Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009791.1 Kokia drynarioides strain JFW-HI SEQ_124512, 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: 50892
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:1667 original size:18 final size:19
Alignment explanation
Indices: 1625--1667 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
1615 TGTTTACCAA
1625 AAAAATTTATGACCAAGTT
1 AAAAATTTATGACCAAGTT
1644 AGAAAATTT-T-ACCAAGTT
1 A-AAAATTTATGACCAAGTT
1662 CAAAAA
1 -AAAAA
1668 CTGAAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 12 0.55
19 3 0.14
20 7 0.32
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (19 bp):
AAAAATTTATGACCAAGTT
Found at i:5281 original size:24 final size:25
Alignment explanation
Indices: 5230--5326 Score: 69
Period size: 24 Copynumber: 4.0 Consensus size: 25
5220 GTCAGTTGAT
*
5230 GACGACGAGGACGA-GGATGATGAA
1 GACGACGAGGACGACGGATGAAGAA
**
5254 GACGACGAGGACGACGG-TGAAGGC
1 GACGACGAGGACGACGGATGAAGAA
* * * * *
5278 GACGGCGATGACGAC-GACGACGAT
1 GACGACGAGGACGACGGATGAAGAA
*
5302 GACGAC-AGTGATGAC-GATGAAGAA
1 GACGACGAG-GACGACGGATGAAGAA
5326 G
1 G
5327 GTGAAGAAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.40, T:0.08
Consensus pattern (25 bp):
GACGACGAGGACGACGGATGAAGAA
Found at i:5295 original size:15 final size:15
Alignment explanation
Indices: 5257--5307 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
5247 TGATGAAGAC
* *
5257 GACGAGGACGACGGT
1 GACGACGACGACGAT
* * *
5272 GAAGGCGACGGCGAT
1 GACGACGACGACGAT
5287 GACGACGACGACGAT
1 GACGACGACGACGAT
5302 GACGAC
1 GACGAC
5308 AGTGATGACG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.41, T:0.06
Consensus pattern (15 bp):
GACGACGACGACGAT
Found at i:6102 original size:21 final size:21
Alignment explanation
Indices: 6053--6102 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6043 ATTTTGAACC
* * *
6053 AGAAGAAAATGGTGAAGAGGA
1 AGAAGAAGATGATGAAGACGA
6074 AGAAGAAGATGATGAAGACGA
1 AGAAGAAGATGATGAAGACGA
*
6095 TGAAGAAG
1 AGAAGAAG
6103 GTAGTGGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.02, G:0.36, T:0.10
Consensus pattern (21 bp):
AGAAGAAGATGATGAAGACGA
Found at i:6423 original size:9 final size:9
Alignment explanation
Indices: 6409--6435 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6399 TGTGGTAATT
6409 ATATTTTGG
1 ATATTTTGG
6418 ATATTTTGG
1 ATATTTTGG
6427 ATATTTTGG
1 ATATTTTGG
6436 TTAATGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (9 bp):
ATATTTTGG
Found at i:7865 original size:27 final size:26
Alignment explanation
Indices: 7817--7869 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
7807 AAAAAATGTT
*
7817 AAATTGTTTAAATTTAATTTTATAAAA
1 AAATTATTTAAATTTAATTTTA-AAAA
7844 AAATTATTTAAATATTAA-TTTAAAAA
1 AAATTATTTAAAT-TTAATTTTAAAAA
7870 TAACATAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATTATTTAAATTTAATTTTAAAAA
Found at i:9378 original size:49 final size:49
Alignment explanation
Indices: 9306--9403 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
9296 TATTATTATT
9306 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
1 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
* * *
9355 ATTAAAAAAAAGTTATTGGATTCAAAGGTTATGATTTGCATGAAAACCA
1 ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
9404 GAAAAATACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (49 bp):
ATTAAAAAAAAGTTAATGGATTCAAAGGCTATGATTTGCATCAAAACCA
Found at i:13795 original size:30 final size:30
Alignment explanation
Indices: 13754--13829 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
13744 GGGTACTTTC
* **
13754 ACTTCTAAATAGTTTAATGACTTAATTGAA
1 ACTTTTAAATAGTTTAATGACTTAATAAAA
*
13784 ACTTTTAAATAGTTCAATGACTTAATAAAA
1 ACTTTTAAATAGTTTAATGACTTAATAAAA
*
13814 ACTTTTGAATAGTTTA
1 ACTTTTAAATAGTTTA
13830 GTGATCATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (30 bp):
ACTTTTAAATAGTTTAATGACTTAATAAAA
Found at i:15714 original size:10 final size:11
Alignment explanation
Indices: 15694--15718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15684 TCGATCTTGT
15694 AAATAAAAAAA
1 AAATAAAAAAA
15705 AAATAAAAAAA
1 AAATAAAAAAA
15716 AAA
1 AAA
15719 CACCATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:32148 original size:21 final size:19
Alignment explanation
Indices: 32111--32156 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
32101 ACCCTCTATG
*
32111 TTATATATATTATTTTATA
1 TTATATATATTAATTTATA
32130 TTATATATTATGTAATTTATA
1 TTATATA-TAT-TAATTTATA
32151 TTATAT
1 TTATAT
32157 GAAACCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATATATTAATTTATA
Found at i:35872 original size:6 final size:6
Alignment explanation
Indices: 35861--35887 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
35851 AAGACTACAC
35861 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
35888 TAAAGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:38155 original size:17 final size:18
Alignment explanation
Indices: 38125--38158 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38115 TTTAAATAAA
*
38125 TTAATAATGGTAAAATTC
1 TTAATAATGATAAAATTC
38143 TTAA-AATGATAAAATT
1 TTAATAATGATAAAATT
38159 TTGATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (18 bp):
TTAATAATGATAAAATTC
Found at i:50219 original size:412 final size:411
Alignment explanation
Indices: 49456--50278 Score: 1601
Period size: 412 Copynumber: 2.0 Consensus size: 411
49446 AGTACAAAGG
49456 ATGACTCGAAGCTATAGCATTTAAGGTATGAACATCTCAATATTAAAGGCCTGAAATTGCTAGTA
1 ATGACTCGAAGCTATAGCATTTAAGGTATGAACATCTCAATATTAAAGGCCTGAAATTGCTAGTA
49521 ATAAAGGTATGAGTTTTGGACTACCAAAAATTAGCACTCTTGGTTTATGTGAGGGCTACATTTAT
66 ATAAAGGTATGAGTTTTGGACTACCAAAAATTAGCACTCTTGGTTTATGTGAGGGCTACATTTAT
49586 GGAAAGCAAACTAGGAAGCCATTTCCTGTTGAAAAGGCATGGAAGGCTACTGAATGTTTAGAATT
131 GGAAAGCAAACTAGGAAGCCATTTCCTGTTGAAAAGGCATGGAAGGCTACTGAATGTTTAGAATT
*
49651 AATTTATGCTAATATATGTGGTCCTATGCAAACTGAGTCTTTGGGTGTGAGTCGTTACTTCTTGT
196 AATTCATGCTAATATATGTGGTCCTATGCAAACTGAGTCTTTGGGTGTGAGTCGTTACTTCTTGT
49716 TGTTCACTGATGATTATAGCCGCATGAGTTGGGTGTATTTTTTGGAAAACAAGTCAGAAACTTAT
261 TGTTCACTGATGATTATAGCCGCATGAGTTGGGTGTATTTTTTGGAAAACAAGTCAGAAACTTAT
*
49781 GAAAAGTTTCAAAAATTCAAGGCTATGGTAGAGAACCAAAGCGGCTGTCGTATCAAAGTTCTTCG
326 GAAAAGTTTCAAAAATTCAAGGCTATGGTAGAGAACCAAAGCAGCTGTCGTATCAAAGTTCTTCG
49846 CACGGATCGAGGGGGAGAGTT
391 CACGGATCGAGGGGGAGAGTT
*
49867 ATGACTCGAAGCTATAGCATTTAAGGTATGGACATCTCAATATTAAAGGCCTGAAATTGCTAAGT
1 ATGACTCGAAGCTATAGCATTTAAGGTATGAACATCTCAATATTAAAGGCCTGAAATTGCT-AGT
49932 AATAAAGGTATGAGTTTTGGACTACCAAAAATTAGCACTCTTGGTTTATGTGAGGGCTACATTTA
65 AATAAAGGTATGAGTTTTGGACTACCAAAAATTAGCACTCTTGGTTTATGTGAGGGCTACATTTA
49997 TGGAAAGCAAACTAGGAAGCCATTTCCTGTTGAAAAGGCATGGAAGGCTACTGAATGTTTAGAAT
130 TGGAAAGCAAACTAGGAAGCCATTTCCTGTTGAAAAGGCATGGAAGGCTACTGAATGTTTAGAAT
*
50062 TAATTCATGCTGATATATGTGGTCCTATGCAAACTGAGTCTTTGGGTGTGAGTCGTTACTTCTTG
195 TAATTCATGCTAATATATGTGGTCCTATGCAAACTGAGTCTTTGGGTGTGAGTCGTTACTTCTTG
50127 TTGTTCACTGATGATTATAGCCGCATGAGTTGGGTGTATTTTTTGGAAAACAAGTCAGAAACTTA
260 TTGTTCACTGATGATTATAGCCGCATGAGTTGGGTGTATTTTTTGGAAAACAAGTCAGAAACTTA
50192 TGAAAAGTTTCAAAAATTCAAGGCTATGGTAGAGAACCAAAGCAGCTGTCGTATCAAAGTTCTTC
325 TGAAAAGTTTCAAAAATTCAAGGCTATGGTAGAGAACCAAAGCAGCTGTCGTATCAAAGTTCTTC
50257 GCACGGATCGAGGGGGAGAGTT
390 GCACGGATCGAGGGGGAGAGTT
50279 CATGTCCAAA
Statistics
Matches: 407, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
411 60 0.15
412 347 0.85
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (411 bp):
ATGACTCGAAGCTATAGCATTTAAGGTATGAACATCTCAATATTAAAGGCCTGAAATTGCTAGTA
ATAAAGGTATGAGTTTTGGACTACCAAAAATTAGCACTCTTGGTTTATGTGAGGGCTACATTTAT
GGAAAGCAAACTAGGAAGCCATTTCCTGTTGAAAAGGCATGGAAGGCTACTGAATGTTTAGAATT
AATTCATGCTAATATATGTGGTCCTATGCAAACTGAGTCTTTGGGTGTGAGTCGTTACTTCTTGT
TGTTCACTGATGATTATAGCCGCATGAGTTGGGTGTATTTTTTGGAAAACAAGTCAGAAACTTAT
GAAAAGTTTCAAAAATTCAAGGCTATGGTAGAGAACCAAAGCAGCTGTCGTATCAAAGTTCTTCG
CACGGATCGAGGGGGAGAGTT
Done.