Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000526.1 Kokia drynarioides strain JFW-HI SEQ_111415, 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: 32244
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:445 original size:13 final size:13
Alignment explanation
Indices: 429--454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
419 AAATTGGCCC
429 AAAAAATTTAAAT
1 AAAAAATTTAAAT
442 AAAAAATTTAAAT
1 AAAAAATTTAAAT
455 GATTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAATTTAAAT
Found at i:618 original size:30 final size:30
Alignment explanation
Indices: 542--776 Score: 174
Period size: 29 Copynumber: 8.0 Consensus size: 30
532 AAAAGGTCTC
* * * * * *
542 TAAACTCTTAAAAAATCATATTTTGATCCT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* *
572 TAAACTTTTC-AAAATTACATTTTGACCTT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
*
601 TAAACTTTTCAAAAATTACATTTTAACCCC
1 TAAACTTTTCAAAAATTACATTTTAACCCT
*
631 TAAACTTTTTTAAAAATTACATTTTAACCCT
1 TAAAC-TTTTCAAAAATTACATTTTAACCCT
* * * **
662 CAAACTTCTCAAAAATTCCATTTTTGCCC-
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* * * * *
691 TCAACTTCT-AAAAATTATATTTTCACCCC
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* * * * *
720 CAAAC-ATCCAAAAATTACATTTTTACCCC
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* * *
749 TAAAC-TTCCAAAAATTCCATTTTTACCC
1 TAAACTTTTCAAAAATTACATTTTAACCC
777 CCGAACTTTC
Statistics
Matches: 168, Mismatches: 33, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
28 15 0.09
29 78 0.46
30 48 0.29
31 27 0.16
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
TAAACTTTTCAAAAATTACATTTTAACCCT
Found at i:697 original size:29 final size:30
Alignment explanation
Indices: 573--851 Score: 202
Period size: 29 Copynumber: 9.5 Consensus size: 30
563 TTTGATCCTT
* * * *
573 AAACTTTTC-AAAATTACATTTTGACCTTT
1 AAACTTCTCAAAAATTACATTTTTACCCTC
* *
602 AAACTTTTCAAAAATTACATTTTAACCC-C
1 AAACTTCTCAAAAATTACATTTTTACCCTC
* * *
631 TAAACTTTTTTAAAAATTACATTTTAACCCTC
1 -AAAC-TTCTCAAAAATTACATTTTTACCCTC
* *
663 AAACTTCTCAAAAATTCCATTTTTGCCCTC
1 AAACTTCTCAAAAATTACATTTTTACCCTC
* * *
693 -AACTTCT-AAAAATTATATTTTCACCCCC
1 AAACTTCTCAAAAATTACATTTTTACCCTC
*
721 AAACATC-CAAAAATTACATTTTTACCC-C
1 AAACTTCTCAAAAATTACATTTTTACCCTC
* *
749 TAAACTTC-CAAAAATTCCATTTTTACCCCC
1 -AAACTTCTCAAAAATTACATTTTTACCCTC
* * * *
779 GAACTT-TCAAAAATCATATTTATACCC-C
1 AAACTTCTCAAAAATTACATTTTTACCCTC
* * * * *
807 GAATTTC-CCAAAATGACATTTTTACCCCTA
1 AAACTTCTCAAAAATTACATTTTTA-CCCTC
*
837 AAACTT-TCCAAAATT
1 AAACTTCTCAAAAATT
852 GTGTTTTAAC
Statistics
Matches: 204, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
28 36 0.18
29 87 0.43
30 53 0.26
31 27 0.13
32 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
AAACTTCTCAAAAATTACATTTTTACCCTC
Found at i:754 original size:87 final size:88
Alignment explanation
Indices: 642--851 Score: 245
Period size: 86 Copynumber: 2.4 Consensus size: 88
632 AAACTTTTTT
* * * *
642 AAAAATTACA-TTTTAACCCTCAAACTTCTCAAAAATTCCATTTTTGCCCTC-AAC-TTCTAAAA
1 AAAAATTACATTTTTACCCCTAAAACTTCTCAAAAATTCCATTTTTACCCCCGAACTTTC-AAAA
*
704 ATTATATTT-TCACCCCCAAACATCC
65 ATCATATTTAT-A-CCCCAAACATCC
729 AAAAATTACATTTTTACCCCT-AAACTTC-CAAAAATTCCATTTTTACCCCCGAACTTTCAAAAA
1 AAAAATTACATTTTTACCCCTAAAACTTCTCAAAAATTCCATTTTTACCCCCGAACTTTCAAAAA
* **
792 TCATATTTATACCCCGAATTTCC
66 TCATATTTATACCCCAAACATCC
* * *
815 CAAAATGACATTTTTACCCCTAAAACTT-TCCAAAATT
1 AAAAATTACATTTTTACCCCTAAAACTTCTCAAAAATT
852 GTGTTTTAAC
Statistics
Matches: 107, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
86 48 0.45
87 46 0.43
88 13 0.12
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (88 bp):
AAAAATTACATTTTTACCCCTAAAACTTCTCAAAAATTCCATTTTTACCCCCGAACTTTCAAAAA
TCATATTTATACCCCAAACATCC
Found at i:1296 original size:97 final size:98
Alignment explanation
Indices: 1125--1314 Score: 278
Period size: 97 Copynumber: 1.9 Consensus size: 98
1115 AAAATATTTA
*
1125 AAAATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGA
1 AAAATCGAGGCAATATTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGA
* *
1190 TTTTTCTTCAAA-CTGGGATAATTGAATACTCTT
66 CTTTTCTTCAAATC-GGGATAATCGAATACTCTT
* * * *
1223 AAAA-CGAGGCAATGTTTCTTTATCTCTGA-TTTTGAAAATTTGTGCCTTAACTTACTAGGTGTG
1 AAAATCGAGGCAATATTCCTTTATCTC-GAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCG
1286 ACTTTTCTTCAAATCGGGATAATCGAATA
65 ACTTTTCTTCAAATCGGGATAATCGAATA
1315 TCCTTTTCCA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
97 76 0.92
98 7 0.08
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (98 bp):
AAAATCGAGGCAATATTCCTTTATCTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGA
CTTTTCTTCAAATCGGGATAATCGAATACTCTT
Found at i:7660 original size:12 final size:12
Alignment explanation
Indices: 7643--7675 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
7633 ATTCGATTTT
7643 CAATCAACAAAA
1 CAATCAACAAAA
7655 CAATCAACAAAA
1 CAATCAACAAAA
7667 CAA-CAACAA
1 CAATCAACAA
7676 CATCTTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.06
Consensus pattern (12 bp):
CAATCAACAAAA
Found at i:21466 original size:15 final size:15
Alignment explanation
Indices: 21436--21481 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
21426 GAAATTTAGA
*
21436 TAAAAATTAGTTTTTT
1 TAAATATTA-TTTTTT
*
21452 TAAATTTTATTTTTT
1 TAAATATTATTTTTT
21467 TAAATATTATCTTTT
1 TAAATATTAT-TTTT
21482 ACATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TAAATATTATTTTTT
Found at i:22563 original size:28 final size:25
Alignment explanation
Indices: 22525--22583 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
22515 GAACTTGACA
22525 TTTTTTTCTAATTAGAAACCTAAATT
1 TTTTTTTCTAATTAGAAACCT-AATT
* **
22551 TTTTTTTACCTAATTTGGTACCTAATT
1 TTTTTTT--CTAATTAGAAACCTAATT
22578 TTTTTT
1 TTTTTT
22584 AGATTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.25
27 10 0.36
28 11 0.39
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (25 bp):
TTTTTTTCTAATTAGAAACCTAATT
Found at i:29345 original size:36 final size:36
Alignment explanation
Indices: 29305--29393 Score: 124
Period size: 36 Copynumber: 2.5 Consensus size: 36
29295 CTTTTGGGTT
* *
29305 AATAGGGTGTAAAACGAGCATCATGACCTCTAGGTC
1 AATAGGGAGTAAAACGAACATCATGACCTCTAGGTC
* * *
29341 AATAGGGAGTAAAATGAACATTATGACCTTTAGGTC
1 AATAGGGAGTAAAACGAACATCATGACCTCTAGGTC
*
29377 AACAGGGAGTAAAACGA
1 AATAGGGAGTAAAACGA
29394 TTAACGAACG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (36 bp):
AATAGGGAGTAAAACGAACATCATGACCTCTAGGTC
Found at i:30088 original size:21 final size:21
Alignment explanation
Indices: 30064--30125 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
30054 TTTGTGTCGG
*
30064 TAGAAGTAAGACTTGTATCAA
1 TAGAAGTGAGACTTGTATCAA
* * *
30085 TAGAAGTGAGACCTGTTTCGA
1 TAGAAGTGAGACTTGTATCAA
* *
30106 TAGAACTGACACTTGTATCA
1 TAGAAGTGAGACTTGTATCA
30126 GTAAAAAACT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (21 bp):
TAGAAGTGAGACTTGTATCAA
Found at i:32185 original size:21 final size:21
Alignment explanation
Indices: 32134--32202 Score: 50
Period size: 24 Copynumber: 3.1 Consensus size: 21
32124 TTAATATATG
* *
32134 AAAAATTAATTTTAAATATTACT
1 AAAAATTAATATTAATTATT--T
*
32157 AAGCAATTAATATTAATTATTT
1 AA-AAATTAATATTAATTATTT
* *
32179 AAAAATTTA-ATTAGATTATAT
1 AAAAATTAATATTA-ATTATTT
32200 AAA
1 AAA
32203 CTATATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.11
21 14 0.37
22 3 0.08
23 2 0.05
24 15 0.39
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAAATTAATATTAATTATTT
Done.