Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009336.1 Kokia drynarioides strain JFW-HI SEQ_124043, 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: 15386
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Found at i:1456 original size:22 final size:19
Alignment explanation
Indices: 1431--1472 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1421 AGTTTGAATG
1431 AGTTACATTATTTTATTTGTTT
1 AGTTAC-TT-TTTTATTT-TTT
1453 AGTTACTTTTTTATTTTTT
1 AGTTACTTTTTTATTTTTT
1472 A
1 A
1473 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 2 0.10
22 6 0.30
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (19 bp):
AGTTACTTTTTTATTTTTT
Found at i:3211 original size:99 final size:98
Alignment explanation
Indices: 3102--3343 Score: 265
Period size: 99 Copynumber: 2.4 Consensus size: 98
3092 AAGATACGAA
** * *
3102 GGGAAAGGTTGAGACAGCAACGATG-AACTTGGTACCGTGAAGATTTGAAGGGAAGGATTGAGGC
1 GGGAAAGGTTGAGACAGCAA-GA-GAAACCCGGTACCATGAAGATTTGAAAGGAAGGATTGAGGC
** * * * *
3166 CGTGATGATGAATCTGGTACCTTAGAAGATGTGAT
64 CACGACGACGAATCCGATACCTTAGAAGATGTGAT
* * *
3201 GGGAAAGGTTGAGGCCGCAAGAGCAAACCCGGTACCATGAAGATTTGAAAGGAAGGATTGAGGTC
1 GGGAAAGGTTGAGACAGCAAGAG-AAACCCGGTACCATGAAGATTTGAAAGGAAGGATTGAGGCC
3266 ACGACGACGAATCCGATACCTTAGAAGATGTGAT
65 ACGACGACGAATCCGATACCTTAGAAGATGTGAT
* * *
3300 GGGAAAGATTGAGCCCA-CAACG-GCGAACCCGGTACCATGAAGAT
1 GGGAAAGGTTGAG-ACAGCAA-GAG-AAACCCGGTACCATGAAGAT
3344 ATAAAGGGAA
Statistics
Matches: 122, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
97 1 0.01
98 2 0.02
99 117 0.96
100 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (98 bp):
GGGAAAGGTTGAGACAGCAAGAGAAACCCGGTACCATGAAGATTTGAAAGGAAGGATTGAGGCCA
CGACGACGAATCCGATACCTTAGAAGATGTGAT
Found at i:3213 original size:50 final size:49
Alignment explanation
Indices: 3123--3217 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
3113 AGACAGCAAC
*
3123 GATGAACTTGGTACCGTGAAGATTTGAAGGGAAGGATTGAGGCCGTGAT
1 GATGAACTTGGTACCGTGAAGATGTGAAGGGAAGGATTGAGGCCGTGAT
* *
3172 GATGAA-TCTGGTACCTTAGAAGATGTGATGGGAAAGG-TTGAGGCCG
1 GATGAACT-TGGTACCGT-GAAGATGTGAAGGG-AAGGATTGAGGCCG
3218 CAAGAGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
48 1 0.03
49 14 0.35
50 21 0.52
51 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.37, T:0.24
Consensus pattern (49 bp):
GATGAACTTGGTACCGTGAAGATGTGAAGGGAAGGATTGAGGCCGTGAT
Found at i:3372 original size:99 final size:98
Alignment explanation
Indices: 3132--3390 Score: 285
Period size: 99 Copynumber: 2.6 Consensus size: 98
3122 CGATGAACTT
* * * * * * *
3132 GGTACCGTGAAGATTTGAAGGGAAGGATTGAGGCCGTGATGATGAATCTGGTACCTTAGAAGATG
1 GGTACCATGAAGATTTAAAGGGAAGGATTGAGACCGT-ACGACGAATCCGATACCTTAGAAGATG
* * *
3197 TGATGGGAAAGGTTGAGGCCGCAAGAGCAAACCC
65 TGATGGGAAAGATTGAGCCCACAAGAGCAAACCC
*
3231 GGTACCATGAAGATTTGAAA-GGAAGGATTGAGGTCACG-ACGACGAATCCGATACCTTAGAAGA
1 GGTACCATGAAGATTT-AAAGGGAAGGATTGA-GAC-CGTACGACGAATCCGATACCTTAGAAGA
*
3294 TGTGATGGGAAAGATTGAGCCCACAACG-GCGAACCC
63 TGTGATGGGAAAGATTGAGCCCACAA-GAGCAAACCC
* *
3330 GGTACCATGAAGATATAAAGGGAAAGG-TTGAGACCGTAACGACGAA-CCTAGTACCTTAGAA
1 GGTACCATGAAGATTTAAAGGG-AAGGATTGAGACCGT-ACGACGAATCCGA-TACCTTAGAA
3391 ACATGACAGG
Statistics
Matches: 137, Mismatches: 14, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
97 2 0.01
98 8 0.06
99 116 0.85
100 9 0.07
101 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (98 bp):
GGTACCATGAAGATTTAAAGGGAAGGATTGAGACCGTACGACGAATCCGATACCTTAGAAGATGT
GATGGGAAAGATTGAGCCCACAAGAGCAAACCC
Found at i:3384 original size:49 final size:49
Alignment explanation
Indices: 2993--3384 Score: 233
Period size: 49 Copynumber: 8.0 Consensus size: 49
2983 TCTAATACAT
* *
2993 TGAAGATATGAAGGGAAAGGTTGAGGCCACAAC-ATCGAACCCAGTACCT
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGA-CGAACCCAGTACCA
* * * * *
3042 TAGAAGATGTAGTA-GGAAAGGTTGAGG-TGCAATGGCGAA-CCAGTACCA
1 T-GAAGATAT-GAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCA
* * * * *** *
3090 TGAAGATACGAAGGGAAAGGTTGAGACAGCAACGATGAACTTGGTACCG
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCA
* ** * * * ** *
3139 TGAAGATTTGAAGGG-AAGGATTGAGGCCGTGATGATGAATCTGGTACCT
1 TGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGACGAACCCAGTACCA
* * * *
3188 TAGAAGATGTGATGGGAAAGGTTGAGGCCGCAA-GAGCAAACCCGGTACCA
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGA-CGAACCCAGTACCA
* * * * * * *
3238 TGAAGATTTGAAAGG-AAGGATTGAGGTCACGACGACGAATCC-GATACCT
1 TGAAGATATGAAGGGAAAGG-TTGAGGCCGCAACGACGAACCCAG-TACCA
* * * * * * *
3287 TAGAAGATGTGATGGGAAAGATTGAGCCCACAACGGCGAACCCGGTACCA
1 T-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCA
* * * *
3337 TGAAGATATAAAGGGAAAGGTTGAGACCGTAACGACGAACCTAGTACC
1 TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACC
3385 TTAGAAACAT
Statistics
Matches: 260, Mismatches: 67, Indels: 32
0.72 0.19 0.09
Matches are distributed among these distances:
46 2 0.01
47 18 0.07
48 26 0.10
49 117 0.45
50 87 0.33
51 10 0.04
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (49 bp):
TGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCA
Found at i:3526 original size:49 final size:49
Alignment explanation
Indices: 3405--3517 Score: 199
Period size: 49 Copynumber: 2.3 Consensus size: 49
3395 GACAGGAAAG
*
3405 ATTAAAGCCACAACGACAAATCTTACACCCTAAAGCCGAAAAGGAGTAA
1 ATTAAAGCCACAACGACAAATCTTATACCCTAAAGCCGAAAAGGAGTAA
* *
3454 ATTAAAGCCATAACGACAAATCTTATACCCTAAAGCCGAATAGGAGTAA
1 ATTAAAGCCACAACGACAAATCTTATACCCTAAAGCCGAAAAGGAGTAA
3503 ATTAAAGCCACAACG
1 ATTAAAGCCACAACG
3518 GTAGATCTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.17
Consensus pattern (49 bp):
ATTAAAGCCACAACGACAAATCTTATACCCTAAAGCCGAAAAGGAGTAA
Found at i:4716 original size:12 final size:13
Alignment explanation
Indices: 4699--4732 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
4689 TTCAAAGTAC
4699 ATTAAATAAT-AT
1 ATTAAATAATAAT
4711 ATTAAATAATAAT
1 ATTAAATAATAAT
*
4724 AATAAATAA
1 ATTAAATAA
4733 AAGAGATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTAAATAATAAT
Found at i:6069 original size:23 final size:23
Alignment explanation
Indices: 6043--6088 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6033 TGTTGAGTAA
6043 CAGAGGGCACACAAAGTACTAAT
1 CAGAGGGCACACAAAGTACTAAT
* *
6066 CAGAGGGCACACAGAGTGCTAAT
1 CAGAGGGCACACAAAGTACTAAT
6089 AATAGAAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTACTAAT
Found at i:6099 original size:25 final size:26
Alignment explanation
Indices: 6062--6110 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
6052 CACAAAGTAC
*
6062 TAATCAGAGGGCACACAGAGTGCTAA
1 TAATCAGAAGGCACACAGAGTGCTAA
* *
6088 TAAT-AGAAGGCATACATAGTGCT
1 TAATCAGAAGGCACACAGAGTGCT
6111 GAACAGAGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (26 bp):
TAATCAGAAGGCACACAGAGTGCTAA
Found at i:13490 original size:24 final size:24
Alignment explanation
Indices: 13448--13495 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
13438 GATATTTTTA
13448 ATATGCATCTAAATTTTTTTGAATAT
1 ATATGCATCTAAA-TTTTTT-AATAT
*
13474 ATATGTATCTAAA-TTTTTAATA
1 ATATGCATCTAAATTTTTTAATA
13496 GAATGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
26 12 0.57
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
ATATGCATCTAAATTTTTTAATAT
Found at i:13644 original size:13 final size:13
Alignment explanation
Indices: 13626--13651 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13616 TGTATTAAAT
13626 AATAAAATAATAA
1 AATAAAATAATAA
13639 AATAAAATAATAA
1 AATAAAATAATAA
13652 CATGTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAATAATAA
Done.