTTAAATTTATAATAAACTTAAATTTAAAAC
Found at i:5276 original size:21 final size:21
Alignment explanation
Indices: 5252--5293 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5242 CAATACTTGA
*
5252 GTAAGTTCTACCGATAAAAGT
1 GTAACTTCTACCGATAAAAGT
* *
5273 GTAACTTCTACTGATACAAGT
1 GTAACTTCTACCGATAAAAGT
5294 CATGCTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
GTAACTTCTACCGATAAAAGT
Found at i:6128 original size:52 final size:52
Alignment explanation
Indices: 6045--6321 Score: 387
Period size: 52 Copynumber: 5.4 Consensus size: 52
6035 ATTTCATTTA
** * * *
6045 ATACTCACGATGACACATAACCATCGAACCTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* *
6097 ATACTCAAGATGACACATAGTTATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * *
6149 ATACTCATGATGACACATAGTCATCAGACCTCATAATCTGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* * ** *
6201 ATACTTACGATG--ACAGAGTCATCAAACCTCATTATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
* *
6251 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
6303 ATACTCACGATGACACATA
1 ATACTCACGATGACACATA
6322 ATTATCGAAC
Statistics
Matches: 198, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
50 44 0.22
52 154 0.78
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCAT
Found at i:6271 original size:102 final size:101
Alignment explanation
Indices: 6045--6317 Score: 384
Period size: 102 Copynumber: 2.7 Consensus size: 101
6035 ATTTCATTTA
** *
6045 ATACTCACGATGACACATAACCATCGAACCTCATAATCCGTAAATGATTCATATACTCAAGATGA
1 ATACTCACGATGACACATAGTCATCG-ACCTCATAATCCGTAAATGATTCATATACTCACGATG-
* * **
6110 CACATAGTTATCGGACCTCATAATCTGTAAAGGATTCAT
64 -ACAGAGTCATCAAACCTCATAATCTGTAAAGGATTCAT
* * *
6149 ATACTCATGATGACACATAGTCATCAGACCTCATAATCTGTAAATGATTCATATACTTACGATGA
1 ATACTCACGATGACACATAGTCATC-GACCTCATAATCCGTAAATGATTCATATACTCACGATGA
*
6214 CAGAGTCATCAAACCTCATTATCTGTAAAGGATTCAT
65 CAGAGTCATCAAACCTCATAATCTGTAAAGGATTCAT
* *
6251 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACATAGTCATC-GACCTCATAATCCGTAAATGATTCATATACTCACGATGA
6316 CA
65 CA
6318 CATAATTATC
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
102 94 0.62
104 56 0.37
105 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (101 bp):
ATACTCACGATGACACATAGTCATCGACCTCATAATCCGTAAATGATTCATATACTCACGATGAC
AGAGTCATCAAACCTCATAATCTGTAAAGGATTCAT
Found at i:11647 original size:3 final size:3
Alignment explanation
Indices: 11639--11668 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11629 TGCTTTGGTT
11639 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
11669 GGACGCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:23030 original size:20 final size:20
Alignment explanation
Indices: 22981--23032 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
22971 ATTTGTAATG
22981 ATTATATTTTA-ATATTTAA
1 ATTATATTTTACATATTTAA
* *
23000 AATATAATTTACATATTTAA
1 ATTATATTTTACATATTTAA
*
23020 ATTAGATTTTACA
1 ATTATATTTTACA
23033 AATAATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTATATTTTACATATTTAA
Found at i:24090 original size:30 final size:31
Alignment explanation
Indices: 24055--24135 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
24045 TTTTTTGATC
*
24055 TAATTTAGT-TCTCAAACTTGACA-TTTTTTT
1 TAATTTAGTACCT-AAACTTGACACTTTTTTT
*
24085 TAATTTGGTACCTAAACTTGACACTTTTTTTT
1 TAATTTAGTACCTAAACTTGACAC-TTTTTTT
* * *
24117 TAAGTTGGTACTTAAACTT
1 TAATTTAGTACCTAAACTT
24136 TTTGAGGTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.41
31 2 0.05
32 24 0.55
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (31 bp):
TAATTTAGTACCTAAACTTGACACTTTTTTT
Found at i:24119 original size:32 final size:30
Alignment explanation
Indices: 24068--24135 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 30
24058 TTTAGTTCTC
*
24068 AAACTTGACATTTTTTTTAATTTGGTACCT
1 AAACTTGACATTTTTTTTAAGTTGGTACCT
*
24098 AAACTTGACACTTTTTTTTTAAGTTGGTACTT
1 AAACTTGACA--TTTTTTTTAAGTTGGTACCT
24130 AAACTT
1 AAACTT
24136 TTTGAGGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 10 0.29
32 24 0.71
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (30 bp):
AAACTTGACATTTTTTTTAAGTTGGTACCT
Found at i:24198 original size:60 final size:60
Alignment explanation
Indices: 24086--24197 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 60
24076 CATTTTTTTT
* *
24086 AATTTGGTACCTAAACTTGACACTTTTTTTTTAAGTTGGTACTTAAACTTTTTGAGGTCC
1 AATTTGGTACCTAAACTTGACACTTTTTTCTTAAGTTGGTACATAAACTTTTTGAGGTCC
* * * * *
24146 AATTTGGTATCTGAACTTGACTC-TTTTTCTTAATTTGGTACATAATCTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTTCTTAAGTTGGTACATAAACTTTTT
24198 TAATATTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 25 0.56
60 20 0.44
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.48
Consensus pattern (60 bp):
AATTTGGTACCTAAACTTGACACTTTTTTCTTAAGTTGGTACATAAACTTTTTGAGGTCC
Found at i:24443 original size:61 final size:59
Alignment explanation
Indices: 24354--24503 Score: 196
Period size: 60 Copynumber: 2.5 Consensus size: 59
24344 AAATTGAATC
* * * *
24354 TAAAATAAGCTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTTAAGCATCAAATT-AGG
1 TAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAAGCACCAAATTGA-G
* *
24413 TCCAAAAAAAGTTTAGATACCAAATTAGG-AAAAAATGTCAAGTTCAAGTACCAAATTGAG
1 T--AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAAGCACCAAATTGAG
*
24473 TAAAAAAAGTGTAGGTACCAAATTAGGAAAA
1 TAAAAAAAGTTTAGGTACCAAATTAGGAAAA
24504 TGTATCAAGT
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
58 24 0.30
59 4 0.05
60 27 0.34
61 24 0.30
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (59 bp):
TAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTCAAGCACCAAATTGAG
Found at i:24480 original size:60 final size:59
Alignment explanation
Indices: 24339--24526 Score: 218
Period size: 58 Copynumber: 3.2 Consensus size: 59
24329 ATAAATTTAG
* * * *
24339 GTACCAAATTGAATCTAAAATAAGCTTAGGTACCAAATTAGGAAAAAAATGTCAAGTTTAA
1 GTACCAAATTGAGTC-AAAAAAAGTTTAGGTACCAAATTAGG-AAAAAATGTCAAGTTCAA
* * *
24400 GCATCAAATT-AGGTCCAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTCAA
1 GTACCAAATTGA-GT-CAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
* ** *
24460 GTACCAAATTGAGT-AAAAAAAGTGTAGGTACCAAATTAGGAAAATGTATCAAGTTCAA
1 GTACCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
*
24518 GTATCAAAT
1 GTACCAAAT
24527 ATTATATTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
58 47 0.43
60 28 0.26
61 33 0.30
62 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (59 bp):
GTACCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
Done.