Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010608.1 Kokia drynarioides strain JFW-HI SEQ_125541, 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: 43970
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:19296 original size:72 final size:75
Alignment explanation
Indices: 19220--19361 Score: 245
Period size: 72 Copynumber: 1.9 Consensus size: 75
19210 GCAACTCTTG
* *
19220 TTCTTTTAATTTACTTAAAATCTTTCTCTATGGTTTTATATGAGGCC-A-A-GGTGTTTTTCCAG
1 TTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATACGAGGCCAAGAGGGTGTTTTTCCAG
19282 TGGCTGCTTT
66 TGGCTGCTTT
19292 TTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATACGAGGCCAAGAGGGTGTTTTTCCAG
1 TTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATACGAGGCCAAGAGGGTGTTTTTCCAG
19357 TGGCT
66 TGGCT
19362 TCTGTATGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 45 0.69
73 1 0.02
74 1 0.02
75 18 0.28
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (75 bp):
TTCTTTTAATTTAATTAAAATCTTTCTCTATGGTTTTATACGAGGCCAAGAGGGTGTTTTTCCAG
TGGCTGCTTT
Found at i:21327 original size:14 final size:13
Alignment explanation
Indices: 21294--21327 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
21284 AATTTAATAT
*
21294 TATTTTTGAGAAG
1 TATTTTGGAGAAG
21307 TATTTTGGAGAAG
1 TATTTTGGAGAAG
21320 TGATTTTG
1 T-ATTTTG
21328 AAAAGTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (13 bp):
TATTTTGGAGAAG
Found at i:23132 original size:231 final size:230
Alignment explanation
Indices: 22730--23192 Score: 890
Period size: 231 Copynumber: 2.0 Consensus size: 230
22720 GCATCACCCG
22730 TTAAACTAATACCAGAATGCTTATTTAATGAATCAATGACGCATAAATCTCTGAATTTGGAGGTT
1 TTAAACTAATACCAGAATGCTTATTTAATGAATCAATGACGCATAAATCTCTGAATTTGGAGGTT
*
22795 TACTAAGTAAAGACTTAGCTGATTAACAAATCAATAAGCGATTTGATGCAGCTAACAAATCGTTT
66 TACTAAGTAAAGACTTAACTGATTAACAAATCAATAAGCGATTTGATGCAGCTAACAAATCGTTT
*
22860 TCCATCGAATCGCTTGTTGATTCAGCTAATAGCGAAAATGTTTTTTTCCTTTGTTATTTTCAATG
131 TCCATCGAATCGCTTGTTGATTCAGCTAATAGCGAAAATGTTTTTTTCCTTCGTTATTTTCAATG
22925 ACTCTTAAATCTCTGAATTTCGTTAATCAATTCAT
196 ACTCTTAAATCTCTGAATTTCGTTAATCAATTCAT
22960 TTAAACTAATACCAGAATGCTTATTTTAATGAATCAATGACGCATAAATCTCTGAATTTGGAGGT
1 TTAAACTAATACCAGAATGCTTA-TTTAATGAATCAATGACGCATAAATCTCTGAATTTGGAGGT
23025 TTACTAAGTAAAGACTTAACTGATTAACAAATCAATAAGCGATTTGATGCAGCTAACAAATCGTT
65 TTACTAAGTAAAGACTTAACTGATTAACAAATCAATAAGCGATTTGATGCAGCTAACAAATCGTT
*
23090 TTCCATCGAATCGCTTGTTGATTTAGCTAATAGCGAAAATGTTTTTTTCCTTCGTTATTTTCAAT
130 TTCCATCGAATCGCTTGTTGATTCAGCTAATAGCGAAAATGTTTTTTTCCTTCGTTATTTTCAAT
23155 GACTCTTAAATCTCTGAATTTCGTTAATCAATTCAT
195 GACTCTTAAATCTCTGAATTTCGTTAATCAATTCAT
23191 TT
1 TT
23193 TTACTTGGTA
Statistics
Matches: 229, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
230 23 0.10
231 206 0.90
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (230 bp):
TTAAACTAATACCAGAATGCTTATTTAATGAATCAATGACGCATAAATCTCTGAATTTGGAGGTT
TACTAAGTAAAGACTTAACTGATTAACAAATCAATAAGCGATTTGATGCAGCTAACAAATCGTTT
TCCATCGAATCGCTTGTTGATTCAGCTAATAGCGAAAATGTTTTTTTCCTTCGTTATTTTCAATG
ACTCTTAAATCTCTGAATTTCGTTAATCAATTCAT
Found at i:26532 original size:13 final size:14
Alignment explanation
Indices: 26514--26551 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
26504 CTTAAACTAA
26514 ACTTTTCAAAAAT-
1 ACTTTTCAAAAATC
26527 ACTTTTC-AAAATC
1 ACTTTTCAAAAATC
26540 ACTTTTTCAAAA
1 AC-TTTTCAAAA
26552 CACTTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.23
13 9 0.41
14 5 0.23
15 3 0.14
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (14 bp):
ACTTTTCAAAAATC
Found at i:26548 original size:14 final size:14
Alignment explanation
Indices: 26516--26556 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
26506 TAAACTAAAC
26516 TTTTCAAAAAT-AC-
1 TTTTC-AAAATCACT
26529 TTTTCAAAATCACT
1 TTTTCAAAATCACT
26543 TTTTCAAAA-CACT
1 TTTTCAAAATCACT
26556 T
1 T
26557 ACTAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.19
13 12 0.46
14 9 0.35
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTCAAAATCACT
Found at i:28714 original size:15 final size:15
Alignment explanation
Indices: 28694--28728 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
28684 TCCCAATCTT
*
28694 CACCACCATCACAAC
1 CACCACCACCACAAC
28709 CACCACCACCACAAC
1 CACCACCACCACAAC
28724 CACCA
1 CACCA
28729 ACACAACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.57, G:0.00, T:0.03
Consensus pattern (15 bp):
CACCACCACCACAAC
Found at i:31153 original size:23 final size:23
Alignment explanation
Indices: 31127--31172 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31117 TGATATAATA
* *
31127 TGTAATTATATATACTGATTTTT
1 TGTAATTATATATAATAATTTTT
*
31150 TGTAATTTTATATAATAATTTTT
1 TGTAATTATATATAATAATTTTT
31173 ATTTGATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TGTAATTATATATAATAATTTTT
Found at i:39555 original size:98 final size:98
Alignment explanation
Indices: 39383--39574 Score: 228
Period size: 98 Copynumber: 2.0 Consensus size: 98
39373 TCGAGGCTGC
* * * * *
39383 TTAAGCCATTTCCCACTAAAGCAAAGACGTGGCCTCATCATCATTGTATAATTATGCATAAATGT
1 TTAAGCCACTTCCCACTAAAACAAAGACCTAGCCTCATCATCATTGTACAATTATGCATAAATGT
* **
39448 ATTATCTTGGCTTATGATAATCATCAAATTAAA
66 ATTAGCTTGGCTTAAAATAATCATCAAATTAAA
* * *
39481 TTAAGCCACTTCGCACTAAAACAAAGACCTAGCTTCATCA-C-TTGTACAATTATGCATAGCCAC
1 TTAAGCCACTTCCCACTAAAACAAAGACCTAGCCTCATCATCATTGTACAATTATGCATA---AA
*
39544 T-TATTAGCTTGGCTTAAAATTATCATCAAAT
63 TGTATTAGCTTGGCTTAAAATAATCATCAAAT
39575 CAACTCAACT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
96 16 0.20
97 1 0.01
98 60 0.76
99 2 0.03
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (98 bp):
TTAAGCCACTTCCCACTAAAACAAAGACCTAGCCTCATCATCATTGTACAATTATGCATAAATGT
ATTAGCTTGGCTTAAAATAATCATCAAATTAAA
Done.