Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014810.1 Kokia drynarioides strain JFW-HI SEQ_129852, 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: 65067
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:1442 original size:46 final size:47
Alignment explanation
Indices: 1336--1460 Score: 137
Period size: 46 Copynumber: 2.7 Consensus size: 47
1326 CACTAGCGCG
* * * *
1336 CTCTCTGTTTAGCACGTCT-CGTGCTCTCTGTTATTAGCATTTTGTGTG
1 CTCTCTGTTTAGCAC-TCTGTGTGCTTTCTG-TATTAGCACTTTGTGTA
* * * *
1384 CTCTTTGATTAGCACTTTGTGTGCTTTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTCTGTGTGCTTTCTGTATTAGCACTTTGTGTA
*
1430 CTCTCTGTTTAGCACTGTGTGTGCTTTCTGT
1 CTCTCTGTTTAGCACTCTGTGTGCTTTCTGT
1461 TACCGAGCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
46 40 0.62
47 2 0.03
48 22 0.34
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (47 bp):
CTCTCTGTTTAGCACTCTGTGTGCTTTCTGTATTAGCACTTTGTGTA
Found at i:1459 original size:23 final size:23
Alignment explanation
Indices: 1369--1461 Score: 107
Period size: 23 Copynumber: 4.0 Consensus size: 23
1359 CTCTCTGTTA
* *
1369 TTAGCATTTTGTGTGCTCTT-TGA
1 TTAGCACTTTGTGTGCT-TTCTGT
*
1392 TTAGCACTTTGTGTGCTTTCTGA
1 TTAGCACTTTGTGTGCTTTCTGT
* * *
1415 TTAGTACTTTGTGTACTCTCTGT
1 TTAGCACTTTGTGTGCTTTCTGT
*
1438 TTAGCACTGTGTGTGCTTTCTGT
1 TTAGCACTTTGTGTGCTTTCTGT
1461 T
1 T
1462 ACCGAGCACT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
22 2 0.03
23 58 0.97
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.51
Consensus pattern (23 bp):
TTAGCACTTTGTGTGCTTTCTGT
Found at i:17766 original size:24 final size:24
Alignment explanation
Indices: 17717--17764 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
17707 TTTATTTCTT
17717 ATATTTATATTTTTAAAATTTTAA
1 ATATTTATATTTTTAAAATTTTAA
*
17741 ATATTT-TATTTTTGAAATTTTAA
1 ATATTTATATTTTTAAAATTTTAA
17764 A
1 A
17765 ATTCAGATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
ATATTTATATTTTTAAAATTTTAA
Found at i:22831 original size:18 final size:18
Alignment explanation
Indices: 22808--22846 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
22798 TTTAATTCCT
22808 TTTTTATTTATATTTATA
1 TTTTTATTTATATTTATA
* *
22826 TTTTTATTTTTATTTCTA
1 TTTTTATTTATATTTATA
22844 TTT
1 TTT
22847 CGTGTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTATTTATATTTATA
Found at i:26959 original size:42 final size:42
Alignment explanation
Indices: 26912--26997 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
26902 CATAGAGAGT
*
26912 TATAAAATCGAGGTTGAAGAGAAGTATATTCAATTTTTTAAA
1 TATAAAATCGAGGATGAAGAGAAGTATATTCAATTTTTTAAA
*
26954 TATAAAATCGAGGATGAAGAGAATTATATTCAATTTTTTAAA
1 TATAAAATCGAGGATGAAGAGAAGTATATTCAATTTTTTAAA
26996 TA
1 TA
26998 AGTAATTCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (42 bp):
TATAAAATCGAGGATGAAGAGAAGTATATTCAATTTTTTAAA
Found at i:27344 original size:31 final size:32
Alignment explanation
Indices: 27283--27347 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
27273 CTCAACAATC
* *
27283 AACAAAGTGGAAAAATAATTTCGACCAAAAAA
1 AACAAAGTGGAAAAATAATTTCAACAAAAAAA
**
27315 AACAAAGTGG-AAAATAATTT-AATTAAAAAA
1 AACAAAGTGGAAAAATAATTTCAACAAAAAAA
27345 AAC
1 AAC
27348 CTCGATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 10 0.33
31 10 0.33
32 10 0.33
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (32 bp):
AACAAAGTGGAAAAATAATTTCAACAAAAAAA
Found at i:27773 original size:18 final size:16
Alignment explanation
Indices: 27732--27762 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
27722 CCTCTAAATG
27732 ATATTTATACTTTTTT
1 ATATTTATACTTTTTT
27748 ATATTTATACTTTTT
1 ATATTTATACTTTTT
27763 ATTTTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATTTATACTTTTTT
Found at i:42152 original size:18 final size:18
Alignment explanation
Indices: 42117--42155 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42107 TTGGGGCTAA
*
42117 TTTTAATCATTTTGGAAT
1 TTTTAATCATTATGGAAT
42135 TTTTAATCAATTAT-GAAT
1 TTTTAATC-ATTATGGAAT
42153 TTT
1 TTT
42156 ACTTTTTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (18 bp):
TTTTAATCATTATGGAAT
Found at i:51584 original size:15 final size:15
Alignment explanation
Indices: 51557--51595 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
51547 AGGAACCTCA
51557 TCATCCTCATCTTCT
1 TCATCCTCATCTTCT
* *
51572 TCTTCCTCCTCTTCT
1 TCATCCTCATCTTCT
51587 TCATCCTCA
1 TCATCCTCA
51596 CCATCATCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.10, C:0.44, G:0.00, T:0.46
Consensus pattern (15 bp):
TCATCCTCATCTTCT
Found at i:51642 original size:12 final size:12
Alignment explanation
Indices: 51611--51661 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
51601 ATCGTCATCA
*
51611 TCATCATCTTCG
1 TCATCATCGTCG
**
51623 TCCCCATCGTCG
1 TCATCATCGTCG
51635 TCATCATCGTCG
1 TCATCATCGTCG
* *
51647 TCATCCTCTTCG
1 TCATCATCGTCG
51659 TCA
1 TCA
51662 CTCCCACCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.14, C:0.39, G:0.12, T:0.35
Consensus pattern (12 bp):
TCATCATCGTCG
Found at i:55303 original size:14 final size:13
Alignment explanation
Indices: 55284--55326 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
55274 GTTCCAACTC
55284 AATTAAAAACTAAT
1 AATTAAAAA-TAAT
*
55298 AATTAAAAATTATT
1 AATTAAAAA-TAAT
*
55312 ATTTAAAAATAAT
1 AATTAAAAATAAT
55325 AA
1 AA
55327 ATATTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTAAAAATAAT
Found at i:57579 original size:21 final size:21
Alignment explanation
Indices: 57552--57596 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
57542 ACCCAGATAA
57552 TTAAAAAGGAAAAAAGAAATTG
1 TTAAAAA-GAAAAAAGAAATTG
**
57574 TTAAAAAGTTAAAAGAAATTG
1 TTAAAAAGAAAAAAGAAATTG
57595 TT
1 TT
57597 TTTTAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.27
Consensus pattern (21 bp):
TTAAAAAGAAAAAAGAAATTG
Done.