Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004088.1 Kokia drynarioides strain JFW-HI SEQ_117258, 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: 49782
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:8806 original size:19 final size:20
Alignment explanation
Indices: 8788--8828 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
8778 ATTTAATAAT
8788 ATTTTTA-ATA-ATTTTT-A
1 ATTTTTATATATATTTTTAA
8805 ATTTTTATATATATTTTTAA
1 ATTTTTATATATATTTTTAA
8825 ATTT
1 ATTT
8829 AATAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 6 0.29
20 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTATATATATTTTTAA
Found at i:8827 original size:20 final size:17
Alignment explanation
Indices: 8788--8833 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
8778 ATTTAATAAT
8788 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTTTA
8805 ATTTTTATATATATTTTTA
1 ATTTTTA-ATA-ATTTTTA
*
8824 A-ATTTAATAA
1 ATTTTTAATAA
8834 AATAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 7 0.27
19 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Found at i:13678 original size:29 final size:27
Alignment explanation
Indices: 13577--13678 Score: 62
Period size: 29 Copynumber: 3.4 Consensus size: 27
13567 ATACTTTTTT
* **
13577 AATTTGGTACCTAATTTTTTTTTGGACCC
1 AATTTGGTACCTAACTTTTTTTT--ATTC
13606 AATTTGGTACCTAAACTTGGTATTTTT-TTCC
1 AATTTGGTACCT-AACTT--T-TTTTTATT-C
**
13637 TAATTTGAAACCTAAGCTTTTTTTTAATTC
1 -AATTTGGTACCTAA-CTTTTTTTT-ATTC
13667 AATTTGGTACCT
1 AATTTGGTACCT
13679 GAATTTATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
29 27 0.47
30 6 0.11
31 5 0.09
32 14 0.25
33 5 0.09
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.48
Consensus pattern (27 bp):
AATTTGGTACCTAACTTTTTTTTATTC
Found at i:13933 original size:60 final size:59
Alignment explanation
Indices: 13823--13934 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 59
13813 TTAATATTAA
* * *
13823 AAAAAGATTAAGTACTAAATTAAGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCC
1 AAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTCAGCTACCAAATTGGACCCC
* * * *
13882 AAAAAGTTTAAGTACCAACTTAAAAAAAA-AGTATCAAGTTTAGCTAGCAAATT
1 AAAAAGATTAAGTACCAAATTAAAAAAAAGAG--TCAAGTTCAGCTACCAAATT
13935 AGGAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.05
59 25 0.57
60 17 0.39
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.23
Consensus pattern (59 bp):
AAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTCAGCTACCAAATTGGACCCC
Found at i:30764 original size:3 final size:3
Alignment explanation
Indices: 30756--30819 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
30746 ATGGTATGAC
30756 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30804 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
30820 ATTGTTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31365 original size:23 final size:23
Alignment explanation
Indices: 31320--31380 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
31310 TCATTAACAT
* *
31320 TGTTCATGAACATGTTCATTTAA
1 TGTTCATGAACATGTACAATTAA
* *
31343 TGTTCTTGAGCATGTACAATTAA
1 TGTTCATGAACATGTACAATTAA
*
31366 -GTTAAATGAACATGT
1 TGTT-CATGAACATGT
31381 TCGTGAACAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (23 bp):
TGTTCATGAACATGTACAATTAA
Found at i:31947 original size:61 final size:61
Alignment explanation
Indices: 31830--31948 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
31820 CATCCTTCTT
31830 TGCTAACAGTAGTTAGCTGCACACCAAAGAGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAG
1 TGCTAACAGTAGTTAGCTGCACACCAAAGAGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAG
31891 TGCTAACAGTAGTTAGCTGCACACCAAAGAGA-GGAGGGAGGGAGAGAGAGAG-GAGAGA
1 TGCTAACAGTAGTTAGCTGCACACCAAAGAGAGGGAGGGAGGGAGAGAGAGAGAGAGAGA
31949 TGGTATCGCT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 6 0.10
60 20 0.34
61 32 0.55
ACGTcount: A:0.38, C:0.12, G:0.40, T:0.10
Consensus pattern (61 bp):
TGCTAACAGTAGTTAGCTGCACACCAAAGAGAGGGAGGGAGGGAGAGAGAGAGAGAGAGAG
Found at i:35455 original size:17 final size:17
Alignment explanation
Indices: 35429--35481 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
35419 GACGTGCCAC
*
35429 AAAAACAAATAAAAATT
1 AAAAAAAAATAAAAATT
*
35446 AAAAAAAAATCAAAA-T
1 AAAAAAAAATAAAAATT
* *
35462 ATAAAAAAATAACAATT
1 AAAAAAAAATAAAAATT
35479 AAA
1 AAA
35482 TATAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAAAAATAAAAATT
Found at i:35460 original size:18 final size:17
Alignment explanation
Indices: 35429--35470 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
35419 GACGTGCCAC
*
35429 AAAAACAAATAAAA-ATT
1 AAAAAAAAATAAAATA-T
35446 AAAAAAAAATCAAAATAT
1 AAAAAAAAAT-AAAATAT
35464 AAAAAAA
1 AAAAAAA
35471 TAACAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAAAAAATAAAATAT
Found at i:35470 original size:21 final size:21
Alignment explanation
Indices: 35446--35490 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35436 AATAAAAATT
35446 AAAA-AAAAATCAAAATATAAA
1 AAAATAAAAAT-AAAATATAAA
* *
35467 AAAATAACAATTAAATATAAA
1 AAAATAAAAATAAAATATAAA
35488 AAA
1 AAA
35491 TTAAGGGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAATAAAAATAAAATATAAA
Found at i:35674 original size:30 final size:30
Alignment explanation
Indices: 35631--35692 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
35621 TAAATCTTAT
*
35631 ATTTTAATAAAATGAATTAAACAAGATAAC
1 ATTTCAATAAAATGAATTAAACAAGATAAC
*
35661 ATTTCAATCAAATGAATTAAACAAGATAAC
1 ATTTCAATAAAATGAATTAAACAAGATAAC
35691 AT
1 AT
35693 AACATATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (30 bp):
ATTTCAATAAAATGAATTAAACAAGATAAC
Found at i:45380 original size:23 final size:23
Alignment explanation
Indices: 45354--45398 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
45344 AATTTCGAAT
**
45354 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
45377 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
45399 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Done.