Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006820.1 Kokia drynarioides strain JFW-HI SEQ_121419, 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: 9235
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:241 original size:33 final size:33
Alignment explanation
Indices: 168--242 Score: 82
Period size: 33 Copynumber: 2.2 Consensus size: 33
158 AAGAAGTTTG
*
168 TTTATTTGATGATTTTTGAATCTTTTCCTTGTTA
1 TTTATTT-ATGATTTTCGAATCTTTTCCTTGTTA
*
202 GATTATTT-TGATTTTCGAATCTTTTCTTCTTGTT-
1 -TTTATTTATGATTTTCGAATCTTTTC--CTTGTTA
236 TTTATTT
1 TTTATTT
243 CATTTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 23 0.66
35 12 0.34
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (33 bp):
TTTATTTATGATTTTCGAATCTTTTCCTTGTTA
Found at i:1607 original size:26 final size:27
Alignment explanation
Indices: 1573--1634 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
1563 ATGTTTTCGT
1573 AAAGTGATTTTTGATGAAATTACGA-TA
1 AAAG-GATTTTTGATGAAATTACGATTA
*
1600 AAAGGATTTTTGATGAAATTAGGATTA
1 AAAGGATTTTTGATGAAATTACGATTA
1627 AAA-GATTT
1 AAAGGATTT
1635 AAATGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 24 0.73
27 9 0.27
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (27 bp):
AAAGGATTTTTGATGAAATTACGATTA
Found at i:2140 original size:52 final size:52
Alignment explanation
Indices: 2055--2246 Score: 278
Period size: 52 Copynumber: 3.7 Consensus size: 52
2045 TAAATGAAAA
* *
2055 AGGTTCGATGACTATGTGTCATCGTGAGTATATAAATCTTTTACGGATTATG
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATAAATCCTTTACGGATTATG
* * * * *
2107 AGGTTCGATGACTACGTATCATCATGAGCATATAAACCCTTTACGGATAATG
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATAAATCCTTTACGGATTATG
* * *
2159 AGGTTCGATGACTACGTGTTATCGTGAGTATATGAATCCTTTACGGATTGTG
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATAAATCCTTTACGGATTATG
*
2211 AGGTTCGATGACTATGTGTCATCGTGAGTAT-TAAAT
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATAAAT
2247 GAAATGAATC
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
51 4 0.03
52 118 0.97
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AGGTTCGATGACTACGTGTCATCGTGAGTATATAAATCCTTTACGGATTATG
Found at i:2878 original size:24 final size:21
Alignment explanation
Indices: 2850--2900 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2840 TGCATGATAG
*
2850 GTATCGATAGTTCAGTGTATGCTT
1 GTATCGATAGTT-AG-G-ATACTT
*
2874 GTATCGGTAGTTAGGATACTT
1 GTATCGATAGTTAGGATACTT
2895 GTATCG
1 GTATCG
2901 TTAGAAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 2 0.08
24 11 0.44
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (21 bp):
GTATCGATAGTTAGGATACTT
Found at i:4829 original size:35 final size:36
Alignment explanation
Indices: 4790--4865 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
4780 ATATTATCAA
*
4790 TCACATGG-TATGAA-AACATACCCACATATTTACTG
1 TCACATGGCT-TGAATAACATACCCACATATTCACTG
*
4825 TCACATGGCTTGAATAACATACCCACATATTCACTT
1 TCACATGGCTTGAATAACATACCCACATATTCACTG
4861 TCACA
1 TCACA
4866 ATAGTCATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 12 0.32
36 25 0.68
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (36 bp):
TCACATGGCTTGAATAACATACCCACATATTCACTG
Found at i:7450 original size:17 final size:18
Alignment explanation
Indices: 7419--7452 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
7409 AATTTAACTT
7419 TAATTAAATTGTTTAAAA
1 TAATTAAATTGTTTAAAA
*
7437 TAATT-AATTTTTTAAA
1 TAATTAAATTGTTTAAA
7453 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATTAAATTGTTTAAAA
Found at i:8528 original size:8 final size:7
Alignment explanation
Indices: 8510--8550 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
8500 CTTTTTGATG
8510 AAAATAA
1 AAAATAA
*
8517 AAATTAA
1 AAAATAA
8524 AAAATAA
1 AAAATAA
*
8531 AATATAAA
1 AAAAT-AA
8539 AAAATAA
1 AAAATAA
8546 AAAAT
1 AAAAT
8551 CTCAAGGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:8542 original size:15 final size:14
Alignment explanation
Indices: 8510--8548 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
8500 CTTTTTGATG
*
8510 AAAATAAAAATTAA
1 AAAATAAAAATAAA
8524 AAAATAAAATATAAA
1 AAAATAAAA-ATAAA
8539 AAAATAAAAA
1 AAAATAAAAA
8549 ATCTCAAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAATAAAAATAAA
Done.