Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011136.1 Kokia drynarioides strain JFW-HI SEQ_126109, 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: 9167
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2054 original size:4 final size:4
Alignment explanation
Indices: 2045--2079 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2035 GGCACCAAGT
*
2045 AGAA AGAA AGGA AGAA AGAA AGAA AG-A AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
2080 GGAAGAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:2076 original size:7 final size:7
Alignment explanation
Indices: 2048--2087 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
2038 ACCAAGTAGA
2048 AAGAAAGG
1 AAGAAA-G
2056 AAGAAAG
1 AAGAAAG
2063 AAAGAAAG
1 -AAGAAAG
2071 AAGAAAG
1 AAGAAAG
*
2078 AAGGAAG
1 AAGAAAG
2085 AAG
1 AAG
2088 GAGAGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 17 0.57
8 13 0.43
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:2076 original size:11 final size:11
Alignment explanation
Indices: 2048--2086 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2038 ACCAAGTAGA
*
2048 AAGAAAGGAAG
1 AAGAAAGAAAG
2059 AAAGAAAGAAAG
1 -AAGAAAGAAAG
*
2071 AAGAAAGAAGG
1 AAGAAAGAAAG
2082 AAGAA
1 AAGAA
2087 GGAGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:2108 original size:20 final size:20
Alignment explanation
Indices: 2078--2115 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2068 AAGAAGAAAG
2078 AAGGAAGAAGGAGAGAAAAAA
1 AAGGAAGAAGGAGA-AAAAAA
2099 AAGG-AGAAGGAGAAAAA
1 AAGGAAGAAGGAGAAAAA
2116 GGTAGTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGGAAGAAGGAGAAAAAAA
Found at i:2352 original size:14 final size:14
Alignment explanation
Indices: 2333--2402 Score: 58
Period size: 13 Copynumber: 5.1 Consensus size: 14
2323 TAAGTGCTTA
2333 TTATTTTAATTT-AT
1 TTATTTT-ATTTAAT
2347 TTATTTTATTTAAT
1 TTATTTTATTTAAT
**
2361 TTAATTTTTAAATAAT
1 TT-A-TTTTATTTAAT
2377 TTA--TTATTTAAT
1 TTATTTTATTTAAT
*
2389 GT-TTTTATTTAAT
1 TTATTTTATTTAAT
2402 T
1 T
2403 GAATAAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
12 8 0.18
13 13 0.29
14 11 0.24
15 2 0.04
16 11 0.24
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (14 bp):
TTATTTTATTTAAT
Found at i:3026 original size:47 final size:46
Alignment explanation
Indices: 2952--3045 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 46
2942 TATGTGGATA
*
2952 TCATTTTGGTATATAAATATTTATTTTGTACCATTTTAGTAAATAAC
1 TCATTTTGGTATATAAATATTTATTTTGTACCATATTAGTAAA-AAC
* * **
2999 TCATTTTGGTATTTAATTA-TTATTTTTGTATTATATTAGTAAAAAC
1 TCATTTTGGTATATAAATATTTA-TTTTGTACCATATTAGTAAAAAC
3045 T
1 T
3046 AATAAAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 7 0.17
47 34 0.83
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (46 bp):
TCATTTTGGTATATAAATATTTATTTTGTACCATATTAGTAAAAAC
Found at i:4203 original size:43 final size:43
Alignment explanation
Indices: 4153--4242 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
4143 CATTAACATG
* *
4153 TTAAATTATATTACTTGACTCGTGTTAATATGGTT-ACATGTTA
1 TTAAATTATATTACTTGACTCGTATTAATAT-CTTGACATGTTA
*
4196 TTAAATTATATTACTTGACTCTTATTAATATCTTGACATGTTA
1 TTAAATTATATTACTTGACTCGTATTAATATCTTGACATGTTA
4239 TTAA
1 TTAA
4243 TTGTGCAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (43 bp):
TTAAATTATATTACTTGACTCGTATTAATATCTTGACATGTTA
Found at i:5139 original size:15 final size:14
Alignment explanation
Indices: 5119--5171 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
5109 CTTTAACCCT
5119 AAACCTTAAACCTTC-
1 AAACCTTAAA--TTCA
5134 AAACCTTAAATTCA
1 AAACCTTAAATTCA
* **
5148 AAACCTTAAGTTTT
1 AAACCTTAAATTCA
5162 AAACCTTAAA
1 AAACCTTAAA
5172 CCCTTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 3 0.09
14 20 0.61
15 10 0.30
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (14 bp):
AAACCTTAAATTCA
Found at i:5177 original size:36 final size:34
Alignment explanation
Indices: 5126--5243 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 34
5116 CCTAAACCTT
**
5126 AAACCTTCAAACCTTAAATTCAAAACCTTAAGTTTT
1 AAACCTT-AAACCTTAAATTCAAAACCTTAA-TTCA
* * *
5162 AAACCTTAAACCCTTAAATTTGAAACCCTAAATTCA
1 AAACCTTAAA-CCTTAAA-TTCAAAACCTTAATTCA
**
5198 AAACCCAAAACCTTAAAATTCAAAACCCTTAATTCA
1 AAACCTTAAACCTT-AAATTCAAAA-CCTTAATTCA
5234 AAACCTTAAA
1 AAACCTTAAA
5244 TTTAAAGCCC
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
35 12 0.18
36 44 0.67
37 10 0.15
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.27
Consensus pattern (34 bp):
AAACCTTAAACCTTAAATTCAAAACCTTAATTCA
Found at i:5187 original size:22 final size:22
Alignment explanation
Indices: 5151--5193 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5141 AAATTCAAAA
* * *
5151 CCTTAAGTTTTAAACCTTAAAC
1 CCTTAAATTTGAAACCCTAAAC
5173 CCTTAAATTTGAAACCCTAAA
1 CCTTAAATTTGAAACCCTAAA
5194 TTCAAAACCC
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:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
CCTTAAATTTGAAACCCTAAAC
Found at i:5201 original size:14 final size:15
Alignment explanation
Indices: 5169--5266 Score: 67
Period size: 14 Copynumber: 6.3 Consensus size: 15
5159 TTTAAACCTT
**
5169 AAACCCTTAAATTTG
1 AAACCCTTAAATTCA
5184 AAACCC-TAAATTCA
1 AAACCCTTAAATTCA
5198 AAACCCAAAACCTTAAAATTCA
1 AAA-CC-----CTTA-AATTCA
5220 AAACCCTT-AATTCA
1 AAACCCTTAAATTCA
*
5234 AAA-CCTTAAATTTA
1 AAACCCTTAAATTCA
* *
5248 AAGCCCTAAAATTCA
1 AAACCCTTAAATTCA
5263 AAAC
1 AAAC
5267 ACTAAACCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
13 4 0.06
14 25 0.38
15 20 0.30
16 3 0.05
20 1 0.02
21 4 0.06
22 9 0.14
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (15 bp):
AAACCCTTAAATTCA
Found at i:5260 original size:29 final size:29
Alignment explanation
Indices: 5203--5266 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
5193 ATTCAAAACC
*
5203 CAAAACCTTAAAATTCAAAACCCTTAATT
1 CAAAACCTTAAAATTCAAAACCCTAAATT
* *
5232 CAAAACCTT-AAATTTAAAGCCCTAAAATT
1 CAAAACCTTAAAATTCAAAACCCT-AAATT
5261 CAAAAC
1 CAAAAC
5267 ACTAAACCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (29 bp):
CAAAACCTTAAAATTCAAAACCCTAAATT
Found at i:7490 original size:18 final size:18
Alignment explanation
Indices: 7467--7513 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
7457 GCGTTATAAT
7467 TTTCATCGTCATTCGGCC
1 TTTCATCGTCATTCGGCC
7485 TTTCATCGTCATTCGGCC
1 TTTCATCGTCATTCGGCC
7503 TTTCATCGTCA
1 TTTCATCGTCA
7514 ATCATCCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.13, C:0.32, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTCATCGTCATTCGGCC
Found at i:8375 original size:3 final size:3
Alignment explanation
Indices: 8367--8406 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
8357 TTGGCACCAC
8367 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8407 TTTTAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:8551 original size:24 final size:27
Alignment explanation
Indices: 8524--8584 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 27
8514 GGTATGTATT
*
8524 TAATTTTTTTTTATTC-AAT-AAAT-A
1 TAATTTTTTTTTAGTCAAATAAAATAA
* *
8548 TAATATTATTTTAGTCAAATAAAATAAA
1 TAATTTTTTTTTAGTCAAATAAAAT-AA
8576 TAATTTTTT
1 TAATTTTTT
8585 ATATTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 13 0.46
25 3 0.11
26 4 0.14
28 8 0.29
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (27 bp):
TAATTTTTTTTTAGTCAAATAAAATAA
Found at i:8584 original size:25 final size:23
Alignment explanation
Indices: 8530--8585 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
8520 TATTTAATTT
*
8530 TTTTTTATTCAATAAATATAATA
1 TTTTTTAGTCAATAAATATAATA
8553 TTATTTTAGTCAAATAAA-ATAAATAA
1 TT-TTTTAGTC-AATAAATAT-AAT-A
8579 TTTTTTA
1 TTTTTTA
8586 TATTATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 9 0.32
25 14 0.50
26 3 0.11
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTTTTAGTCAATAAATATAATA
Found at i:8618 original size:28 final size:29
Alignment explanation
Indices: 8569--8628 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
8559 TAGTCAAATA
**
8569 AAATAAATAATTTTTTATATTATTTTAGT
1 AAATAAATAATTTTTTATATTAAATTAGT
* *
8598 AAATGAAT-ATTTTTTGTATTAAATTAGT
1 AAATAAATAATTTTTTATATTAAATTAGT
8626 AAA
1 AAA
8629 AAACCCTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
AAATAAATAATTTTTTATATTAAATTAGT
Done.