Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014505.1 Kokia drynarioides strain JFW-HI SEQ_129544, 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: 70387
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 169 characters in sequence are not A, C, G, or T
Found at i:868 original size:24 final size:26
Alignment explanation
Indices: 841--888 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
831 AGAGAAATGT
841 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
865 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
889 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:979 original size:22 final size:23
Alignment explanation
Indices: 951--1006 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
941 ACGCTAGCGC
*
951 GCTTCTGTT-CAGCACTATGTGT
1 GCTTCTGTTCCAACACTATGTGT
*
973 GCTTCTGTTACCCAACACTGTGTGT
1 GCTTCTGTT--CCAACACTATGTGT
998 GCTTCTGTT
1 GCTTCTGTT
1007 ACCCAGCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
25 20 0.69
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.41
Consensus pattern (23 bp):
GCTTCTGTTCCAACACTATGTGT
Found at i:997 original size:25 final size:25
Alignment explanation
Indices: 963--1021 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
953 TTCTGTTCAG
963 CACTATGTGTGCTTCTGTTACCCAA
1 CACTATGTGTGCTTCTGTTACCCAA
* *
988 CACTGTGTGTGCTTCTGTTACCCAG
1 CACTATGTGTGCTTCTGTTACCCAA
1013 CACTTATGT
1 CAC-TATGT
1022 ACCTCTGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (25 bp):
CACTATGTGTGCTTCTGTTACCCAA
Found at i:5112 original size:125 final size:125
Alignment explanation
Indices: 4890--5140 Score: 466
Period size: 125 Copynumber: 2.0 Consensus size: 125
4880 AGAAACTCCC
*
4890 TGTAGCTTTTAGGATATATTTGGAGTATTACTCAAAACATACCTATTGCTTTAAGCCTAAGAGCA
1 TGTAGCTTTTAGGATATATTTGGAGTAATACTCAAAACATACCTATTGCTTTAAGCCTAAGAGCA
* *
4955 ATAACGATCCTTTGTAAAGGGAATGTAACCATTATCTTTTATTTTAATGAGAATGATGCA
66 ATAACGATCATTTGTAAAGGGAATGTAACCATTATCTTTTATTTTAATGAGAACGATGCA
*
5015 TGTAGCTTTTAGGATATATTTGGAGTAATACTCAAAACATACCTATTGCTTTAAGCCTGAGAGCA
1 TGTAGCTTTTAGGATATATTTGGAGTAATACTCAAAACATACCTATTGCTTTAAGCCTAAGAGCA
5080 ATAACGATCATTTGTAAAGGGAATGTAACCATTATCTTTTATTTTAATGAGAACGATGCA
66 ATAACGATCATTTGTAAAGGGAATGTAACCATTATCTTTTATTTTAATGAGAACGATGCA
5140 T
1 T
5141 TTTCTGTCTC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 122 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (125 bp):
TGTAGCTTTTAGGATATATTTGGAGTAATACTCAAAACATACCTATTGCTTTAAGCCTAAGAGCA
ATAACGATCATTTGTAAAGGGAATGTAACCATTATCTTTTATTTTAATGAGAACGATGCA
Found at i:7806 original size:45 final size:45
Alignment explanation
Indices: 7683--8257 Score: 561
Period size: 45 Copynumber: 12.9 Consensus size: 45
7673 CATCACCTTA
* * * * * **
7683 TCCAATATTTTACCCTTAAGTCAAGAAGGGTAGATTGAAGCTATTG
1 TCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCG
** * * * *
7729 TATAATATTTTACCCTCTAATCAAGAGGGGTAAATTGAAACCACCG
1 TCCAATCTTTTACCC-CTAATCAAGAGGGGCAGATTGAAGCCACCG
* * *
7775 TCCAATCTTTTACCCCTAATCAAAAGGGGTAAATTGAAGCCACCG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * *
7820 TCCAATCTTTTACCCATAATCAAGAGGAGCAGATTGAA-CTACCG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * *
7864 TCCAATCTTTTACCCATAGTCAAGAGAGGCAGATTGAAGCCACCG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * * * * * **
7909 TCCAATATTTTACCCCCAGTCAAAAGAGGTAGATTGAAGCCATTG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * * **
7954 TCCAATCTTGTACACC---T--AGAGGGGCAGATTGAAGTCACTA
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
** * * * **
7994 TCCAATCTTTTACCTTTAGTCAAGAGGGGTAGATTGAAGTCACTA
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * * * * *
8039 TCCAATCTTTTACCCCTAGTCAAGAGAGACAAATTGAAGGCACCA
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
*
8084 TCCAATCTTTTACCCCTAATTAAGAGGGGCAGATTGAAGCCACCG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* *
8129 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGTCACCG
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * *
8174 TCCAATCTTTTACCCTTAATCTAGAGGGGCAGATTGAAGCCACCA
1 TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
* * *
8219 TCCAATCTTATACTCCTAATTC-AGAGGGGTAGATTGAAG
1 TCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAG
8258 TCACGCACAC
Statistics
Matches: 449, Mismatches: 72, Indels: 17
0.83 0.13 0.03
Matches are distributed among these distances:
40 29 0.06
42 1 0.00
43 1 0.00
44 40 0.09
45 328 0.73
46 47 0.10
47 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
TCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCG
Found at i:19576 original size:24 final size:24
Alignment explanation
Indices: 19547--19601 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
19537 CATTGACATT
19547 TATTTTTGTAT-TT-ATTTATTTTA
1 TATTTTTGT-TGTTAATTTATTTTA
* *
19570 TCATTTTAGTTGTTAATTTTTTTTA
1 T-ATTTTTGTTGTTAATTTATTTTA
19595 TATTTTT
1 TATTTTT
19602 AGGATAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.08
24 14 0.54
25 10 0.38
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (24 bp):
TATTTTTGTTGTTAATTTATTTTA
Found at i:20558 original size:4 final size:4
Alignment explanation
Indices: 20549--20603 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
20539 GAAGAGAGAA
20549 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT
20597 GAAT GAA
1 GAAT GAA
20604 AGGAAAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (4 bp):
GAAT
Found at i:20803 original size:16 final size:16
Alignment explanation
Indices: 20784--20821 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
20774 GTAGGGTATA
20784 TTTTT-AAATTTTTATT
1 TTTTTGAAA-TTTTATT
20800 TTTTTGAAATTTTATT
1 TTTTTGAAATTTTATT
20816 TATTTT
1 T-TTTT
20822 TTAACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTGAAATTTTATT
Found at i:21215 original size:24 final size:24
Alignment explanation
Indices: 21181--21228 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21171 TGATGTGGAA
*
21181 CCAGTATAAAATGAAGATCCAACT
1 CCAGTAGAAAATGAAGATCCAACT
21205 CCAGTAGAAAATGAAGATCCAACT
1 CCAGTAGAAAATGAAGATCCAACT
21229 TCTTGTATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.19
Consensus pattern (24 bp):
CCAGTAGAAAATGAAGATCCAACT
Found at i:25521 original size:6 final size:6
Alignment explanation
Indices: 25512--25553 Score: 56
Period size: 5 Copynumber: 7.7 Consensus size: 6
25502 TCTATTCAAT
25512 TTTTTC TTTTTC TTTTT- TTTTTC -TTTTC TTTTT- TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
25554 ACATTAATGN
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 19 0.56
6 15 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (6 bp):
TTTTTC
Found at i:25522 original size:1 final size:1
Alignment explanation
Indices: 25511--25553 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
25501 TTCTATTCAA
* * * *
25511 TTTTTTCTTTTTCTTTTTTTTTTCTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25554 ACATTAATGN
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:25531 original size:17 final size:17
Alignment explanation
Indices: 25511--25553 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
25501 TTCTATTCAA
25511 TTTTTTCTTTTTCTTTT
1 TTTTTTCTTTTTCTTTT
25528 TTTTTTC-TTTTCTTTT
1 TTTTTTCTTTTTCTTTT
25544 TTTTTT-TTTT
1 TTTTTTCTTTT
25554 ACATTAATGN
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTT
Found at i:25541 original size:22 final size:21
Alignment explanation
Indices: 25513--25553 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
25503 CTATTCAATT
25513 TTTTCTTTTTCTTTTTTTTTTC
1 TTTTCTTTTT-TTTTTTTTTTC
25535 TTTTCTTTTTTTTTTTTTT
1 TTTTCTTTTTTTTTTTTTT
25554 ACATTAATGN
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (21 bp):
TTTTCTTTTTTTTTTTTTTTC
Found at i:27081 original size:44 final size:45
Alignment explanation
Indices: 27017--27104 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
27007 AATCCTTGAA
* *
27017 TTTTCTTAACCTTTCCTA-TTTAGACTACACATTCTAATTCTTAAT
1 TTTTCTTAACCTTTCCTATTTTA-ACCACACATTCTAACTCTTAAT
* * *
27062 TTTTCTTAATC-TTCTTATTTTAACCACATATTCTAACTCTTAA
1 TTTTCTTAACCTTTCCTATTTTAACCACACATTCTAACTCTTAA
27105 CTCGACACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 23 0.62
45 14 0.38
ACGTcount: A:0.27, C:0.22, G:0.01, T:0.50
Consensus pattern (45 bp):
TTTTCTTAACCTTTCCTATTTTAACCACACATTCTAACTCTTAAT
Found at i:29264 original size:12 final size:11
Alignment explanation
Indices: 29217--29260 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
29207 TAATTTACTC
29217 AATTAAATAAAAA
1 AATTAAAT--AAA
29230 AATTAAATAACA
1 AATTAAATAA-A
*
29242 AATCAAATAAA
1 AATTAAATAAA
29253 AATTAAAT
1 AATTAAAT
29261 TAAACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.36
12 10 0.36
13 8 0.29
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AATTAAATAAA
Found at i:29266 original size:25 final size:23
Alignment explanation
Indices: 29227--29276 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
29217 AATTAAATAA
29227 AAAAATTAAATAAC-AAATCAAAT
1 AAAAATTAAATAACAAAAT-AAAT
29250 AAAAATTAAATTAAACAAAATAAAT
1 AAAAATTAAA-T-AACAAAATAAAT
29275 AA
1 AA
29277 GTTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 9 0.38
26 4 0.17
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAATTAAATAACAAAATAAAT
Found at i:29315 original size:24 final size:26
Alignment explanation
Indices: 29288--29337 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
29278 TTAAAATAAT
*
29288 AATTACTAA-AAAA-ATTTAAATTTA
1 AATTACCAATAAAATATTTAAATTTA
*
29312 AATTACCAATAAAATATTTACATTTA
1 AATTACCAATAAAATATTTAAATTTA
29338 CCTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 4 0.18
26 10 0.45
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
AATTACCAATAAAATATTTAAATTTA
Found at i:36181 original size:2 final size:2
Alignment explanation
Indices: 36168--36203 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
36158 ACATGACAAT
*
36168 GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
36204 AGGTAGGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:45595 original size:17 final size:17
Alignment explanation
Indices: 45573--45611 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
45563 AGGTGGAGAA
* *
45573 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
45590 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
45607 CTTGT
1 CTTGT
45612 CAAAGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:45664 original size:41 final size:41
Alignment explanation
Indices: 45601--45697 Score: 167
Period size: 41 Copynumber: 2.4 Consensus size: 41
45591 TTGTTCGTAG
* *
45601 AGAATTCTTGTCAAAGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAAGTAGAGATTGTTAGAATTGGGTGACT
*
45642 AGAATTCTTGTTAAGGTAGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAAGTAGAGATTGTTAGAATTGGGTGACT
45683 AGAATTCTTGTTAAA
1 AGAATTCTTGTTAAA
45698 ATAAAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAAGTAGAGATTGTTAGAATTGGGTGACT
Done.