Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000546.1 Kokia drynarioides strain JFW-HI SEQ_111450, 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: 53285
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1048 original size:23 final size:23
Alignment explanation
Indices: 1022--1187 Score: 132
Period size: 23 Copynumber: 7.4 Consensus size: 23
1012 ACACTAGCGC
*
1022 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * *
1045 GCTCTCTATTCAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
1068 GCTCTCTGTTTAGCACATCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
* *
1091 GCTCTCTGTTATTAGCACTTCGCGT
1 GCTCTCTG-T-TTAGCACTTTGTGT
** *
1116 GCTCTCTAATTAACACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
1139 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
1155 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
1178 GCTCTCTGTT
1 GCTCTCTGTT
1188 GCCCAGCACT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
21 3 0.03
23 77 0.68
24 4 0.04
25 17 0.15
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:1097 original size:25 final size:25
Alignment explanation
Indices: 1069--1122 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1059 ACTGTGTGTG
*
1069 CTCTCTGT-TTAGCACATCTCGTGCT
1 CTCTCT-TATTAGCACATCGCGTGCT
* *
1094 CTCTGTTATTAGCACTTCGCGTGCT
1 CTCTCTTATTAGCACATCGCGTGCT
1119 CTCT
1 CTCT
1123 AATTAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.11, C:0.31, G:0.17, T:0.41
Consensus pattern (25 bp):
CTCTCTTATTAGCACATCGCGTGCT
Found at i:3887 original size:39 final size:40
Alignment explanation
Indices: 3811--3890 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
3801 AAGAGGTATG
*
3811 TCCAATATGAAAAGGGTTGTGACTCTTCAAAATGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
*
3851 TCCAAT-TTAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
3890 T
1 T
3891 TGAGTGCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 32 0.84
40 6 0.16
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
Found at i:5114 original size:27 final size:28
Alignment explanation
Indices: 5084--5148 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
5074 AAATAATTTG
5084 TTTTATAAAAGAAATTAAAAAA-TTATA
1 TTTTATAAAAGAAATTAAAAAATTTATA
* *
5111 TTTTAAAAAATAAATTAAAAAATTTTATA
1 TTTTATAAAAGAAATTAAAAAA-TTTATA
5140 TTTT-TAAAA
1 TTTTATAAAA
5149 ATAATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.61
28 4 0.12
29 9 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTTATAAAAGAAATTAAAAAATTTATA
Found at i:5142 original size:29 final size:29
Alignment explanation
Indices: 5084--5166 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
5074 AAATAATTTG
* *
5084 TTTTATAAAAGAAATTAAAAAA--TTATA
1 TTTTAAAAAATAAATTAAAAAATTTTATA
5111 TTTTAAAAAATAAATTAAAAAATTTTATA
1 TTTTAAAAAATAAATTAAAAAATTTTATA
* * * *
5140 TTTTTAAAAATAATTTTAATAATTTTA
1 TTTTAAAAAATAAATTAAAAAATTTTA
5167 AAATCATTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 20 0.42
29 28 0.58
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (29 bp):
TTTTAAAAAATAAATTAAAAAATTTTATA
Found at i:5156 original size:20 final size:20
Alignment explanation
Indices: 5127--5169 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5117 AAAATAAATT
*
5127 AAAAAATTTT-ATATTTTTA
1 AAAAAATTTTAATAATTTTA
5146 AAAATAATTTTAATAATTTTA
1 AAAA-AATTTTAATAATTTTA
5167 AAA
1 AAA
5170 TCATTTGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAAATTTTAATAATTTTA
Found at i:5170 original size:20 final size:19
Alignment explanation
Indices: 5125--5175 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5115 AAAAAATAAA
*
5125 TTAAAA-AATTTTATATTT
1 TTAAAATAATTTTATAATT
5143 TTAAAAATAATTTTAATAATT
1 TT-AAAATAATTTT-ATAATT
*
5164 TTAAAATCATTT
1 TTAAAATAATTT
5176 GCTGATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 15 0.54
21 7 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATAATTTTATAATT
Found at i:5727 original size:23 final size:24
Alignment explanation
Indices: 5701--5748 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
5691 TTTTCCAATA
5701 TTCAATT-AATACTTGA-ATTTTTT
1 TTCAATTAAATACTT-ATATTTTTT
5724 TTCAATTAAATACTTATATTTTTT
1 TTCAATTAAATACTTATATTTTTT
5748 T
1 T
5749 AACTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.58
Consensus pattern (24 bp):
TTCAATTAAATACTTATATTTTTT
Found at i:5839 original size:12 final size:12
Alignment explanation
Indices: 5822--5848 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5812 TGAGACAAAA
5822 AAATTAAATATT
1 AAATTAAATATT
5834 AAATTAAATATT
1 AAATTAAATATT
5846 AAA
1 AAA
5849 ACTAATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATTAAATATT
Found at i:10086 original size:22 final size:22
Alignment explanation
Indices: 10061--10103 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10051 AGAGTAATTA
10061 TTTTTTGTTAAAAAATAAGTAT
1 TTTTTTGTTAAAAAATAAGTAT
* * *
10083 TTTTTTTTTGAGAAATAAGTA
1 TTTTTTGTTAAAAAATAAGTA
10104 AATATTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTTTTGTTAAAAAATAAGTAT
Found at i:23035 original size:57 final size:55
Alignment explanation
Indices: 22937--23131 Score: 221
Period size: 57 Copynumber: 3.4 Consensus size: 55
22927 TATCATATAA
* * * * *
22937 TTTTTTATCTGAAAAAAGAGTATCGACCATAACATGGGCGACACCAAAAAATATTT
1 TTTTTTATCTGAAAAAGGGGTGTCGATCATAGCATGGGCGACACCAAAAAATA-TT
* *
22993 TTTTTTATTTGAAAAAGAGGGTGTCGATCATGGCATGGGCGACACCAAAACAATATT
1 TTTTTTATCTGAAAAAG-GGGTGTCGATCATAGCATGGGCGACACCAAAA-AATATT
* * *
23050 TTTTTTATCTGAAAAAGGGGTGTTTG-TCATAGCATGGACGATATCCAAACAAATATT
1 TTTTTTATCTGAAAAAGGGGTG-TCGATCATAGCATGGGCGACA-CCAAA-AAATATT
*
23107 TTTTTTATTTGAAAAAGGAGGTGTC
1 TTTTTTATCTGAAAAAGG-GGTGTC
23132 AGGCATAGCT
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
56 34 0.29
57 76 0.64
58 9 0.08
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (55 bp):
TTTTTTATCTGAAAAAGGGGTGTCGATCATAGCATGGGCGACACCAAAAAATATT
Found at i:23156 original size:58 final size:56
Alignment explanation
Indices: 22980--23156 Score: 151
Period size: 57 Copynumber: 3.1 Consensus size: 56
22970 ATGGGCGACA
* * * * * * *
22980 CCAAAAAATATTTTTTTTTATTTGAAAAAGAGGGTGTC-GATCATGGCATGGGCGACAC
1 CCAAACAATA-TTTTTTTTATCTGAAAAAG-GGGTGTCAG-GCATAGCATGGACAATAC
* ** * * *
23038 CAAAACAATATTTTTTTTATCTGAAAAAGGGGTGTTTGTCATAGCATGGACGATAT
1 CCAAACAATATTTTTTTTATCTGAAAAAGGGGTGTCAGGCATAGCATGGACAATAC
* *
23094 CCAAACAAATATTTTTTTTATTTGAAAAAGGAGGTGTCAGGCATAGC-TTGACAAATAC
1 CCAAAC-AATATTTTTTTTATCTGAAAAAGG-GGTGTCAGGCATAGCATGGAC-AATAC
23152 CCAAA
1 CCAAA
23157 TTTTTTTTGG
Statistics
Matches: 99, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
56 25 0.25
57 46 0.46
58 28 0.28
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (56 bp):
CCAAACAATATTTTTTTTATCTGAAAAAGGGGTGTCAGGCATAGCATGGACAATAC
Found at i:38677 original size:6 final size:6
Alignment explanation
Indices: 38666--38694 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38656 TGATCAAAAT
38666 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
38695 TTGGAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:38707 original size:18 final size:18
Alignment explanation
Indices: 38662--38710 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
38652 TTTGTGATCA
38662 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
38680 AAAGTGAAAGTGAAATTG
1 AAATTGAAAGTGAAAGTG
* *
38698 GAATTAAAAGTGA
1 AAATTGAAAGTGA
38711 TATGAATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:42015 original size:31 final size:31
Alignment explanation
Indices: 41966--42038 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
41956 AGAAAAACAT
* *
41966 AATAGCCTAGCGACTTAAATAAAAACTTTGG
1 AATAGTCTAGTGACTTAAATAAAAACTTTGG
* * *
41997 AATAGTCTAGTGATTTAAATGAAAACTTTTG
1 AATAGTCTAGTGACTTAAATAAAAACTTTGG
*
42028 AATAGTTTAGT
1 AATAGTCTAGT
42039 AATCATTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
AATAGTCTAGTGACTTAAATAAAAACTTTGG
Found at i:48724 original size:28 final size:28
Alignment explanation
Indices: 48660--48730 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
48650 TTTTATTAAG
*
48660 ATATTAA-AATTTTA-ATATTATTTTAT
1 ATATTAATAATTATATATATTATTTTAT
* * *
48686 GTATGACTAATTATATATATGTATTTT-T
1 ATATTAATAATTATATATAT-TATTTTAT
48714 ATATTAATAATTATATA
1 ATATTAATAATTATATA
48731 ATATATAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 4 0.11
27 6 0.17
28 19 0.54
29 6 0.17
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (28 bp):
ATATTAATAATTATATATATTATTTTAT
Found at i:48740 original size:15 final size:15
Alignment explanation
Indices: 48693--48744 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
48683 TATGTATGAC
*
48693 TAATTATAT-ATATG
1 TAATTATATAATATA
* * *
48707 TATTTTTATATTA-A
1 TAATTATATAATATA
48721 TAATTATATAATATA
1 TAATTATATAATATA
48736 TAATTATAT
1 TAATTATAT
48745 TATGTAACAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATTATATAATATA
Done.