Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004244.1 Kokia drynarioides strain JFW-HI SEQ_117516, 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: 67480
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:6922 original size:18 final size:19
Alignment explanation
Indices: 6879--6916 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6869 ATGAATTTAA
6879 AAAAATTAAAATAATATAT
1 AAAAATTAAAATAATATAT
*
6898 AAAAATTGAAAT-ATATAT
1 AAAAATTAAAATAATATAT
6916 A
1 A
6917 TTAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATTAAAATAATATAT
Found at i:9435 original size:6 final size:6
Alignment explanation
Indices: 9426--9451 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9416 AAAAAACGAT
9426 GAAGAG GAAGAG GAAGAG GAAGAG GA
1 GAAGAG GAAGAG GAAGAG GAAGAG GA
9452 GGATGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:12503 original size:16 final size:16
Alignment explanation
Indices: 12458--12504 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
12448 TTACCTGAAT
12458 AATAATTAATTACGAA
1 AATAATTAATTACGAA
*
12474 AA-AA-T-A-T-GGAA
1 AATAATTAATTACGAA
12485 AATAATTAATTACGAA
1 AATAATTAATTACGAA
12501 AATA
1 AATA
12505 GGAATTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 10
0.67 0.06 0.28
Matches are distributed among these distances:
11 5 0.21
12 3 0.12
13 2 0.08
14 2 0.08
15 3 0.12
16 9 0.38
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (16 bp):
AATAATTAATTACGAA
Found at i:14270 original size:2 final size:2
Alignment explanation
Indices: 14263--14294 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14253 TCACTCAAAA
14263 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
14295 TTGTGTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:19378 original size:2 final size:2
Alignment explanation
Indices: 19371--19396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19361 TCACTCAAAA
19371 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
19397 TTTGTGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20322 original size:12 final size:10
Alignment explanation
Indices: 20293--20326 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
20283 ACAACAAATT
20293 AAATTTTAAA
1 AAATTTTAAA
20303 AAATTTTAAA
1 AAATTTTAAA
20313 AACTATTTTAAA
1 AA--ATTTTAAA
20325 AA
1 AA
20327 TTAAAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:26170 original size:17 final size:18
Alignment explanation
Indices: 26145--26180 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
26135 AAATATTTAG
*
26145 TATTTAAAAA-AAAATAT
1 TATTAAAAAATAAAATAT
26162 TATTAAAAAATAAAATAT
1 TATTAAAAAATAAAATAT
26180 T
1 T
26181 TATTTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATTAAAAAATAAAATAT
Found at i:26501 original size:19 final size:20
Alignment explanation
Indices: 26459--26507 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
26449 TAATTATTTG
*
26459 TAAAATATAATTTGAATATA
1 TAAAATATAATTTAAATATA
* *
26479 TAAATTATATTTTAAATAT-
1 TAAAATATAATTTAAATATA
26498 TAAAATATAA
1 TAAAATATAA
26508 CCATTATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAATATAATTTAAATATA
Found at i:43653 original size:6 final size:6
Alignment explanation
Indices: 43642--43670 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43632 TAATTCTCAC
43642 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
43671 CACAACGTTA
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:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:48467 original size:9 final size:9
Alignment explanation
Indices: 48453--48484 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
48443 TAAAATTGTA
*
48453 TATTATGTT
1 TATTATTTT
48462 TATTATTTT
1 TATTATTTT
48471 TATTATTTT
1 TATTATTTT
48480 TATTA
1 TATTA
48485 GTAATCGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (9 bp):
TATTATTTT
Found at i:55208 original size:20 final size:20
Alignment explanation
Indices: 55183--55224 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
55173 ACAAAGACTG
55183 AGGGTTTTTGGTTGATTATT
1 AGGGTTTTTGGTTGATTATT
55203 AGGGTTTTTGGTTGATTATT
1 AGGGTTTTTGGTTGATTATT
55223 AG
1 AG
55225 AAACTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (20 bp):
AGGGTTTTTGGTTGATTATT
Found at i:59978 original size:79 final size:79
Alignment explanation
Indices: 59651--59970 Score: 354
Period size: 79 Copynumber: 4.1 Consensus size: 79
59641 CTATTATCAT
* * * * * *
59651 TCACACATCACTAATG-AATTAACAAATTTTATTACTT-A-ATT-T-TTTAGCTGTACTAAAAGA
1 TCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTCTCTTTA-TTGTAATAAAA-A
*
59711 CATCTTTAATAATCGC
64 TATCTTTAATAATCGC
*
59727 TCA-ACGTCATTAACGAAATTAACGAATTTTATTAGTTAATATT-T-TTTATTGTAATAAAAGAT
1 TCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAA-AT
*
59789 ATCTTTCATAATCGC
65 ATCTTTAATAATCGC
* *
59804 TCACACGTCACTAACGAAATTAACGAGTTTTAGTAGTTAATATTCTCTTTATTGTAATAAAAA-A
1 TCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAATA
* *
59868 CTCTTTGATGAGT-GC
66 -TCTTTAAT-AATCGC
* * *
59883 TCACACGTCACTAATGAAATTAACGAATTTTATTAGTTAATATTCTCCTTATCGTAATGAAAAAT
1 TCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAAT-AAAAAT
* *
59948 ATATTTAATGATCGC
65 ATCTTTAATAATCGC
59963 TCACACGT
1 TCACACGT
59971 GTTAATGATT
Statistics
Matches: 210, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
75 9 0.04
76 22 0.10
77 29 0.14
78 46 0.22
79 65 0.31
80 38 0.18
81 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (79 bp):
TCACACGTCACTAACGAAATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAATA
TCTTTAATAATCGC
Found at i:60501 original size:23 final size:25
Alignment explanation
Indices: 60475--60522 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
60465 CTACCTCAAC
60475 GTTA-CCT-TTTTTGTCTTTTACTA
1 GTTATCCTCTTTTTGTCTTTTACTA
*
60498 GTTATCTTCTTTTTGTCTTTTACTA
1 GTTATCCTCTTTTTGTCTTTTACTA
60523 ATTTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 2 0.09
25 16 0.73
ACGTcount: A:0.12, C:0.17, G:0.08, T:0.62
Consensus pattern (25 bp):
GTTATCCTCTTTTTGTCTTTTACTA
Found at i:61136 original size:28 final size:31
Alignment explanation
Indices: 61080--61136 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 31
61070 TTATGATTGA
* *
61080 ATCATAATTAAAATTTCATATGTATAATTTC
1 ATCATAATTAAAATTTCATATATACAATTTC
61111 ATCA-AATT-AAATTT-ATATATACAATT
1 ATCATAATTAAAATTTCATATATACAATT
61137 ACATATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 6 0.25
30 4 0.17
31 4 0.17
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (31 bp):
ATCATAATTAAAATTTCATATATACAATTTC
Found at i:62116 original size:29 final size:30
Alignment explanation
Indices: 62060--62118 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
62050 TAATTGAATC
* *
62060 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAAGTTTATGTATAAAACTGCACA
* *
62090 AAATC-AAAGTTTATGTGTACAACTGCACA
1 AAATCAAAAGTTTATGTATAAAACTGCACA
62119 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTTATGTATAAAACTGCACA
Found at i:63007 original size:45 final size:45
Alignment explanation
Indices: 62957--63094 Score: 195
Period size: 45 Copynumber: 3.1 Consensus size: 45
62947 TCAATTGGTT
* * * *
62957 TCATGTTCTTCAGGATCTTGTTTAAGCCCCTTGTTGTTATCGTCA
1 TCATGTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCA
*
63002 TCATGTTCTTCGGGATCTTGTTTAACCCCCTCGGTGTTATCATCA
1 TCATGTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCA
* * * *
63047 TCACGTTCTTCAGGAACTTGTTTGACCCCCTCGGTGTTCTCATCA
1 TCATGTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCA
63092 TCA
1 TCA
63095 ACTTTCCTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (45 bp):
TCATGTTCTTCAGGATCTTGTTTAACCCCCTCGGTGTTATCATCA
Found at i:64507 original size:81 final size:81
Alignment explanation
Indices: 64414--64641 Score: 250
Period size: 80 Copynumber: 2.8 Consensus size: 81
64404 CTCACACGTC
* *
64414 ATTAACGAATTTTATTAGTTAATGTTCTCTTTATTTTAATAAAAAAATTTCTTCGATGATCTCTT
1 ATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAAAATTTCTT-GATGATCTCTT
*
64479 ACAT-GTCACTAACGAT
65 ACATAGTCACTAACGAA
* * * * *
64495 ATTAACGAATTTTAGTAGTTAATATTCTCTTTATTGTAAT-AAAAAATTTCTTTAATTA-GTGTT
1 ATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAAAATTTC-TTGATGATCTCTT
* *
64558 -CATACGTTACTAATGAA
65 ACATA-GTCACTAACGAA
* * * * *
64575 ACTAACGAATTTTATTAGTTAATATTTTCTTTAGTGTAATAAAAAACATAT-TTGATGATCGCTT
1 ATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAAA-ATTTCTTGATGATCTCTT
64639 ACA
65 ACA
64642 CATGTTAACG
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
78 3 0.03
79 3 0.03
80 63 0.52
81 46 0.38
82 5 0.04
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.44
Consensus pattern (81 bp):
ATTAACGAATTTTATTAGTTAATATTCTCTTTATTGTAATAAAAAAATTTCTTGATGATCTCTTA
CATAGTCACTAACGAA
Found at i:64817 original size:21 final size:21
Alignment explanation
Indices: 64793--64835 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
64783 ATTGTTAAAG
*
64793 AAATATTTTA-TTTTATTTATA
1 AAATA-TTTACTTTTACTTATA
64814 AAATATTTACTTTTACTTATA
1 AAATATTTACTTTTACTTATA
64835 A
1 A
64836 TCTTTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTTACTTTTACTTATA
Found at i:65413 original size:18 final size:19
Alignment explanation
Indices: 65370--65410 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
65360 AAATTCATGC
* *
65370 ATTTGATGTAAAATTAAAT
1 ATTTAATGTAAAATAAAAT
65389 ATTTAATGTAAAATAAAAT
1 ATTTAATGTAAAATAAAAT
65408 ATT
1 ATT
65411 AATATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
ATTTAATGTAAAATAAAAT
Found at i:65824 original size:2 final size:2
Alignment explanation
Indices: 65817--65843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65807 AATTAAAAAT
65817 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
65844 CTGTGACTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.