Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009033.1 Kokia drynarioides strain JFW-HI SEQ_123731, 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: 10340
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1192 original size:30 final size:28
Alignment explanation
Indices: 1146--1455 Score: 266
Period size: 30 Copynumber: 10.5 Consensus size: 28
1136 TAAACTATTT
1146 AAAAATTCCATTTTTACCCCTGAACTTCC
1 AAAAATTCCATTTTTA-CCCTGAACTTCC
* *
1175 AAAAATACCATTTTTTACCTTGAAACTTCC
1 AAAAATTCCA-TTTTTACCCTG-AACTTCC
* *
1205 AAAAATTTCATTTTAACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCT-GAACTTCC
* *
1234 AAAAATTCTATTTTTAACCCTAAAAC-TCTC
1 AAAAATTCCATTTTT-ACCCT-GAACTTC-C
*
1264 AAAAATTCCATTTTTAACCCTAAAAC-TCC
1 AAAAATTCCATTTTT-ACCCT-GAACTTCC
1293 TAAAAATTCCATTTTTACCCCTGAACTTCC
1 -AAAAATTCCATTTTTA-CCCTGAACTTCC
* **
1323 AAATATTCCATTTTTGACCCCAAAACTTCC
1 AAAAATTCCATTTTT-A-CCCTGAACTTCC
* *
1353 AAAAATTCCATTTTTTATCCTCAAACTTCC
1 AAAAATTCCA-TTTTTACCCT-GAACTTCC
* *
1383 GAAAATTCCATTTTTTACTCTGAAACTTCC
1 AAAAATTCCA-TTTTTACCCTG-AACTTCC
** *
1413 AAAAATTACCA-TTTTACCCCCAAATGTCC
1 AAAAATT-CCATTTTTACCCTGAACT-TCC
*
1442 AAAAACTCCATTTT
1 AAAAATTCCATTTT
1456 CAACCTCGAA
Statistics
Matches: 237, Mismatches: 29, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.03
29 82 0.35
30 141 0.59
31 8 0.03
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCCTGAACTTCC
Found at i:1238 original size:59 final size:61
Alignment explanation
Indices: 1146--1465 Score: 294
Period size: 59 Copynumber: 5.4 Consensus size: 61
1136 TAAACTATTT
* * *
1146 AAAAATTCCATTTTTACCCCT-GAACTTCCAAAAATACCATTTTTTA-CCTTGAAACTTCC
1 AAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCCATTTTTTACCCCTGAAACTTCC
* * * *
1205 AAAAATTTCA-TTTTAACCCTCGAACTTCCAAAAATTCTA-TTTTTAACCCTAAAAC-TCTC
1 AAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCCATTTTTTACCCCTGAAACTTC-C
**
1264 AAAAATTCCATTTTTAACCCTAAAAC-TCCTAAAAATTCCA-TTTTTACCCCTG-AACTTCC
1 AAAAATTCCATTTTTAACCCTCGAACTTCC-AAAAATTCCATTTTTTACCCCTGAAACTTCC
* * * * *
1323 AAATATTCCATTTTTGACCC-CAAAACTTCCAAAAATTCCATTTTTTA-TCCTCAAACTTCC
1 AAAAATTCCATTTTTAACCCTC-GAACTTCCAAAAATTCCATTTTTTACCCCTGAAACTTCC
* * * *
1383 GAAAATTCCATTTTTTACTCT-GAAACTTCCAAAAATTACCA--TTTTACCCC-CAAA-TGTCC
1 AAAAATTCCATTTTTAACCCTCG-AACTTCCAAAAATT-CCATTTTTTACCCCTGAAACT-TCC
* *
1442 AAAAACTCCATTTTCAA-CCTCGAA
1 AAAAATTCCATTTTTAACCCTCGAA
1466 ACGCTTAAAA
Statistics
Matches: 217, Mismatches: 28, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
58 22 0.10
59 110 0.51
60 82 0.38
61 3 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (61 bp):
AAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCCATTTTTTACCCCTGAAACTTCC
Found at i:1432 original size:89 final size:87
Alignment explanation
Indices: 1146--1455 Score: 335
Period size: 89 Copynumber: 3.5 Consensus size: 87
1136 TAAACTATTT
** * *
1146 AAAAATTCCATTTTT-ACCCCTGAACTTCCAAAAATACCATTTTTTACCTTGAAACTTCCAAAAA
1 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTTACC-TAAAACTTCCAAAAA
* *
1210 TTTCATTTTAACCCTCGAACTTCC
65 TTCCATTTTTACCCT-GAACTTCC
* * *
1234 AAAAATTCTATTTTTAACCCTAAAAC-TCTCAAAAATTCCATTTTTAACCCTAAAAC-TCCTAAA
1 AAAAATTCCATTTTTAACCCCAAAACTTC-CAAAAATTCCATTTTTTA-CCTAAAACTTCC-AAA
1297 AATTCCATTTTTACCCCTGAACTTCC
63 AATTCCATTTTTA-CCCTGAACTTCC
* * * *
1323 AAATATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTTATCCTCAAACTTCCGAAAA
1 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTTA-CCTAAAACTTCCAAAAA
*
1388 TTCCATTTTTTACTCTGAAACTTCC
65 TTCCA-TTTTTACCCTG-AACTTCC
* *
1413 AAAAATTACCA-TTTT-ACCCCCAAA-TGTCCAAAAACTCCATTTT
1 AAAAATT-CCATTTTTAACCCCAAAACT-TCCAAAAATTCCATTTT
1456 CAACCTCGAA
Statistics
Matches: 190, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
88 20 0.11
89 133 0.70
90 34 0.18
91 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (87 bp):
AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTTACCTAAAACTTCCAAAAAT
TCCATTTTTACCCTGAACTTCC
Found at i:1442 original size:29 final size:29
Alignment explanation
Indices: 1410--1580 Score: 91
Period size: 29 Copynumber: 5.9 Consensus size: 29
1400 CTCTGAAACT
1410 TCCAAAAATTACCATTTTACCCCCAAATG
1 TCCAAAAATTACCATTTTACCCCCAAATG
* * * *
1439 TCCAAAAACT-CCATTTTCAACCTCGAAACG
1 TCCAAAAATTACCATTTT--ACCCCCAAATG
** ** * * *
1469 -CTTAAAATTACCCGTTCACTCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCAAATG
* * * * *
1497 TCTAAAAATTCCCTTTTTAACCCCAAATTT
1 TCCAAAAATTACCATTTTACCCCCAAA-TG
* *
1527 TCCCAAAATTACCATTTCACCCCCGAGAA--
1 TCCAAAAATTACCATTTTACCCCC-A-AATG
*
1556 TCC-AAAATTACCATTTTGCCCCCAA
1 TCCAAAAATTACCATTTTACCCCCAA
1581 GTATCCGAAA
Statistics
Matches: 103, Mismatches: 32, Indels: 17
0.68 0.21 0.11
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 31 0.30
29 36 0.35
30 31 0.30
31 1 0.01
32 2 0.02
ACGTcount: A:0.34, C:0.33, G:0.05, T:0.28
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCAAATG
Found at i:1586 original size:28 final size:28
Alignment explanation
Indices: 1529--1591 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1519 CCAAATTTTC
*
1529 CCAAAATTACCATTTCACCCCCGAGAAT
1 CCAAAATTACCATTTCACCCCCAAGAAT
** *
1557 CCAAAATTACCATTTTGCCCCCAAGTAT
1 CCAAAATTACCATTTCACCCCCAAGAAT
1585 CCGAAAA
1 CC-AAAA
1592 GTCTCGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (28 bp):
CCAAAATTACCATTTCACCCCCAAGAAT
Found at i:3578 original size:6 final size:6
Alignment explanation
Indices: 3560--3602 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
3550 TTTTGAACTC
* *
3560 AATTTA AAATTA AATTTA AA-ATA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
3603 ACAAATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:3588 original size:23 final size:23
Alignment explanation
Indices: 3560--3635 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
3550 TTTTGAACTC
*
3560 AATTTAAAATTAAATTTAAAATA
1 AATTTAAATTTAAATTTAAAATA
*
3583 AATTTAAATTTAAATTTAAAACA
1 AATTTAAATTTAAATTTAAAATA
* * *
3606 AATTTATATTTGAACTTAAAATA
1 AATTTAAATTTAAATTTAAAATA
3629 AATTTAA
1 AATTTAA
3636 TTAAAGATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (23 bp):
AATTTAAATTTAAATTTAAAATA
Found at i:3589 original size:17 final size:17
Alignment explanation
Indices: 3564--3596 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3554 GAACTCAATT
3564 TAAAATTAAATTTAAAA
1 TAAAATTAAATTTAAAA
*
3581 TAAATTTAAATTTAAA
1 TAAAATTAAATTTAAA
3597 TTTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTAAATTTAAAA
Found at i:3685 original size:53 final size:53
Alignment explanation
Indices: 3624--3728 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
3614 TTTGAACTTA
3624 AAATAAATTTAATTAAAGATTAGACTTGATTTGGATTCACAGTTTGGGCCCGG
1 AAATAAATTTAATTAAAGATTAGACTTGATTTGGATTCACAGTTTGGGCCCGG
*
3677 AAATAAATTTAATTAAAGATTGGACTTGATTTGGATTCACAGTTTGGGCCCG
1 AAATAAATTTAATTAAAGATTAGACTTGATTTGGATTCACAGTTTGGGCCCG
3729 ATCAAAATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (53 bp):
AAATAAATTTAATTAAAGATTAGACTTGATTTGGATTCACAGTTTGGGCCCGG
Found at i:4034 original size:18 final size:18
Alignment explanation
Indices: 4011--4053 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4001 GAATAGGTTT
4011 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
4029 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
4047 TTAATTA
1 TTAATTA
4054 CACTTTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:6850 original size:31 final size:30
Alignment explanation
Indices: 6776--6856 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 30
6766 ATCTTAGAAG
* * *
6776 TATACTTGAAATTTTAATTTGGTGTAATTA
1 TATATTTGAAATTTTAATTTAGTGTAAATA
* * *
6806 TACATGTGAAATTTTAATTATAGTTTAAATA
1 TATATTTGAAATTTTAATT-TAGTGTAAATA
6837 TATATTTGAAATTTTAATTT
1 TATATTTGAAATTTTAATTT
6857 TGATTTAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 17 0.40
31 25 0.60
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (30 bp):
TATATTTGAAATTTTAATTTAGTGTAAATA
Found at i:7745 original size:23 final size:24
Alignment explanation
Indices: 7664--7752 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
7654 ATTAGAAAAT
*
7664 ATATAATTTTATATATTATGTTAA
1 ATATTATTTTATATATTATGTTAA
* * * * *
7688 ATAATATGTAATTATATAATG-AAA
1 ATATTATTTTA-TATATTATGTTAA
7712 ATATATAATTTTATATATTATGTTAA
1 ATAT-T-ATTTTATATATTATGTTAA
7738 A-ATTATTTTAT-TATT
1 ATATTATTTTATATATT
7753 CAAAAGCATC
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
22 4 0.08
23 7 0.14
24 13 0.26
25 19 0.38
26 7 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATTATTTTATATATTATGTTAA
Found at i:10083 original size:18 final size:18
Alignment explanation
Indices: 10056--10098 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
10046 AGTTTATTTT
10056 ATTT-TTATT-AATTTACA
1 ATTTATTATTAAATTTA-A
10073 ATTTATTATTAAATTTAA
1 ATTTATTATTAAATTTAA
10091 ATTGTATT
1 ATT-TATT
10099 TATATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTATTATTAAATTTAA
Found at i:10199 original size:24 final size:25
Alignment explanation
Indices: 10167--10219 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
10157 TGTGTGCTTA
*
10167 ATATTTTATCAAAATTTA-TAT-AAT
1 ATATCTTAT-AAAATTTATTATAAAT
*
10191 ATATCTTATAAATTTTATTATAAAT
1 ATATCTTATAAAATTTATTATAAAT
10216 ATAT
1 ATAT
10220 AATACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 11 0.44
25 7 0.28
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATCTTATAAAATTTATTATAAAT
Done.