Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006672.1 Kokia drynarioides strain JFW-HI SEQ_121265, 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: 75513
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2793 original size:43 final size:43
Alignment explanation
Indices: 2744--2840 Score: 194
Period size: 43 Copynumber: 2.3 Consensus size: 43
2734 TCAGACAGCA
2744 ATATTCGTTATATAATCTACAAAACAAGGAATAAAGAGAAATT
1 ATATTCGTTATATAATCTACAAAACAAGGAATAAAGAGAAATT
2787 ATATTCGTTATATAATCTACAAAACAAGGAATAAAGAGAAATT
1 ATATTCGTTATATAATCTACAAAACAAGGAATAAAGAGAAATT
2830 ATATTCGTTAT
1 ATATTCGTTAT
2841 CCAGTTCCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.31
Consensus pattern (43 bp):
ATATTCGTTATATAATCTACAAAACAAGGAATAAAGAGAAATT
Found at i:16436 original size:20 final size:20
Alignment explanation
Indices: 16393--16436 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16383 TAAATTCCTG
* *
16393 AAAA-TTTAAATAGAGAGAC
1 AAAATTTTAAATACAGAGAA
*
16412 TAAATTTTAAATACAGAGAA
1 AAAATTTTAAATACAGAGAA
16432 AAAAT
1 AAAAT
16437 ACATGAACTC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (20 bp):
AAAATTTTAAATACAGAGAA
Found at i:22114 original size:6 final size:6
Alignment explanation
Indices: 22105--22132 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
22095 ACCACCACCA
22105 CCACTG CCACTG CCACTG CCACTG CCAC
1 CCACTG CCACTG CCACTG CCACTG CCAC
22133 AACCTACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.54, G:0.14, T:0.14
Consensus pattern (6 bp):
CCACTG
Found at i:35615 original size:29 final size:28
Alignment explanation
Indices: 35573--35627 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
35563 CACTTATTAA
*
35573 AAAAAAAAAGAGATTAAATTCTTAAATTT
1 AAAAAAAAAGAGATTAAAAT-TTAAATTT
* *
35602 AAAAATAAATAGATTAAAATTTAAAT
1 AAAAAAAAAGAGATTAAAATTTAAAT
35628 GCGCGATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAAAAAAAGAGATTAAAATTTAAATTT
Found at i:37368 original size:15 final size:16
Alignment explanation
Indices: 37348--37377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37338 TATAAAACAT
37348 ATTT-AAAAATTTAAA
1 ATTTAAAAAATTTAAA
37363 ATTTAAAAAATTTAA
1 ATTTAAAAAATTTAA
37378 TACAAGACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTAAAAAATTTAAA
Found at i:38086 original size:13 final size:13
Alignment explanation
Indices: 38066--38098 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38056 TTTAATTATA
38066 TATGTTTTTTGTTT
1 TATGTTTTTT-TTT
38080 T-TGTTTTTTTTT
1 TATGTTTTTTTTT
38092 TATGTTT
1 TATGTTT
38099 AGTATTAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 13 0.72
14 1 0.06
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.82
Consensus pattern (13 bp):
TATGTTTTTTTTT
Found at i:51686 original size:10 final size:10
Alignment explanation
Indices: 51671--51696 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
51661 ACATAGATTT
51671 TTTTTTATTA
1 TTTTTTATTA
51681 TTTTTTATTA
1 TTTTTTATTA
51691 TTTTTT
1 TTTTTT
51697 TTTTTTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:51710 original size:13 final size:13
Alignment explanation
Indices: 51667--51703 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
51657 CAGTACATAG
51667 ATTTTTTTTTATT
1 ATTTTTTTTTATT
*
51680 ATTTTTTATTATT
1 ATTTTTTTTTATT
*
51693 TTTTTTTTTTA
1 ATTTTTTTTTA
51704 GTGTTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTTTTTATT
Found at i:54596 original size:15 final size:15
Alignment explanation
Indices: 54576--54638 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
54566 AAAAAATCTT
54576 TAAAAATATAAATTC
1 TAAAAATATAAATTC
54591 TAAAAATAATAAAATTGTC
1 TAAAAAT-AT-AAA-T-TC
*
54610 TAAAATTA-AATATTC
1 TAAAAATATAA-ATTC
54625 TAAAATATATAAAT
1 TAAAA-ATATAAAT
54639 ATAAATTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 14 0.36
16 9 0.23
17 6 0.15
18 2 0.05
19 8 0.21
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (15 bp):
TAAAAATATAAATTC
Found at i:74375 original size:40 final size:40
Alignment explanation
Indices: 74331--74410 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
74321 TGCTAAACTA
* * *
74331 TAAATATCTATCTTCTCTGTAACTCTTCTCATTCGTCAAT
1 TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
*
74371 TAAATATCCATTTTCTCTGCAACTCTTCTCATTCATCAAT
1 TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
74411 CACCTTCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.44
Consensus pattern (40 bp):
TAAATATCCATCTTCTCTGCAACTCTTCTCATTCATCAAT
Done.