Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014653.1 Kokia drynarioides strain JFW-HI SEQ_129692, 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: 120143
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:329 original size:41 final size:41
Alignment explanation
Indices: 234--392 Score: 176
Period size: 41 Copynumber: 3.9 Consensus size: 41
224 TGCTCTGACC
* * *
234 TTTAGCGACGCTTTCCCATAAGCGTCGTTAATGCTCTCAATT
1 TTTAGCGGCGCTTTCCCACAAGCGTCGCTAATGCTCT-AATT
* *
276 TTTAGCAGCGCTTTTCCACAAGCGTCGCTAATGCTCTAATT
1 TTTAGCGGCGCTTTCCCACAAGCGTCGCTAATGCTCTAATT
* * * **
317 TTTAGCGGCGCTTTTCCACAAACG-CTTCTAATGCTCTAACC
1 TTTAGCGGCGCTTTCCCACAAGCGTC-GCTAATGCTCTAATT
* * *
358 TTTAGTGGCGCTTTCCCATAAGCGTCACTAATGCT
1 TTTAGCGGCGCTTTCCCACAAGCGTCGCTAATGCT
393 TTACCTTTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
40 1 0.01
41 66 0.66
42 33 0.33
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGCTTTCCCACAAGCGTCGCTAATGCTCTAATT
Found at i:3957 original size:19 final size:19
Alignment explanation
Indices: 3933--3971 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3923 ATTTCTATTG
3933 AGTAAAAATAAAAAGGACC
1 AGTAAAAATAAAAAGGACC
*
3952 AGTAAAAATAAAAGGGACC
1 AGTAAAAATAAAAAGGACC
3971 A
1 A
3972 AAGTGGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.18, T:0.10
Consensus pattern (19 bp):
AGTAAAAATAAAAAGGACC
Found at i:11580 original size:21 final size:21
Alignment explanation
Indices: 11555--11594 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11545 TAGAGTAGTA
11555 TCGGTAGTCTGAATAATTGTG
1 TCGGTAGTCTGAATAATTGTG
11576 TCGGTAGTCTGAATAATTG
1 TCGGTAGTCTGAATAATTG
11595 GTTACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.10, G:0.28, T:0.38
Consensus pattern (21 bp):
TCGGTAGTCTGAATAATTGTG
Found at i:16814 original size:13 final size:13
Alignment explanation
Indices: 16796--16823 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
16786 AGTCTCAATG
16796 CATTATTATTGTT
1 CATTATTATTGTT
16809 CATTATTATTGTT
1 CATTATTATTGTT
16822 CA
1 CA
16824 AGCCCATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (13 bp):
CATTATTATTGTT
Found at i:20146 original size:23 final size:23
Alignment explanation
Indices: 20089--20139 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
20079 CACTCAAGAC
20089 CCTAAACCCAAAAAAAACCTTAATT
1 CCTAAA-CC-AAAAAAACCTTAATT
20114 CCTAAACCAAAAAAACC-TAA-T
1 CCTAAACCAAAAAAACCTTAATT
20135 CCTAA
1 CCTAA
20140 TAACCAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 9 0.35
24 2 0.08
25 6 0.23
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (23 bp):
CCTAAACCAAAAAAACCTTAATT
Found at i:20417 original size:14 final size:13
Alignment explanation
Indices: 20395--20437 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
20385 TTAAAGTGAT
*
20395 TAAATTAAAAAAA
1 TAAAATAAAAAAA
20408 TAAAAATAAAAATAA
1 T-AAAATAAAAA-AA
20423 TAAAATAAAATAAA
1 TAAAATAAAA-AAA
20437 T
1 T
20438 TTTATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 21 0.81
15 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:23390 original size:22 final size:24
Alignment explanation
Indices: 23365--23411 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
23355 ATATTAATTT
23365 ATTTTTATAT-TAGATAA-ATATA
1 ATTTTTATATGTAGATAATATATA
* *
23387 ATTTTTTTATGTATATAATATATA
1 ATTTTTATATGTAGATAATATATA
23411 A
1 A
23412 ACATGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTTTTATATGTAGATAATATATA
Found at i:24168 original size:13 final size:14
Alignment explanation
Indices: 24150--24179 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
24140 AATTCACATT
24150 TAAAAGTAAAAA-A
1 TAAAAGTAAAAATA
24163 TAAAAGTAAAAATA
1 TAAAAGTAAAAATA
24177 TAA
1 TAA
24180 GTTGTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
TAAAAGTAAAAATA
Found at i:26718 original size:28 final size:28
Alignment explanation
Indices: 26664--26718 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
26654 TTTTCGTAAC
* *
26664 GAAGCCTTTATGGCTATCTCAGTTAAAG
1 GAAGCCTTTATGGCAATCTCAGCTAAAG
* *
26692 GAAGCCTTTGTGGCAATCTCTGCTAAA
1 GAAGCCTTTATGGCAATCTCAGCTAAA
26719 AAGAAAGTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (28 bp):
GAAGCCTTTATGGCAATCTCAGCTAAAG
Found at i:27607 original size:20 final size:20
Alignment explanation
Indices: 27584--27650 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
27574 TTAAGCCACT
27584 AGTAATGCAGATAAACTGCC
1 AGTAATGCAGATAAACTGCC
* * * *
27604 AGTAGTGCAGACAAGCTGCA
1 AGTAATGCAGATAAACTGCC
* * *
27624 AGTAGTGCAAATAAATTGCC
1 AGTAATGCAGATAAACTGCC
*
27644 AATAATG
1 AGTAATG
27651 TGGTCAAACC
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (20 bp):
AGTAATGCAGATAAACTGCC
Found at i:27870 original size:27 final size:27
Alignment explanation
Indices: 27839--27899 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
27829 ACATGCAATT
*
27839 TACACATTATCTTGATGTATCAAAACA
1 TACACATTATCTCGATGTATCAAAACA
*
27866 TACACATTATCTCGATGTATCAAGACA
1 TACACATTATCTCGATGTATCAAAACA
27893 T-CACATT
1 TACACATT
27900 TTAATGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
TACACATTATCTCGATGTATCAAAACA
Found at i:32175 original size:29 final size:29
Alignment explanation
Indices: 32113--32169 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
32103 TGACAGTGTT
*
32113 TATCTCTGTTAAAAGGAAGCCTTTGTGGC
1 TATCTCAGTTAAAAGGAAGCCTTTGTGGC
*
32142 TATCTCAGTTAAAAGGATGCCTTTGTGG
1 TATCTCAGTTAAAAGGAAGCCTTTGTGG
32170 TGATCTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (29 bp):
TATCTCAGTTAAAAGGAAGCCTTTGTGGC
Found at i:38204 original size:18 final size:18
Alignment explanation
Indices: 38177--38211 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38167 CAGGGAGATC
* *
38177 AACAAGGAAAAATGAAAA
1 AACAAAGAAAAACGAAAA
38195 AACAAAGAAAAACGAAA
1 AACAAAGAAAAACGAAA
38212 GGGAGAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (18 bp):
AACAAAGAAAAACGAAAA
Found at i:56609 original size:17 final size:18
Alignment explanation
Indices: 56587--56626 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
56577 AGATTGCATA
56587 CATTTT-TATTGTCATCG
1 CATTTTATATTGTCATCG
* *
56604 CATTTTATTTTGTCATTG
1 CATTTTATATTGTCATCG
56622 CATTT
1 CATTT
56627 CTTTTGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (18 bp):
CATTTTATATTGTCATCG
Found at i:57239 original size:6 final size:6
Alignment explanation
Indices: 57228--57271 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
57218 ATGTTGAATG
57228 AGAAAA AG-AAA AGAAAA AGAGAAA AGAGAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGA-AAA AGAAAA AGAAAA A
57272 TTGCTATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 18 0.50
7 13 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:57259 original size:20 final size:19
Alignment explanation
Indices: 57227--57271 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
57217 AATGTTGAAT
57227 GAGAAAAAGAAAAGAAAAA
1 GAGAAAAAGAAAAGAAAAA
57246 GAGAAAAGAGAAAAGAAAAA
1 GAGAAAA-AGAAAAGAAAAA
57266 GA-AAAA
1 GAGAAAA
57272 TTGCTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (19 bp):
GAGAAAAAGAAAAGAAAAA
Found at i:64962 original size:13 final size:12
Alignment explanation
Indices: 64935--64967 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
64925 GCCAATTTGG
64935 TTAG-TTTTATT
1 TTAGTTTTTATT
64946 TTAGTTTTTAGTT
1 TTAGTTTTTA-TT
64959 TTAGTTTTT
1 TTAGTTTTT
64968 GATGCAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 5 0.25
13 11 0.55
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (12 bp):
TTAGTTTTTATT
Found at i:84321 original size:46 final size:47
Alignment explanation
Indices: 84253--84343 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 47
84243 GGTTCATTCC
* **
84253 CTTGCTTTCTGCCTTGGCTTTGCCCTTCCTCGTCTTGCTTGTTTTAG
1 CTTGCTTTCTGCCTTGGCTTTGCCCTTCCACCACTTGCTTGTTTTAG
*
84300 CTTGCTTTTTG-CTTGGCTTTGCCCTTCCACCACTTGCTTGTTTT
1 CTTGCTTTCTGCCTTGGCTTTGCCCTTCCACCACTTGCTTGTTTT
84344 CGCCTCTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 30 0.75
47 10 0.25
ACGTcount: A:0.03, C:0.30, G:0.18, T:0.49
Consensus pattern (47 bp):
CTTGCTTTCTGCCTTGGCTTTGCCCTTCCACCACTTGCTTGTTTTAG
Found at i:96003 original size:18 final size:18
Alignment explanation
Indices: 95960--96003 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
95950 GCAGGCACAT
* *
95960 CATGATCAGATGTAGTCG
1 CATGCTCAGATGTAGTCA
*
95978 CATACTCAGATGTAGTCA
1 CATGCTCAGATGTAGTCA
95996 CATGCTCA
1 CATGCTCA
96004 TATGCAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (18 bp):
CATGCTCAGATGTAGTCA
Found at i:107263 original size:46 final size:47
Alignment explanation
Indices: 107198--107291 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 47
107188 TGCATTTAGG
* *
107198 TTGTAGTTTTTATTTTGCCATAATATTGTTT-TGTTGTCATGACATTT
1 TTGTAGTTTTCATTTTGCCATAATATTATTTCT-TTGTCATGACATTT
*
107245 TTGTAG-TTTCATTTTGCCATGATATTATTTCTTTGTCATGACATTT
1 TTGTAGTTTTCATTTTGCCATAATATTATTTCTTTGTCATGACATTT
107291 T
1 T
107292 CATATTTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 36 0.84
47 7 0.16
ACGTcount: A:0.19, C:0.11, G:0.14, T:0.56
Consensus pattern (47 bp):
TTGTAGTTTTCATTTTGCCATAATATTATTTCTTTGTCATGACATTT
Found at i:117694 original size:12 final size:12
Alignment explanation
Indices: 117672--117710 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
117662 AGTTAATTTG
117672 AAAGCATAAAATA
1 AAAG-ATAAAATA
117685 AAAGATAAAATA
1 AAAGATAAAATA
* *
117697 AAATAGAAAATA
1 AAAGATAAAATA
117709 AA
1 AA
117711 GAAAAAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAGATAAAATA
Found at i:117716 original size:17 final size:17
Alignment explanation
Indices: 117677--117710 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
117667 ATTTGAAAGC
117677 ATAAAATAAAAGATAAA
1 ATAAAATAAAAGATAAA
117694 ATAAAATAGAAA-ATAAA
1 ATAAAATA-AAAGATAAA
117711 GAAAAAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAATAAAAGATAAA
Found at i:119919 original size:15 final size:15
Alignment explanation
Indices: 119877--119944 Score: 91
Period size: 15 Copynumber: 4.4 Consensus size: 15
119867 AGTCTGGTTT
119877 GCTGTAATGGAATAGA
1 GCTGT-ATGGAATAGA
*
119893 GTTGTAATGGAATAGA
1 GCTGT-ATGGAATAGA
*
119909 GCTGTATGGAATAGG
1 GCTGTATGGAATAGA
*
119924 GCTGTATGGAATAGG
1 GCTGTATGGAATAGA
119939 GCTGTA
1 GCTGTA
119945 ATCAGTAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
15 30 0.61
16 19 0.39
ACGTcount: A:0.31, C:0.06, G:0.35, T:0.28
Consensus pattern (15 bp):
GCTGTATGGAATAGA
Found at i:120020 original size:44 final size:46
Alignment explanation
Indices: 119929--120022 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
119919 ATAGGGCTGT
* *
119929 ATGGAATAGGGCTGTAATCAGTAATTCAGTTGTTTGGTTGAATGAA
1 ATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTGGTAGAATGAA
*
119975 ATGGAATAGAGCTGTAAT-AGT-ATTC-TTCTGTTTGGTAGAATGAA
1 ATGGAATAGAGCTGTAATCAGTAATTCAGT-TGTTTGGTAGAATGAA
120019 ATGG
1 ATGG
120023 TGTTGTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 3 0.07
46 17 0.39
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (46 bp):
ATGGAATAGAGCTGTAATCAGTAATTCAGTTGTTTGGTAGAATGAA
Done.