Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003616.1 Kokia drynarioides strain JFW-HI SEQ_116506, 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: 43613
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:2478 original size:80 final size:80
Alignment explanation
Indices: 2345--2508 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 80
2335 AAGAGTGCTC
* * ** *
2345 CCTCCTCACCCATCCCCGCCAAGAATTTTTATCCTTATCATCTCCCTGCAACCCGCACCAGG-TA
1 CCTCCGCACCCATCCCCGCCAAGAATTTTTATCCTTATCATCGCCCCACAACCCGCAAC-GGCTA
2409 CAAAACCCAAAACCAT
65 CAAAACCCAAAACCAT
*
2425 CCTCCGCACTCATCCCCGCCAAGAATTTTTATCCTTATCATCGCCCCACAACCCGCAACGGCTAC
1 CCTCCGCACCCATCCCCGCCAAGAATTTTTATCCTTATCATCGCCCCACAACCCGCAACGGCTAC
*
2490 AAAATCCAAAACCAT
66 AAAACCCAAAACCAT
2505 CCTC
1 CCTC
2509 ACCCCACAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
79 2 0.03
80 74 0.97
ACGTcount: A:0.29, C:0.43, G:0.08, T:0.21
Consensus pattern (80 bp):
CCTCCGCACCCATCCCCGCCAAGAATTTTTATCCTTATCATCGCCCCACAACCCGCAACGGCTAC
AAAACCCAAAACCAT
Found at i:4319 original size:16 final size:16
Alignment explanation
Indices: 4268--4320 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
4258 TAGGTAACCC
4268 AATAAGATAATTACATGTA
1 AATAA-ATAA-TACAT-TA
* *
4287 AA-AAATAATAAAATA
1 AATAAATAATACATTA
4302 AATAAATAATACATTA
1 AATAAATAATACATTA
4318 AAT
1 AAT
4321 TAAAAAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
15 4 0.14
16 17 0.59
17 4 0.14
18 2 0.07
19 2 0.07
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (16 bp):
AATAAATAATACATTA
Found at i:7105 original size:101 final size:101
Alignment explanation
Indices: 6930--7243 Score: 477
Period size: 101 Copynumber: 3.1 Consensus size: 101
6920 ACACATCGGT
* * *
6930 TTGGCACCCTGTGTCTCATTGGATAAATCCGAAGTAATAAATCGCG-CTCTACACTAAAATAAAG
1 TTGGCACCCTGTGCCTCATTGGATAAATCCGAAGTAATAAATCGCGCCT-TGCGCTAAAATAAAG
* *
6994 TTCAAACCCAGTGTCTCATCGGATAAACCGAAGTAAA
65 TTGACACCCAGTGTCTCATCGGATAAACCGAAGTAAA
* * *
7031 TTGGCACCCTGTGCCTCATCGGATAAATCTGAAGTAATAAATCGTGCCTTGCGCTAAAATAAAGT
1 TTGGCACCCTGTGCCTCATTGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGT
7096 TGACACCCAGTGTCTCATCGGATAAACCGAAGTAAA
66 TGACACCCAGTGTCTCATCGGATAAACCGAAGTAAA
* * *
7132 TTGGCACCCTATGCGTCATTGGATAAATCCAAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGT
1 TTGGCACCCTGTGCCTCATTGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGT
** * *
7197 TGACACATAGTGTCTCATTGGTTAAACCGAAGTAAA
66 TGACACCCAGTGTCTCATCGGATAAACCGAAGTAAA
7233 TTGGCACCCTG
1 TTGGCACCCTG
7244 AACTCTTTCT
Statistics
Matches: 193, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 191 0.99
102 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (101 bp):
TTGGCACCCTGTGCCTCATTGGATAAATCCGAAGTAATAAATCGCGCCTTGCGCTAAAATAAAGT
TGACACCCAGTGTCTCATCGGATAAACCGAAGTAAA
Found at i:11320 original size:37 final size:36
Alignment explanation
Indices: 11234--11414 Score: 215
Period size: 37 Copynumber: 5.0 Consensus size: 36
11224 CTTACACAAA
* * *
11234 TTCAAGCTATATGCCTAGTAGGCTGTGTGACGGTATTT
1 TTCAAGCTATGTGCCTAGTAGGCT-TGTGCCGGT-GTT
11272 TTCAAGCTATGTGCCTAGTAGGCTGTGTGCCGGTGTT
1 TTCAAGCTATGTGCCTAGTAGGCT-TGTGCCGGTGTT
* * *
11309 TTCAGGTTATGTGCCTAGTAGGCTTCGTGCCGATGTT
1 TTCAAGCTATGTGCCTAGTAGGCTT-GTGCCGGTGTT
11346 TTCAAGCTATGTGCCTAGTAGGC-TGT--CGGTGTT
1 TTCAAGCTATGTGCCTAGTAGGCTTGTGCCGGTGTT
* * *
11379 TTCAGGCTATATCCCTAGTAGGCTTCGTGCCGGTGT
1 TTCAAGCTATGTGCCTAGTAGGCTT-GTGCCGGTGT
11415 ATTTGGCCTT
Statistics
Matches: 126, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
33 26 0.21
34 1 0.01
35 4 0.03
36 2 0.02
37 61 0.48
38 32 0.25
ACGTcount: A:0.15, C:0.19, G:0.29, T:0.36
Consensus pattern (36 bp):
TTCAAGCTATGTGCCTAGTAGGCTTGTGCCGGTGTT
Found at i:11406 original size:70 final size:72
Alignment explanation
Indices: 11234--11410 Score: 236
Period size: 70 Copynumber: 2.4 Consensus size: 72
11224 CTTACACAAA
* *
11234 TTCAAGCTATATGCCTAGTAGGCTGT-GTGACGGTATTTTTCAAGCTATGTGCCTAGTAGGCTGT
1 TTCAGGCTATATGCCTAGTAGGCT-TCGTG-CCGTATTTTTCAAGCTATGTGCCTAGTAGGC-GT
11298 GTGCCGGTGTT
63 GT-CCGGTGTT
* *
11309 TTCAGGTTATGTGCCTAGTAGGCTTCGTGCCG-ATGTTTTCAAGCTATGTGCCTAGTAGGC-TGT
1 TTCAGGCTATATGCCTAGTAGGCTTCGTGCCGTAT-TTTTCAAGCTATGTGCCTAGTAGGCGTGT
11372 -CGGTGTT
65 CCGGTGTT
*
11379 TTCAGGCTATATCCCTAGTAGGCTTCGTGCCG
1 TTCAGGCTATATGCCTAGTAGGCTTCGTGCCG
11411 GTGTATTTGG
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
70 36 0.39
72 3 0.03
73 2 0.02
74 28 0.30
75 24 0.26
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (72 bp):
TTCAGGCTATATGCCTAGTAGGCTTCGTGCCGTATTTTTCAAGCTATGTGCCTAGTAGGCGTGTC
CGGTGTT
Found at i:11431 original size:107 final size:109
Alignment explanation
Indices: 11234--11447 Score: 251
Period size: 107 Copynumber: 2.0 Consensus size: 109
11224 CTTACACAAA
* * *
11234 TTCAAGCTATATGCCTAGTAGGCTGTGTGACGGTATTTTTCAAGCTATGTGCCTAGTAGGCTGTG
1 TTCAAGCTATATGCCTAGTAGGC-GTGT-ACGGTAGTTTTCAAGCTATATCCCTAGTAGGCTGTG
* *
11299 TGCCGGTGTTTTCAGGTTATGTGCCTAGTAGGCTTCGTGCCGATGTT
64 TGCCGGTGTTTT-AGGTTATATGCCTAGCAGGCTTCGTGCCGATGTT
* *
11346 TTCAAGCTATGTGCCTAGTAGGC-TGT-CGGT-GTTTTCAGGCTATATCCCTAGTAGGCT-TCGT
1 TTCAAGCTATATGCCTAGTAGGCGTGTACGGTAGTTTTCAAGCTATATCCCTAGTAGGCTGT-GT
*
11407 GCCGGTGTATTT-GGCCTT-TATGCCTAGCAGGCTTTGTGCCG
65 GCCGGTGT-TTTAGG--TTATATGCCTAGCAGGCTTCGTGCCG
11448 GTGATTCAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
106 3 0.03
107 53 0.59
108 9 0.10
110 3 0.03
112 22 0.24
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (109 bp):
TTCAAGCTATATGCCTAGTAGGCGTGTACGGTAGTTTTCAAGCTATATCCCTAGTAGGCTGTGTG
CCGGTGTTTTAGGTTATATGCCTAGCAGGCTTCGTGCCGATGTT
Found at i:11439 original size:70 final size:69
Alignment explanation
Indices: 11234--11439 Score: 175
Period size: 70 Copynumber: 2.9 Consensus size: 69
11224 CTTACACAAA
* * * * *
11234 TTCAAGCTATATGCCTAGTAGGCTGT-GTGACGGTAT-TTTTCAAGCTATGTGCCTAGTAGGCTG
1 TTCAGGCTATATCCCTAGTAGGCT-TCGTG-CCG-ATGTTTT-AAGCTATATGCCTAGCAGGC--
11297 TGTGCCGGTGTT
60 TGT--CGGTGTT
* * * * *
11309 TTCAGGTTATGTGCCTAGTAGGCTTCGTGCCGATGTTTTCAAGCTATGTGCCTAGTAGGCTGTCG
1 TTCAGGCTATATCCCTAGTAGGCTTCGTGCCGATGTTTT-AAGCTATATGCCTAGCAGGCTGTCG
11374 GTGTT
65 GTGTT
* * *
11379 TTCAGGCTATATCCCTAGTAGGCTTCGTGCCGGTGTATTT-GGCCTTTATGCCTAGCAGGCT
1 TTCAGGCTATATCCCTAGTAGGCTTCGTGCCGATGT-TTTAAG-CTATATGCCTAGCAGGCT
11440 TTGTGCCGGT
Statistics
Matches: 115, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
69 1 0.01
70 54 0.47
71 3 0.03
72 3 0.03
73 2 0.02
74 28 0.24
75 24 0.21
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (69 bp):
TTCAGGCTATATCCCTAGTAGGCTTCGTGCCGATGTTTTAAGCTATATGCCTAGCAGGCTGTCGG
TGTT
Found at i:15567 original size:19 final size:20
Alignment explanation
Indices: 15531--15569 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15521 TTTGGCATTA
*
15531 AAGTATCGATACTTTGACAT
1 AAGTATCAATACTTTGACAT
15551 AAGTATCAATA-TTTGACAT
1 AAGTATCAATACTTTGACAT
15570 TTTCAATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
AAGTATCAATACTTTGACAT
Found at i:15675 original size:19 final size:19
Alignment explanation
Indices: 15628--15675 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
15618 CATATTAAAA
15628 TATCGATACCTATATCAAGG
1 TATCGATA-CTATATCAAGG
* *
15648 TACCGATACTTTA-CAAGG
1 TATCGATACTATATCAAGG
15666 CTATCGATAC
1 -TATCGATAC
15676 ACTTATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
20 7 0.29
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (19 bp):
TATCGATACTATATCAAGG
Found at i:19631 original size:6 final size:6
Alignment explanation
Indices: 19622--19647 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19612 AAATGAAAAA
19622 GAGAGC GAGAGC GAGAGC GAGAGC GA
1 GAGAGC GAGAGC GAGAGC GAGAGC GA
19648 TTTCCTGAAA
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:0.35, C:0.15, G:0.50, T:0.00
Consensus pattern (6 bp):
GAGAGC
Found at i:29813 original size:7 final size:8
Alignment explanation
Indices: 29797--29822 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29787 TATTTTTTCT
29797 CCCCTCCC
1 CCCCTCCC
29805 CCCCTCCC
1 CCCCTCCC
29813 CCCCTCCC
1 CCCCTCCC
29821 CC
1 CC
29823 TTCTCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.88, G:0.00, T:0.12
Consensus pattern (8 bp):
CCCCTCCC
Found at i:37578 original size:18 final size:18
Alignment explanation
Indices: 37555--37596 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
37545 TTCAAGGTGT
37555 AATTAATTTAAATTT-TTC
1 AATTAA-TTAAATTTGTTC
*
37573 AATTAATTAAATTTGTTT
1 AATTAATTAAATTTGTTC
37591 AATTAA
1 AATTAA
37597 AAACTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AATTAATTAAATTTGTTC
Found at i:38344 original size:2 final size:2
Alignment explanation
Indices: 38337--38363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38327 ACTTAATTGC
38337 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38364 AATCTATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42215 original size:83 final size:83
Alignment explanation
Indices: 42076--42245 Score: 322
Period size: 83 Copynumber: 2.0 Consensus size: 83
42066 TACTTGCGTA
* *
42076 ATCTGTCATCGGATTGACGTCTTTCTCTCACCATTCCACCACTGACAGCTGTCTCTTTACAAATG
1 ATCTGTCATCGGATTGACGCCTTTCTCTCACCATTCCACCACTGACAGCTATCTCTTTACAAATG
42141 GTTTACAAACTCAATGCC
66 GTTTACAAACTCAATGCC
42159 ATCTGTCATCGGATTGACGCCTTTCTCTCACCATTCCACCACTGACAGCTATCTCTTTACAAATG
1 ATCTGTCATCGGATTGACGCCTTTCTCTCACCATTCCACCACTGACAGCTATCTCTTTACAAATG
42224 GTTTACAAACTCAATGCC
66 GTTTACAAACTCAATGCC
42242 ATCT
1 ATCT
42246 TCTTCTTCTT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (83 bp):
ATCTGTCATCGGATTGACGCCTTTCTCTCACCATTCCACCACTGACAGCTATCTCTTTACAAATG
GTTTACAAACTCAATGCC
Done.