Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014313.1 Kokia drynarioides strain JFW-HI SEQ_129350, 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: 13466
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1055 original size:24 final size:24
Alignment explanation
Indices: 1006--1056 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
996 GAAGATTTAG
* *
1006 TAGCATAATATATTTAGTATTTAT
1 TAGCATAATATATTTAGCATTGAT
*
1030 TAGCATAATATATTTTGCATTGAT
1 TAGCATAATATATTTAGCATTGAT
1054 TAG
1 TAG
1057 AATTAGGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (24 bp):
TAGCATAATATATTTAGCATTGAT
Found at i:3471 original size:29 final size:29
Alignment explanation
Indices: 3429--3549 Score: 154
Period size: 29 Copynumber: 4.1 Consensus size: 29
3419 CTCAAGAGGT
* *
3429 CCCTAAACCTTTCCAAAATTACATTTTTA
1 CCCTAAACTTTTCCAAAATTACATTTTGA
3458 CCCTAAACTTTTCCAAAATTACATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTGA
* *
3487 CCCCCAAACTTTTCC-AAATTCACATTTTAA
1 -CCCTAAACTTTTCCAAAATT-ACATTTTGA
* * *
3517 CCCAAAAATTTTCCAAAATCACATTTTGA
1 CCCTAAACTTTTCCAAAATTACATTTTGA
3546 CCCT
1 CCCT
3550 CGAGCTTTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
29 55 0.69
30 25 0.31
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTGA
Found at i:3498 original size:30 final size:30
Alignment explanation
Indices: 3433--3566 Score: 139
Period size: 29 Copynumber: 4.5 Consensus size: 30
3423 AGAGGTCCCT
* * *
3433 AAACCTTTCCAAAATTACATTTTTA-CCCT
1 AAACTTTTCCAAAATTACATTTTGACCCCC
3462 AAACTTTTCCAAAATTACATTTTGACCCCC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* *
3492 AAACTTTTCC-AAATTCACATTTT-AACCCA
1 AAACTTTTCCAAAATT-ACATTTTGACCCCC
* * *
3521 AAAATTTTCCAAAATCACATTTTGACCCTC
1 AAACTTTTCCAAAATTACATTTTGACCCCC
* * *
3551 GAGCTTTTCTAAAATT
1 AAACTTTTCCAAAATT
3567 TCATCCCGAG
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
29 48 0.56
30 38 0.44
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTGACCCCC
Found at i:3558 original size:59 final size:59
Alignment explanation
Indices: 3433--3566 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 59
3423 AGAGGTCCCT
* * * * *
3433 AAACCTTTCCAAAATTACATTTTTACCCTAAACTTTTCCAAAATTACATTTTGACCCCC
1 AAACTTTTCCAAAATTACATTTTAACCCAAAAATTTTCCAAAATCACATTTTGACCCCC
*
3492 AAACTTTTCC-AAATTCACATTTTAACCCAAAAATTTTCCAAAATCACATTTTGACCCTC
1 AAACTTTTCCAAAATT-ACATTTTAACCCAAAAATTTTCCAAAATCACATTTTGACCCCC
* * *
3551 GAGCTTTTCTAAAATT
1 AAACTTTTCCAAAATT
3567 TCATCCCGAG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 5 0.08
59 54 0.84
60 5 0.08
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
AAACTTTTCCAAAATTACATTTTAACCCAAAAATTTTCCAAAATCACATTTTGACCCCC
Found at i:7721 original size:3 final size:3
Alignment explanation
Indices: 7713--7765 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
7703 AAATAGGAAA
*
7713 AAG AAG AAG AAG AAG AAC AAG AAG AAG AAG AAG AAG AA- AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
7759 AA- AAG AA
1 AAG AAG AA
7766 AGAAAAGGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:7767 original size:9 final size:8
Alignment explanation
Indices: 7711--7772 Score: 58
Period size: 9 Copynumber: 7.6 Consensus size: 8
7701 TAAAATAGGA
7711 AAAAGAAG
1 AAAAGAAG
7719 AAGAAGAAG
1 AA-AAGAAG
7728 AACAAGAAG
1 AA-AAGAAG
7737 AAGAAGAAG
1 AA-AAGAAG
7746 AAGAA-AAG
1 AA-AAGAAG
7754 AAAAGAA-
1 AAAAGAAG
*
7761 AAGA-AAG
1 AAAAGAAG
7768 AAAAG
1 AAAAG
7773 GTCAAGATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 2 0.04
7 8 0.17
8 9 0.20
9 27 0.59
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:7769 original size:4 final size:5
Alignment explanation
Indices: 7711--7772 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 5
7701 TAAAATAGGA
7711 AAAAG AAGAAG AAGAAG AACAAG --AAG AAGAAG AAGAAG AAAAG AAAAG
1 AAAAG AA-AAG AA-AAG AA-AAG AAAAG AA-AAG AA-AAG AAAAG AAAAG
7759 AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG
7773 GTCAAGATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
3 3 0.06
4 4 0.08
5 19 0.37
6 25 0.49
ACGTcount: A:0.73, C:0.02, G:0.26, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:7846 original size:62 final size:63
Alignment explanation
Indices: 7751--7871 Score: 194
Period size: 62 Copynumber: 1.9 Consensus size: 63
7741 AGAAGAAGAA
7751 AAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACCCGCAAAGGGCATCTTTTAAAAAAAAAAG
1 AAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACCCGCAAAGGGCATC--TTAAAAAAAAAAG
*
7816 AAGAAAAG-AAA-AAGGAAAA-GTCAAGATGAAAACCCGCAAAGGGCATCTTAAAAAAA
1 AAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACCCGCAAAGGGCATCTTAAAAAAA
7872 TCTCCTTCAC
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
60 9 0.16
62 28 0.51
63 7 0.13
64 3 0.05
65 8 0.15
ACGTcount: A:0.59, C:0.12, G:0.20, T:0.10
Consensus pattern (63 bp):
AAGAAAAGAAAAGAAAGAAAAGGTCAAGATGAAAACCCGCAAAGGGCATCTTAAAAAAAAAAG
Found at i:9849 original size:49 final size:48
Alignment explanation
Indices: 9787--10248 Score: 228
Period size: 49 Copynumber: 9.5 Consensus size: 48
9777 GGATATATAG
* * *
9787 AGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCACAGAAACATGA
* ** * *
9836 AGGGAAAGATTTAAGCCGCAACGGTAAATCC-AGTACCACA-AGGATAT-A
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTA-TACCACAGA-AACATGA
* * * * *
9884 GAGGGAAGGGTTTAAGTCGCAACGGCGAACCCTGTACCTCAGAAGCATGA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTATACCACAGAAACATGA
* * * * * *
9934 CGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTA-TACCACAGAA-ACATGA
* * * * * * *
9983 AGGGAAAGGTTTAAGTCGCAACGGCAAATCTTGTACCCCCGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTATACCACAGAAACATGA
* * * * * *
10032 AGGGCAAGATTTAAGCCACAACGGCGAATCC-AGTACCACA-AGGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTA-TACCACAGA-AACATGA
** * * * * *
10081 AGAAAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCACAGAAACATGA
* * * * *
10130 AGGGAAAGATTTAAGCCACAACGGCAAATCC-AGTACCACA-AGGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTA-TACCACAGA-AACATGA
* * * * *
10179 AGAGAAAGACTTAAGT---AACGACAAACCTTATACCTC-GAAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCACAGAAA-CATGA
*
10225 AGGGAAAGATTTAAGTTGCAACGG
1 AGGGAAAGATTTAAGTCGCAACGG
10249 TGAATCCAGT
Statistics
Matches: 297, Mismatches: 90, Indels: 52
0.68 0.21 0.12
Matches are distributed among these distances:
45 3 0.01
46 32 0.11
47 1 0.00
48 12 0.04
49 238 0.80
50 11 0.04
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTATACCACAGAAACATGA
Found at i:9924 original size:98 final size:98
Alignment explanation
Indices: 9736--10284 Score: 651
Period size: 98 Copynumber: 5.6 Consensus size: 98
9726 AAAGATATGG
* * *
9736 AGGGAAAGATTTAAGCCGCAATGGCAGATCCAGTACCAAAAGGATATATAGAGGGAAAGGTTTAA
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGG--ATATAGAGGGAAAGGTTTAA
*
9801 GTCGCAACGACGAACCTTATACCTCAGAAACATGA
64 GTCGCAACGACGAACCTTGTACCTCAGAAACATGA
* *
9836 AGGGAAAGATTTAAGCCGCAACGGTAAATCCAGTACCACAAGGATATAGAGGGAAGGGTTTAAGT
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGGATATAGAGGGAAAGGTTTAAGT
* * *
9901 CGCAACGGCGAACCCTGTACCTCAGAAGCATGA
66 CGCAACGACGAACCTTGTACCTCAGAAACATGA
* * * * *
9934 CGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAA-GATATGGAGGGAAAGGTTTAAG
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCAC-AAGGATATAGAGGGAAAGGTTTAAG
* * * * * *
9998 TCGCAACGGCAAATCTTGTACCCCCGAAGCATGA
65 TCGCAACGACGAACCTTGTACCTCAGAAACATGA
* * * * **
10032 AGGGCAAGATTTAAGCCACAACGGCGAATCCAGTACCACAAGGATATGGAGAAAAAGGTTTAAGT
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGGATATAGAGGGAAAGGTTTAAGT
*
10097 CGCAACGACGAACCTTGTACCTCAGAAGCATGA
66 CGCAACGACGAACCTTGTACCTCAGAAACATGA
* * **
10130 AGGGAAAGATTTAAGCCACAACGGCAAATCCAGTACCACAAGGATAT-GAAGAGAAAGACTTAAG
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGGATATAG-AGGGAAAGGTTTAAG
* *
10194 T---AACGACAAACCTTATACCTC-GAAAGCATGA
65 TCGCAACGACGAACCTTGTACCTCAGAAA-CATGA
** ** * * *
10225 AGGGAAAGATTTAAGTTGCAACGGTGAATCCAGTAGCATAAAGATATAGAGGGAAAGGTT
1 AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGGATATAGAGGGAAAGGTT
10285 ACGACCGCAA
Statistics
Matches: 392, Mismatches: 52, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
94 3 0.01
95 70 0.18
96 1 0.00
97 3 0.01
98 274 0.70
99 2 0.01
100 39 0.10
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (98 bp):
AGGGAAAGATTTAAGCCGCAACGGCAAATCCAGTACCACAAGGATATAGAGGGAAAGGTTTAAGT
CGCAACGACGAACCTTGTACCTCAGAAACATGA
Found at i:11209 original size:11 final size:12
Alignment explanation
Indices: 11187--11220 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
11177 TTTACCCACG
11187 AAAAATACAAAA
1 AAAAATACAAAA
11199 AAAAATA-AAAA
1 AAAAATACAAAA
*
11210 ATAAATACAAA
1 AAAAATACAAA
11221 TAATGAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAATACAAAA
Found at i:12298 original size:30 final size:29
Alignment explanation
Indices: 12253--12331 Score: 122
Period size: 30 Copynumber: 2.7 Consensus size: 29
12243 CTTAAGAGGT
*
12253 CCCTAAACCTTTCTAAAATTACATTTTGA
1 CCCTAAACTTTTCTAAAATTACATTTTGA
12282 CCCTCAAACTTTTCTAAAATTACATTTTGA
1 CCCT-AAACTTTTCTAAAATTACATTTTGA
*
12312 CCCTTAAACTTTTCCAAAAT
1 CCC-TAAACTTTTCTAAAAT
12332 ATTCTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 4 0.09
30 41 0.89
31 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCTAAAATTACATTTTGA
Found at i:12337 original size:40 final size:40
Alignment explanation
Indices: 12293--12372 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
12283 CCTCAAACTT
* *
12293 TTCTAAAATTACATTTTGACCCTTAAACTTTTCCAAAATA
1 TTCTAAAATTACATTTTAACCCTTAAAATTTTCCAAAATA
*
12333 TTCTAATATTACATTTTAACCCTTAAAATTTTCCAAAATA
1 TTCTAAAATTACATTTTAACCCTTAAAATTTTCCAAAATA
12373 ACATTTTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (40 bp):
TTCTAAAATTACATTTTAACCCTTAAAATTTTCCAAAATA
Found at i:12347 original size:70 final size:70
Alignment explanation
Indices: 12263--12402 Score: 199
Period size: 70 Copynumber: 2.0 Consensus size: 70
12253 CCCTAAACCT
* * * * * * *
12263 TTCTAAAATTACATTTTGACCCTCAAACTTTTCTAAAATTACATTTTGACCCTTAAACTTTTCCA
1 TTCTAAAATTACATTTTAACCCTCAAAATTTTCCAAAATAACATTTTAACCCCTAAAATTTTCCA
12328 AAATA
66 AAATA
* *
12333 TTCTAATATTACATTTTAACCCTTAAAATTTTCCAAAATAACATTTTAACCCCTAAAATTTTCCA
1 TTCTAAAATTACATTTTAACCCTCAAAATTTTCCAAAATAACATTTTAACCCCTAAAATTTTCCA
12398 AAATA
66 AAATA
12403 ACATTTTGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 61 1.00
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.39
Consensus pattern (70 bp):
TTCTAAAATTACATTTTAACCCTCAAAATTTTCCAAAATAACATTTTAACCCCTAAAATTTTCCA
AAATA
Found at i:12377 original size:30 final size:30
Alignment explanation
Indices: 12343--12415 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
12333 TTCTAATATT
12343 ACATTTTAACCCTTAAAATTTTCCAAAATA
1 ACATTTTAACCCTTAAAATTTTCCAAAATA
*
12373 ACATTTTAACCCCTAAAATTTTCCAAAATA
1 ACATTTTAACCCTTAAAATTTTCCAAAATA
*
12403 ACATTTTGACCCT
1 ACATTTTAACCCT
12416 CGAGATTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.36
Consensus pattern (30 bp):
ACATTTTAACCCTTAAAATTTTCCAAAATA
Found at i:12431 original size:30 final size:30
Alignment explanation
Indices: 12343--12431 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
12333 TTCTAATATT
*
12343 ACATTTTAACCCTTAAAATTTTCCAAAATA
1 ACATTTTAACCCTCAAAATTTTCCAAAATA
12373 ACATTTTAACCC-CTAAAATTTTCCAAAATA
1 ACATTTTAACCCTC-AAAATTTTCCAAAATA
* * * *
12403 ACATTTTGACCCTCGAGATTTTCTAAAAT
1 ACATTTTAACCCTCAAAATTTTCCAAAAT
12432 TTCATCTCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 51 0.98
31 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (30 bp):
ACATTTTAACCCTCAAAATTTTCCAAAATA
Found at i:13170 original size:21 final size:20
Alignment explanation
Indices: 13127--13171 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
13117 ATTTCGAAAG
* *
13127 TAAAATTTTGCAGGGTTCCT
1 TAAAATTCTGCAGGCTTCCT
*
13147 TAAAATTCTGCAGTCTTACCT
1 TAAAATTCTGCAGGCTT-CCT
13168 TAAA
1 TAAA
13172 TTTTACGGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
TAAAATTCTGCAGGCTTCCT
Done.