Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009553.1 Kokia drynarioides strain JFW-HI SEQ_124265, 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: 42983
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:5363 original size:23 final size:22
Alignment explanation
Indices: 5333--5380 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
5323 ATCTTTGATG
*
5333 TTTTTTTAATTTGATATTTAATA
1 TTTTTTTAATTTAATATTTAA-A
5356 TTTTTTTAATTTAATATTTAAA
1 TTTTTTTAATTTAATATTTAAA
5378 TTT
1 TTT
5381 GTCAAATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTTAATTTAATATTTAAA
Found at i:10864 original size:59 final size:60
Alignment explanation
Indices: 10797--10909 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
10787 TTGAAAGACT
* *
10797 ATTTTGTAACTTTTCATGGTTAGATGATC-AAAATGAAATTTACTAATACTTGGATGATC
1 ATTTTGTAACTTTTCATGGTTAGATGACCAAAAATGAAATTTAATAATACTTGGATGATC
* * * *
10856 ATTTTGTAACTTTTCATTGTTAGGTTACCAAAAATGAAATTTAATAATAGTTGG
1 ATTTTGTAACTTTTCATGGTTAGATGACCAAAAATGAAATTTAATAATACTTGG
10910 GTGACTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 25 0.53
60 22 0.47
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (60 bp):
ATTTTGTAACTTTTCATGGTTAGATGACCAAAAATGAAATTTAATAATACTTGGATGATC
Found at i:11345 original size:22 final size:21
Alignment explanation
Indices: 11311--11357 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
11301 TAAATAAATT
11311 AAAATTATGAAAATATTCA-AAA
1 AAAATTATGAAAA-A-TCATAAA
11333 AAAATTTAT-AAAAATCATAAA
1 AAAA-TTATGAAAAATCATAAA
11354 AAAA
1 AAAA
11358 ATTAGCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.13
21 8 0.35
22 8 0.35
23 4 0.17
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATTATGAAAAATCATAAA
Found at i:16525 original size:17 final size:17
Alignment explanation
Indices: 16490--16531 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
16480 GGAAAAAGTA
*
16490 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
16508 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
16525 GTTAAAG
1 GTTAAAG
16532 GTCAATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:16531 original size:24 final size:24
Alignment explanation
Indices: 16504--16551 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16494 CAAGAATATG
* * *
16504 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAAATGAAAGGTT
*
16528 AAAGGTCAATGAAAATGAAAGGTT
1 AAAGGTCAAAGAAAATGAAAGGTT
16552 GAACATCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (24 bp):
AAAGGTCAAAGAAAATGAAAGGTT
Found at i:21915 original size:18 final size:17
Alignment explanation
Indices: 21864--21906 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
21854 GAAAAAAATA
* *
21864 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGGAAG
21882 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGGAAG
21899 GTTAAAGA
1 GTTAAAGA
21907 TCAATGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGGAAG
Found at i:23143 original size:12 final size:12
Alignment explanation
Indices: 23128--23215 Score: 76
Period size: 12 Copynumber: 7.6 Consensus size: 12
23118 GTTCAATTAT
*
23128 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
23140 ATGTTCGTTTA-
1 ATGTTCGTGAAC
23151 ATGTTCGTGAAC
1 ATGTTCGTGAAC
**
23163 ATGTTCGTTTA-
1 ATGTTCGTGAAC
23174 ATGTTCGTGAAC
1 ATGTTCGTGAAC
*
23186 ATGTTCGAT-TA-
1 ATGTTCG-TGAAC
*
23197 ATGTCCGTGAAC
1 ATGTTCGTGAAC
23209 ATGTTCG
1 ATGTTCG
23216 ATTAAGTTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
10 1 0.02
11 25 0.43
12 31 0.53
13 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:23156 original size:11 final size:11
Alignment explanation
Indices: 23140--23200 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
23130 GTTCATGAAC
23140 ATGTTCGTTTA
1 ATGTTCGTTTA
**
23151 ATGTTCGTGAA
1 ATGTTCGTTTA
23162 CATGTTCGTTTA
1 -ATGTTCGTTTA
**
23174 ATGTTCGTGAA
1 ATGTTCGTTTA
*
23185 CATGTTCGATTA
1 -ATGTTCGTTTA
23197 ATGT
1 ATGT
23201 CCGTGAACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 22 0.56
12 17 0.44
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.44
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:23161 original size:23 final size:23
Alignment explanation
Indices: 23105--23238 Score: 171
Period size: 23 Copynumber: 5.8 Consensus size: 23
23095 TTATTAACAT
* *
23105 TGTTCGTGAACGTGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
23129 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
23152 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
23175 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
*
23198 TGTCCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
23221 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
23239 TGAACATTAA
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
22 2 0.02
23 79 0.80
24 18 0.18
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:23248 original size:23 final size:23
Alignment explanation
Indices: 23204--23249 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
23194 TTAATGTCCG
* *
23204 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
23227 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
23250 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:24913 original size:25 final size:24
Alignment explanation
Indices: 24864--24915 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
24854 TATTGTTGTT
*
24864 ATTGATACATTCTATTAGATCTGA
1 ATTGATACATTCTATTACATCTGA
*
24888 ATTG-TACATTCGTAATTACATGTGA
1 ATTGATACATTC-T-ATTACATCTGA
24913 ATT
1 ATT
24916 ATATATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 5 0.21
25 12 0.50
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (24 bp):
ATTGATACATTCTATTACATCTGA
Found at i:25173 original size:6 final size:6
Alignment explanation
Indices: 25162--25229 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
25152 AAACTGCATT
* * *
25162 TGTATC TGTATC TGTATC TGTATT TGTATC TG-AGTC TATATC TATATC
1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTA-TC TGTATC TGTATC
** * *
25210 CATATT TGTATT TGTATC TG
1 TGTATC TGTATC TGTATC TG
25230 ATCATCTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
5 1 0.02
6 50 0.96
7 1 0.02
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (6 bp):
TGTATC
Found at i:25203 original size:24 final size:24
Alignment explanation
Indices: 25159--25204 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25149 AGAAAACTGC
*
25159 ATTTGTATCTGTATCTGTATCTGT
1 ATTTGTATCTGTATCTATATCTGT
25183 ATTTGTATCTG-AGTCTATATCT
1 ATTTGTATCTGTA-TCTATATCT
25205 ATATCCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.20, C:0.13, G:0.15, T:0.52
Consensus pattern (24 bp):
ATTTGTATCTGTATCTATATCTGT
Found at i:26660 original size:16 final size:16
Alignment explanation
Indices: 26639--26671 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
26629 TTCTCCACCC
26639 AAACCCAATCAAATAT
1 AAACCCAATCAAATAT
*
26655 AAACCCAATCCAATAT
1 AAACCCAATCAAATAT
26671 A
1 A
26672 TATATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACCCAATCAAATAT
Found at i:26674 original size:2 final size:2
Alignment explanation
Indices: 26667--26691 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26657 ACCCAATCCA
26667 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26692 AACCCAAGTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32465 original size:21 final size:21
Alignment explanation
Indices: 32441--32487 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
32431 CAGTTCTTCT
*
32441 GATACAAGTGA-GACATCTACC
1 GATACAAGTCATG-CATCTACC
*
32462 GATACAAGTCATGCTTCTACC
1 GATACAAGTCATGCATCTACC
32483 GATAC
1 GATAC
32488 TAAAAACTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
GATACAAGTCATGCATCTACC
Done.