Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004638.1 Kokia drynarioides strain JFW-HI SEQ_118165, 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: 33154
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Found at i:49 original size:38 final size:38
Alignment explanation
Indices: 6--78 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1 AAAAA
*
6 AAAAACTT-ATAAACATTCATAA-AAATTTATAAAAATAT
1 AAAAACTTCA-AAAAATTCATAATAAA-TTATAAAAATAT
*
44 AAAAACTTCAAAAAATTCCTAATAAATTATAAAAA
1 AAAAACTTCAAAAAATTCATAATAAATTATAAAAA
79 AAACTGACGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 27 0.87
39 4 0.13
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (38 bp):
AAAAACTTCAAAAAATTCATAATAAATTATAAAAATAT
Found at i:576 original size:2 final size:2
Alignment explanation
Indices: 569--605 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
559 TAAATGAATT
569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
606 TTATTAGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:632 original size:10 final size:9
Alignment explanation
Indices: 618--686 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 9
608 ATTAGAACTT
618 ATTTTTATA
1 ATTTTTATA
*
627 AGTTTTATA
1 ATTTTTATA
*
636 ATTATTGATA
1 ATT-TTTATA
646 A-TTTTATA
1 ATTTTTATA
654 TATGTTTTATAA
1 -AT-TTTTAT-A
* *
666 ATTATTAGAA
1 ATTTTTA-TA
676 ATTTTTATA
1 ATTTTTATA
685 AT
1 AT
687 ATATATATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 5 0.11
9 15 0.33
10 17 0.37
11 8 0.17
12 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (9 bp):
ATTTTTATA
Found at i:661 original size:29 final size:29
Alignment explanation
Indices: 618--685 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
608 ATTAGAACTT
618 ATTTTTATAAGTTTTAT-AATTATT-GATA
1 ATTTTTATAAGTTTTATAAATTATTAGA-A
*
646 ATTTTATATATGTTTTATAAATTATTAGAA
1 ATTTT-TATAAGTTTTATAAATTATTAGAA
676 ATTTTTATAA
1 ATTTTTATAA
686 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 5 0.14
29 15 0.43
30 13 0.37
31 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (29 bp):
ATTTTTATAAGTTTTATAAATTATTAGAA
Found at i:665 original size:19 final size:18
Alignment explanation
Indices: 617--696 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 18
607 TATTAGAACT
617 TATTTTTATAAGTTTTATA
1 TATTTTTATAA-TTTTATA
*
636 -ATTATTGATAATTTTATA
1 TATT-TTTATAATTTTATA
*
654 TATGTTTTATAAATTATTAGA
1 TAT-TTTTAT-AATT-TTATA
* *
675 AATTTTTATAATATATATA
1 TATTTTTATAAT-TTTATA
694 TAT
1 TAT
697 ATAGTTTATA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 10 0.21
19 20 0.42
20 12 0.25
21 6 0.12
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTTTTATAATTTTATA
Found at i:11713 original size:18 final size:18
Alignment explanation
Indices: 11678--11723 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
11668 ATTTAAAATA
*
11678 ATATTTTTATATTCTTTT
1 ATATTTTTATAATCTTTT
11696 ATATTTTTATGAAT-TTTT
1 ATATTTTTAT-AATCTTTT
11714 A-ATTATTTAT
1 ATATT-TTTAT
11724 TTAATTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 20 0.80
19 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATATTTTTATAATCTTTT
Found at i:13905 original size:20 final size:21
Alignment explanation
Indices: 13876--13920 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13866 TAACATTTGA
*
13876 AAATTAAAT-AATCAAATATT
1 AAATTAAATAAATAAAATATT
*
13896 AAATTTAATAAATAAAATATT
1 AAATTAAATAAATAAAATATT
13917 AAAT
1 AAAT
13921 ATTCATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTAAATAAATAAAATATT
Found at i:14079 original size:14 final size:14
Alignment explanation
Indices: 14062--14103 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
14052 TTAGAATTTA
14062 ATTTTTATATTTTT
1 ATTTTTATATTTTT
*
14076 ATTTTTATATATTTA
1 ATTTTTATAT-TTTT
14091 ATTTTT-TATTTTT
1 ATTTTTATATTTTT
14104 TAAAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 3 0.12
14 13 0.52
15 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTATATTTTT
Found at i:14103 original size:23 final size:22
Alignment explanation
Indices: 14071--14114 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
14061 AATTTTTATA
* *
14071 TTTTTATTTTTATATATTTAAT
1 TTTTTATTTTTAAAAATTTAAT
14093 TTTTTATTTTTTAAAAATTTAA
1 TTTTTA-TTTTTAAAAATTTAA
14115 AATTTAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTTTTAAAAATTTAAT
Found at i:20796 original size:23 final size:23
Alignment explanation
Indices: 20744--20809 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
20734 AATAAAAAAC
* *
20744 ATCATAAAATTATAACTATTAAA
1 ATCATAAAATTATAATTTTTAAA
* *
20767 ATGATAAAATTATAATTTTTATA
1 ATCATAAAATTATAATTTTTAAA
20790 ATCATAAAAATATATAATTT
1 ATCAT-AAAAT-TATAATTT
20810 AATTTCGTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 23 0.64
24 5 0.14
25 8 0.22
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (23 bp):
ATCATAAAATTATAATTTTTAAA
Found at i:29483 original size:21 final size:21
Alignment explanation
Indices: 29457--29496 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29447 AACCAATAAA
29457 AAAAATTCACTAAAATTTGTT
1 AAAAATTCACTAAAATTTGTT
29478 AAAAATTCACTAAAATTTG
1 AAAAATTCACTAAAATTTG
29497 AGTCAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAATTCACTAAAATTTGTT
Found at i:31089 original size:7 final size:8
Alignment explanation
Indices: 31007--31096 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 8
30997 TTATATACAA
31007 ATTTTTAT
1 ATTTTTAT
31015 AATTTTTAAT
1 -ATTTTT-AT
*
31025 ATTTTTAG
1 ATTTTTAT
31033 ATTTTT-T
1 ATTTTTAT
31040 -TTTATTA-
1 ATTT-TTAT
*
31047 ATATTTAAT
1 AT-TTTTAT
31056 AATTTTTAT
1 -ATTTTTAT
*
31065 AACTTTTATT
1 -ATTTTTA-T
31075 GATTTTTAT
1 -ATTTTTAT
31084 -TTTTTAT
1 ATTTTTAT
31091 ATTTTT
1 ATTTTT
31097 TCCACATGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
6 3 0.05
7 9 0.14
8 15 0.23
9 27 0.42
10 11 0.17
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (8 bp):
ATTTTTAT
Found at i:31394 original size:92 final size:94
Alignment explanation
Indices: 31275--31464 Score: 233
Period size: 92 Copynumber: 2.0 Consensus size: 94
31265 ATTTTTTTTT
* * ** *
31275 AAGTTTGAGGGCCTTTTTGATGTATTTTGAAATTTCAAGTATCCAATTAAGTGCAAA-AAAAAAA
1 AAGTTTGAGGCCCTTTTTGATGCATTTTGAAAGCTCAAGTACCCAATTAAGTGCAAAGAAAAAAA
*
31339 AGTAAGGGCTTAATTGC-TTTTTTTGAAA
66 ACTAAGGGCTTAATTGCTTTTTTTTGAAA
* * *
31367 AAGTTTGAGGCCCTTTTTTGA-GCATTTTGTAAGCTCAAGTACCCAATTGAGTGCAAAGATAAAA
1 AAGTTTGAGGCCC-TTTTTGATGCATTTTGAAAGCTCAAGTACCCAATTAAGTGCAAAGAAAAAA
* * * *
31431 AACTAGGGGTTTGATTGCTTTTTTTTGGAA
65 AACTAAGGGCTTAATTGCTTTTTTTTGAAA
31461 AAGT
1 AAGT
31465 GTGACGGCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 42 0.51
93 26 0.32
94 14 0.17
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.36
Consensus pattern (94 bp):
AAGTTTGAGGCCCTTTTTGATGCATTTTGAAAGCTCAAGTACCCAATTAAGTGCAAAGAAAAAAA
ACTAAGGGCTTAATTGCTTTTTTTTGAAA
Found at i:31477 original size:92 final size:91
Alignment explanation
Indices: 31309--31477 Score: 214
Period size: 93 Copynumber: 1.8 Consensus size: 91
31299 TTTTGAAATT
* * *
31309 TCAAGTATCCAATTAAGTGCAAAAAAAAAAAGTAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
1 TCAAGTACCCAATTAAGTGCAAAAAAAAAAACTAAGGGCTTAATTGCTTTTTTTGAAAAAGTGTG
31374 AGGCCCTTTTTTGAGCATTTTGTAAGC
66 AGG-CCTTTTTTGAGCATTTTGTAAGC
* * * * * *
31401 TCAAGTACCCAATTGAGTGCAAAGATAAAAAACTAGGGGTTTGATTGCTTTTTTTTGGAAAAGTG
1 TCAAGTACCCAATTAAGTGCAAA-AAAAAAAACTAAGGGCTTAATTGC-TTTTTTTGAAAAAGTG
31466 TGACGG-CTTTTT
64 TGA-GGCCTTTTT
31478 ACACCTTAAG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
92 21 0.32
93 25 0.38
94 17 0.26
95 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (91 bp):
TCAAGTACCCAATTAAGTGCAAAAAAAAAAACTAAGGGCTTAATTGCTTTTTTTGAAAAAGTGTG
AGGCCTTTTTTGAGCATTTTGTAAGC
Found at i:31678 original size:2 final size:2
Alignment explanation
Indices: 31673--31697 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31663 AATTTTTTAC
31673 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31698 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.