Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004681.1 Kokia drynarioides strain JFW-HI SEQ_118232, 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: 60085
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:346 original size:6 final size:6
Alignment explanation
Indices: 335--360 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
325 GAGAAAGGGT
335 AGTTGG AGTTGG AGTTGG AGTTGG AG
1 AGTTGG AGTTGG AGTTGG AGTTGG AG
361 GAGTTGTGGT
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:0.19, C:0.00, G:0.50, T:0.31
Consensus pattern (6 bp):
AGTTGG
Found at i:4531 original size:39 final size:39
Alignment explanation
Indices: 4477--4672 Score: 193
Period size: 39 Copynumber: 5.0 Consensus size: 39
4467 GACCTAACTA
*
4477 ACCTAGAATAATCATCCCTTTTCAGATCATCTTTCTCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
* *
4516 ACCTAGAATATTCATCCCTCTTCTGATCATCTTT-TCCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCT-CCC
* * * ** *
4555 ATCTAGAGTATTCAT-CCTTATTCCAG-TCACCCATCCCCC
1 ACCTAGAATATTCATCCCTT-TT-CAGATCATCTTTCTCCC
* * *
4594 ACCTAGAATATTCAT-CCTTATTCCGGTCATCTTTCCCCC
1 ACCTAGAATATTCATCCCTT-TTCAGATCATCTTTCTCCC
* * *
4633 ACCTAGAATATTCATCCCTATTCCGATCATCATTCTCCC
1 ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
4672 A
1 A
4673 ATAAGCTTTG
Statistics
Matches: 130, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
38 6 0.05
39 119 0.92
40 5 0.04
ACGTcount: A:0.23, C:0.36, G:0.06, T:0.35
Consensus pattern (39 bp):
ACCTAGAATATTCATCCCTTTTCAGATCATCTTTCTCCC
Found at i:4608 original size:78 final size:78
Alignment explanation
Indices: 4477--4656 Score: 218
Period size: 78 Copynumber: 2.3 Consensus size: 78
4467 GACCTAACTA
* * * ** * * *
4477 ACCTAGAATAATCATCCCT-TTTCAGATCATCTTTCTCCCACCTAGAATATTCATCCCTCTTCTG
1 ACCTAGAATATTCATCCCTATTCCAG-TCACCCATCCCCCACCTAGAATATTCATCCCTATTCCG
*
4541 ATCATCTTTTCCCC
65 ATCATCTTTCCCCC
* * * * *
4555 ATCTAGAGTATTCATCCTTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCTTATTCCGG
1 ACCTAGAATATTCATCCCTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCCTATTCCGA
4620 TCATCTTTCCCCC
66 TCATCTTTCCCCC
4633 ACCTAGAATATTCATCCCTATTCC
1 ACCTAGAATATTCATCCCTATTCC
4657 GATCATCATT
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 79 0.94
79 5 0.06
ACGTcount: A:0.23, C:0.36, G:0.06, T:0.35
Consensus pattern (78 bp):
ACCTAGAATATTCATCCCTATTCCAGTCACCCATCCCCCACCTAGAATATTCATCCCTATTCCGA
TCATCTTTCCCCC
Found at i:5664 original size:189 final size:187
Alignment explanation
Indices: 5344--5900 Score: 817
Period size: 189 Copynumber: 2.9 Consensus size: 187
5334 CTATCCCTGC
* * * *
5344 CTCTCCTCTGGCTCCCAGTCAACTCGATCTTCCCTTTCTGAACTTCACCTCTCTTCTTTTCCCTC
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCTT-CCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
* * * *
5409 TCAACATCAGAATCAGAGTCATCCTCACTGGAGTCATTCCTACGACGACCTTTCTTAACCATTTC
65 CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
* *
5474 CTTCTTACGACCTCTCGCTCTGTCAGTATCAGAATCAGATTCACTACCCATGTCCCTCT
130 CTT-TTATGACCTCTCGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
5533 CTCTCCTCTGGCTCCCAGTCGACTCAATCTGTCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCT-TCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
* ** * **
5598 CCACCATCAGAATCAAAGTTGTCCTCACTAGAGTTGTGCCTATGACGACCTTTCTTAACCATTTC
65 CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
* *
5663 CTTTCTATGACCTCTTGCTCTGTCAGCATCAGAATCAGATTCACCACCCATGTCCCTCT
130 CTTT-TATGACCTCTCGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
* * *
5722 CTCTCCTCTGGCTCCTAGTTGACTCAATCTTCTGTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
1 CTCTCCTCTGGCTCCCAGTCGACTCAATCTTC-CTTTTTGAACTTCACCTCTCTTCTTTTGCCTC
* * * * *
5787 CTACCATCAGAATCAGAGTCACCCTCGCTGGAGTCATGCCTTTGATGACCTTTCTTAACCATTTC
65 CCACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTC
*
5852 CTTTTTATGACCTCTCGCTCTGTCAGCACCAGAATCAGATTCACTACCC
130 C-TTTTATGACCTCTCGCTCTGTCAGCATCAGAATCAGATTCACTACCC
5901 TCAGACTTCT
Statistics
Matches: 329, Mismatches: 35, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
188 3 0.01
189 322 0.98
190 4 0.01
ACGTcount: A:0.19, C:0.35, G:0.12, T:0.34
Consensus pattern (187 bp):
CTCTCCTCTGGCTCCCAGTCGACTCAATCTTCCTTTTTGAACTTCACCTCTCTTCTTTTGCCTCC
CACCATCAGAATCAGAGTCATCCTCACTGGAGTCATGCCTATGACGACCTTTCTTAACCATTTCC
TTTTATGACCTCTCGCTCTGTCAGCATCAGAATCAGATTCACTACCCATGTCCCTCT
Found at i:10138 original size:23 final size:23
Alignment explanation
Indices: 10111--10162 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
10101 AAAAAGTTGT
10111 AAAGTTAAAGGACTAA-TGTGAAA
1 AAAGTTAAAGGACTAAGT-TGAAA
* * *
10134 AAAGTTCAGGGACTAAGTTGAGA
1 AAAGTTAAAGGACTAAGTTGAAA
10157 AAAGTT
1 AAAGTT
10163 GACAAATGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.23
Consensus pattern (23 bp):
AAAGTTAAAGGACTAAGTTGAAA
Found at i:10955 original size:3 final size:3
Alignment explanation
Indices: 10947--10974 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10937 GCGCGTATGT
10947 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
10975 GATAATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:14618 original size:19 final size:18
Alignment explanation
Indices: 14596--14636 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
14586 TATTTATGAA
*
14596 ATTTTTATAATTTTAATTT
1 ATTTTT-TAATTTTAAATT
*
14615 ATTTTTTATTTTTAAATT
1 ATTTTTTAATTTTAAATT
14633 ATTT
1 ATTT
14637 GTTGACGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTTTAATTTTAAATT
Found at i:15132 original size:2 final size:2
Alignment explanation
Indices: 15127--15151 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15117 CCTCTCTGAT
15127 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
15152 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:27771 original size:7 final size:7
Alignment explanation
Indices: 27759--27793 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
27749 AATTAACTAT
27759 ATTTTAA
1 ATTTTAA
27766 ATTTTAA
1 ATTTTAA
27773 ATTTTAA
1 ATTTTAA
27780 ATTTTAA
1 ATTTTAA
*
27787 ATGTTAA
1 ATTTTAA
27794 GATGATTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (7 bp):
ATTTTAA
Found at i:29562 original size:11 final size:10
Alignment explanation
Indices: 29536--29561 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29526 CTCCGTTAAA
29536 TTTTTTACAT
1 TTTTTTACAT
29546 TTTTTTACAT
1 TTTTTTACAT
29556 TTTTTT
1 TTTTTT
29562 TCAGCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTACAT
Found at i:41421 original size:106 final size:106
Alignment explanation
Indices: 41236--41447 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
41226 AAATTTGAAA
* *
41236 AATTCAGTTTGCTGAATTTTGGTTCTTTGTTTTCTGTGATGGATTTACAATTGAAATCCTTTCTA
1 AATTCAGTATGCTGAATTTTGGTTCTTTGTTTTCTGTGATGGATTTACAATTGAAATCCATTCTA
41301 GTACTCGAGAAGCTCCGTTACTTTCCGACTTTGATGCTTCT
66 GTACTCGAGAAGCTCCGTTACTTTCCGACTTTGATGCTTCT
41342 AATTCAGTATGCTGAATTTTGGTTCTTTGTTTTCTGTGATGGATTTACAATTGAAATCCATTCTA
1 AATTCAGTATGCTGAATTTTGGTTCTTTGTTTTCTGTGATGGATTTACAATTGAAATCCATTCTA
41407 GTACTCGAGAAGCTCCGTTACTTTCCGACTTTGATGCTTCT
66 GTACTCGAGAAGCTCCGTTACTTTCCGACTTTGATGCTTCT
41448 GTCGGCATTG
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (106 bp):
AATTCAGTATGCTGAATTTTGGTTCTTTGTTTTCTGTGATGGATTTACAATTGAAATCCATTCTA
GTACTCGAGAAGCTCCGTTACTTTCCGACTTTGATGCTTCT
Found at i:44529 original size:43 final size:43
Alignment explanation
Indices: 44468--44554 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
44458 AGTTTATGTA
*
44468 TCAAATTACACATTGAATCAAAATTCATGTATAATTTTGATAT
1 TCAAATTACACATTGAATCAAAATTAATGTATAATTTTGATAT
44511 TCAAATTACACATTGAATCAAAATTAATGTATAATTTTGATAT
1 TCAAATTACACATTGAATCAAAATTAATGTATAATTTTGATAT
44554 T
1 T
44555 TATCCCATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (43 bp):
TCAAATTACACATTGAATCAAAATTAATGTATAATTTTGATAT
Found at i:48233 original size:23 final size:23
Alignment explanation
Indices: 48207--48258 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
48197 AAAAGTTTGC
* *
48207 CACAAAGCAGAGGAAAAGCGTGT
1 CACAAAGCAAAGAAAAAGCGTGT
48230 CACAAAGCAAAGAAAAAGCGTGT
1 CACAAAGCAAAGAAAAAGCGTGT
48253 CACAAA
1 CACAAA
48259 AATAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.19, G:0.23, T:0.08
Consensus pattern (23 bp):
CACAAAGCAAAGAAAAAGCGTGT
Found at i:52308 original size:17 final size:17
Alignment explanation
Indices: 52278--52311 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52268 CATTAAGTTG
**
52278 TTTAAATTTTTAAAAAT
1 TTTAAATTAGTAAAAAT
52295 TTTAAATTAGTAAAAAT
1 TTTAAATTAGTAAAAAT
52312 AAAATTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAT
Found at i:53811 original size:3 final size:3
Alignment explanation
Indices: 53766--53797 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53756 GATTAGTGAT
53766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53798 TTAGATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55969 original size:21 final size:22
Alignment explanation
Indices: 55928--55970 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
55918 CCGTAATCAA
*
55928 TTTATAATTTAACTTAATTAAAC
1 TTTAAAATTTAAC-TAATTAAAC
55951 TTTAAAATTTAAC-AATTAAA
1 TTTAAAATTTAACTAATTAAA
55971 TTAAAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAAAATTTAACTAATTAAAC
Done.