Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006897.1 Kokia drynarioides strain JFW-HI SEQ_121498, 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: 72335
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:6674 original size:17 final size:17
Alignment explanation
Indices: 6652--6691 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
6642 AAATAAGATT
6652 GTAGTAGAGTGCGAACG
1 GTAGTAGAGTGCGAACG
6669 GTAGTAGAGTGCGAACG
1 GTAGTAGAGTGCGAACG
6686 GTAGTA
1 GTAGTA
6692 TGTATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.10, G:0.40, T:0.20
Consensus pattern (17 bp):
GTAGTAGAGTGCGAACG
Found at i:9749 original size:59 final size:59
Alignment explanation
Indices: 9657--9775 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
9647 GCAATGGAAA
9657 AAGAAATGTGATTATAATTATACTACAGCTACATGATATGCATGAAAACTAAACTAAGT
1 AAGAAATGTGATTATAATTATACTACAGCTACATGATATGCATGAAAACTAAACTAAGT
9716 AAGAAATGTGATTATAATTATACTACAGCTACATGATATGCATGAAAACTAAACTAAGT
1 AAGAAATGTGATTATAATTATACTACAGCTACATGATATGCATGAAAACTAAACTAAGT
9775 A
1 A
9776 CTGAAAATAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (59 bp):
AAGAAATGTGATTATAATTATACTACAGCTACATGATATGCATGAAAACTAAACTAAGT
Found at i:10146 original size:21 final size:22
Alignment explanation
Indices: 10117--10158 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10107 GCTACAAAAA
10117 CTTTATCTTCCTCTTCCTCTTT
1 CTTTATCTTCCTCTTCCTCTTT
* *
10139 CTTT-TCTTCTTCTTTCTCTT
1 CTTTATCTTCCTCTTCCTCTT
10159 CTTCCTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (22 bp):
CTTTATCTTCCTCTTCCTCTTT
Found at i:10152 original size:15 final size:15
Alignment explanation
Indices: 10128--10167 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
10118 TTTATCTTCC
* *
10128 TCTTCCTCTTTCTTT
1 TCTTCTTCTTTCTCT
10143 TCTTCTTCTTTCTCT
1 TCTTCTTCTTTCTCT
10158 TCTTCCTTCT
1 TCTT-CTTCT
10168 CCTTATCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:24672 original size:22 final size:21
Alignment explanation
Indices: 24606--24663 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
24596 TCGAAATAAG
* **
24606 ACTTGCATCAGTAGAAGAATC
1 ACTTGTATCAGTAGAACTATC
**
24627 ACTTGTATTGGTAGAACTATC
1 ACTTGTATCAGTAGAACTATC
24648 ACTTGTATCAGTAGAA
1 ACTTGTATCAGTAGAA
24664 ACTTGCACTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACTATC
Found at i:32736 original size:29 final size:29
Alignment explanation
Indices: 32693--32753 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
32683 ATTCCACCCT
32693 TAATGGAATGCACATGTCTACTTCTGTGC
1 TAATGGAATGCACATGTCTACTTCTGTGC
*
32722 TAATGGAATGTACATGTCTACTTCTGTGC
1 TAATGGAATGCACATGTCTACTTCTGTGC
32751 TAA
1 TAA
32754 CTATAGGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (29 bp):
TAATGGAATGCACATGTCTACTTCTGTGC
Found at i:41368 original size:15 final size:15
Alignment explanation
Indices: 41348--41377 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41338 AGCAGTCCAT
41348 TGAGAAACAGCAAAG
1 TGAGAAACAGCAAAG
41363 TGAGAAACAGCAAAG
1 TGAGAAACAGCAAAG
41378 GCTTAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.27, T:0.07
Consensus pattern (15 bp):
TGAGAAACAGCAAAG
Found at i:45387 original size:16 final size:16
Alignment explanation
Indices: 45345--45388 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
45335 GAGGTGCTTA
45345 AGAAGAAAGAAAAAGG
1 AGAAGAAAGAAAAAGG
45361 -GAAATGAAAGAAAAAGG
1 AG-AA-GAAAGAAAAAGG
*
45378 AGAAGCAAGAA
1 AGAAGAAAGAA
45389 GATGTGCCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 1 0.04
16 8 0.33
17 14 0.58
18 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (16 bp):
AGAAGAAAGAAAAAGG
Found at i:47012 original size:15 final size:16
Alignment explanation
Indices: 46981--47030 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
46971 AGTCATATAT
46981 AAAAATAGAAAAGAAG
1 AAAAATAGAAAAGAAG
46997 AAAAATA-AAACA-AAG
1 AAAAATAGAAA-AGAAG
* *
47012 AAAAAGAGAAAAGCAG
1 AAAAATAGAAAAGAAG
47028 AAA
1 AAA
47031 GATGTTGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAATAGAAAAGAAG
Found at i:47015 original size:23 final size:22
Alignment explanation
Indices: 46979--47023 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
46969 TCAGTCATAT
*
46979 ATAAAAATAG-AAAAGAAGAAAA
1 ATAAAAAAAGAAAAAG-AGAAAA
47001 ATAAAACAAAGAAAAAGAGAAAA
1 ATAAAA-AAAGAAAAAGAGAAAA
47024 GCAGAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (22 bp):
ATAAAAAAAGAAAAAGAGAAAA
Found at i:48494 original size:61 final size:61
Alignment explanation
Indices: 48424--48546 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
48414 AATTCCTTGT
48424 CGTCACATCTAGCATTGATACTTAGTGAAGTCAATGATCCACTCTATTCTTCGCACTTGAC
1 CGTCACATCTAGCATTGATACTTAGTGAAGTCAATGATCCACTCTATTCTTCGCACTTGAC
48485 CGTCACATCTAGCATTGATACTTAGTGAAGTCAATGATCCACTCTATTCTTCGCACTTGAC
1 CGTCACATCTAGCATTGATACTTAGTGAAGTCAATGATCCACTCTATTCTTCGCACTTGAC
48546 C
1 C
48547 ACACTTTTAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.33
Consensus pattern (61 bp):
CGTCACATCTAGCATTGATACTTAGTGAAGTCAATGATCCACTCTATTCTTCGCACTTGAC
Found at i:49624 original size:9 final size:9
Alignment explanation
Indices: 49610--49639 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
49600 ATCATTTGTA
49610 TTTTTTAATT
1 TTTTTTAA-T
49620 TTTTTTAAT
1 TTTTTTAAT
49629 TTTTTTAAT
1 TTTTTTAAT
49638 TT
1 TT
49640 AATAAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:49625 original size:10 final size:10
Alignment explanation
Indices: 49610--49639 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
49600 ATCATTTGTA
49610 TTTTTTAATT
1 TTTTTTAATT
49620 TTTTTTAA-T
1 TTTTTTAATT
49629 TTTTTTAATT
1 TTTTTTAATT
49639 T
1 T
49640 AATAAGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:59475 original size:16 final size:18
Alignment explanation
Indices: 59442--59490 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 18
59432 GAACTTGAGG
* *
59442 AGAAGAAGGAAAATAAAAA
1 AGAAGAA-GAAGAGAAAAA
59461 AG-AGAAGAA-AG-AAAA
1 AGAAGAAGAAGAGAAAAA
59476 AGAAGAAGAAGAGAA
1 AGAAGAAGAAGAGAA
59491 GGAAGATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 5 0.19
18 5 0.19
19 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (18 bp):
AGAAGAAGAAGAGAAAAA
Found at i:59936 original size:17 final size:17
Alignment explanation
Indices: 59914--59949 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
59904 ATGCATCTTA
*
59914 TTTAGTTGTCATTACAT
1 TTTAGTTGTCAATACAT
*
59931 TTTAGTTGTTAATACAT
1 TTTAGTTGTCAATACAT
59948 TT
1 TT
59950 GCATTGTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (17 bp):
TTTAGTTGTCAATACAT
Found at i:67784 original size:12 final size:11
Alignment explanation
Indices: 67769--67802 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
67759 AAATCATTTG
67769 TATTTTTTGAAT
1 TATTTTTT-AAT
67781 TATTTTTTAAT
1 TATTTTTTAAT
67792 T-TTTTTTAAT
1 TATTTTTTAAT
67802 T
1 T
67803 TAATAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 4 0.18
12 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTTTTTAAT
Found at i:70100 original size:17 final size:17
Alignment explanation
Indices: 70080--70114 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
70070 GAAGAAAAAC
70080 AATTGATGAATGATTTT
1 AATTGATGAATGATTTT
70097 AATTGATGAATGATTTT
1 AATTGATGAATGATTTT
70114 A
1 A
70115 TTATGCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
AATTGATGAATGATTTT
Found at i:71998 original size:19 final size:20
Alignment explanation
Indices: 71976--72013 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71966 TCAAAAAGTA
*
71976 GAGAAAAA-AAGAAAAATAC
1 GAGAAAAATAAAAAAAATAC
71995 GAGAAAAATAAAAAAAATA
1 GAGAAAAATAAAAAAAATA
72014 TTCTGTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (20 bp):
GAGAAAAATAAAAAAAATAC
Done.