Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009645.1 Kokia drynarioides strain JFW-HI SEQ_124363, 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: 86631
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1141 original size:19 final size:20
Alignment explanation
Indices: 1102--1141 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1092 GATCATTAGG
* *
1102 AACATAATATCTCCCTTGAA
1 AACATAAAATCTCCCTCGAA
1122 AACATAAAAT-TCCCTCGAA
1 AACATAAAATCTCCCTCGAA
1141 A
1 A
1142 TTAATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (20 bp):
AACATAAAATCTCCCTCGAA
Found at i:6715 original size:15 final size:15
Alignment explanation
Indices: 6675--6717 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6665 AAACCCTATA
*
6675 ACACTTAGCCCAA-T
1 ACACTAAGCCCAATT
*
6689 ACACTAAACCCAATT
1 ACACTAAGCCCAATT
*
6704 ACCCTAAGCCCAAT
1 ACACTAAGCCCAAT
6718 AAGCCCAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.40, C:0.37, G:0.05, T:0.19
Consensus pattern (15 bp):
ACACTAAGCCCAATT
Found at i:11146 original size:21 final size:21
Alignment explanation
Indices: 11107--11146 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11097 TTTTATATGG
*
11107 AATTTTGAATTGAAGAGTTTT
1 AATTTTGAATTGAAAAGTTTT
11128 AATTATTGAATT-AAAAGTT
1 AATT-TTGAATTGAAAAGTT
11147 AGTATAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (21 bp):
AATTTTGAATTGAAAAGTTTT
Found at i:12320 original size:16 final size:16
Alignment explanation
Indices: 12299--12330 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12289 AGTAATTTTT
12299 ATGTTAAAGGACTAAA
1 ATGTTAAAGGACTAAA
*
12315 ATGTTAAAGGAGTAAA
1 ATGTTAAAGGACTAAA
12331 TTTGTAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGACTAAA
Found at i:13036 original size:53 final size:53
Alignment explanation
Indices: 12794--13014 Score: 334
Period size: 53 Copynumber: 4.2 Consensus size: 53
12784 TAAATATAAA
* *
12794 AGGTCTAATGATTTTGTGTCATCGTGAGTATATGAATCCTATTATGGATTAAC
1 AGGTCTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAC
* * * *
12847 AGGTCCGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTATGAATCAAC
1 AGGTCTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAC
* * *
12900 AGGTCTGATGATTTTGTGTCATCGTGAGTATAAGAATCCTATTACAGATTAAT
1 AGGTCTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAC
* *
12953 AGGTTTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAA
1 AGGTCTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAC
*
13006 AAGTCTGAT
1 AGGTCTGAT
13015 AACTACGTGT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 151 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (53 bp):
AGGTCTGATGATTTTGTGTCATCGTGAGTATATGAATCCTATTACGGATTAAC
Found at i:18340 original size:26 final size:25
Alignment explanation
Indices: 18311--18361 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
18301 TTAAAAGTTT
*
18311 TTAACCCTTTTACTTCGTTTTTTAAA
1 TTAACCCTTTTA-TTCCTTTTTTAAA
**
18337 TTAATTCTTTTATTCCTTTTTTAAA
1 TTAACCCTTTTATTCCTTTTTTAAA
18362 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.59
Consensus pattern (25 bp):
TTAACCCTTTTATTCCTTTTTTAAA
Found at i:18948 original size:107 final size:106
Alignment explanation
Indices: 18807--19009 Score: 257
Period size: 107 Copynumber: 1.9 Consensus size: 106
18797 AGTAATGTTA
* *
18807 TTTTATTTAAGAAATTCGAAAAATTATGCCCTAACGTATTGAGTATGATTTTT-TGTT-GACCTT
1 TTTTATTTAAGAAACTCGAAAAATTATGCCCTAACGTATTGAGTATGATTTTTCT-TTAAACC-T
18870 ACATAATTAAACATCCTATTTTAAAAATCGATAAATATTTAATG
64 ACATAATTAAACATCCTATTTT-AAAATCGATAAATATTTAATG
* * * * * * *
18914 TTTTTTTTAAGAAACTCGAGAAATTATGCTCTAACGTGTTGGGTATGGTTTTTCTTTAAACCTAT
1 TTTTATTTAAGAAACTCGAAAAATTATGCCCTAACGTATTGAGTATGATTTTTCTTTAAACCTAC
* * *
18979 TTAATTGAAGATCCTATTTTAAAATCGATAA
66 ATAATTAAACATCCTATTTTAAAATCGATAA
19010 GTGTTCTTTA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
106 11 0.13
107 67 0.82
108 4 0.05
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (106 bp):
TTTTATTTAAGAAACTCGAAAAATTATGCCCTAACGTATTGAGTATGATTTTTCTTTAAACCTAC
ATAATTAAACATCCTATTTTAAAATCGATAAATATTTAATG
Found at i:28500 original size:19 final size:18
Alignment explanation
Indices: 28461--28500 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
28451 TCATTTTTAA
*
28461 TATATTTTTAAATGATTT
1 TATATTTTTAAATGATGT
*
28479 TATATTATTTAAATTATGT
1 TATATT-TTTAAATGATGT
28498 TAT
1 TAT
28501 CGTCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATTTTTAAATGATGT
Found at i:45412 original size:21 final size:20
Alignment explanation
Indices: 45386--45434 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
45376 GTTATGGCTA
45386 CATCTGATTCTGGTT-TGGATG
1 CATCTGATT-T-GTTGTGGATG
*
45407 CATCTGGCTTTGTTGTGGATG
1 CATCT-GATTTGTTGTGGATG
45428 CATCTGA
1 CATCTGA
45435 GTGTGCTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.14, C:0.16, G:0.29, T:0.41
Consensus pattern (20 bp):
CATCTGATTTGTTGTGGATG
Found at i:48637 original size:40 final size:40
Alignment explanation
Indices: 48588--48666 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
48578 TCTTTAGACG
48588 ATCTAATGCT-TCATAGACTCATAAGTCTTCCTTTTAAACA
1 ATCTAATGCTCT-ATAGACTCATAAGTCTTCCTTTTAAACA
* * *
48628 ATCTTATGCTCTATCGAGTCATAAGTCTTCCTTTTAAAC
1 ATCTAATGCTCTATAGACTCATAAGTCTTCCTTTTAAAC
48667 GTAATCTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (40 bp):
ATCTAATGCTCTATAGACTCATAAGTCTTCCTTTTAAACA
Found at i:48725 original size:43 final size:43
Alignment explanation
Indices: 48606--48838 Score: 192
Period size: 43 Copynumber: 5.5 Consensus size: 43
48596 CTTCATAGAC
* * *
48606 TCATAAGTCTTCCTTTTAAACA-A-TCTTATGCTC-TATCGAG
1 TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATTTCGAG
* * * **
48646 TCATAAGTCTTCCTTTTAAACGTAATCTCACACTCATTTCTGAG
1 TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATTTC-GAG
*
48690 TCATGAGTCTTCC-TTTAAACATATTCTCATTCTCATTGT-GAG
1 TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATT-TCGAG
* * * *
48732 ACATGAGTCTTCC-TTT-AATATATCCTCATGCTCATTTCAAG
1 TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATTTCGAG
* * * * * * *
48773 TCACGAGTCTTCCATTCATACAAATTCTCATGCTCAATCCGAG
1 TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATTTCGAG
* * *
48816 ACATGAATCTTCCTTTTATACAT
1 TCATGAGTCTTCCTTTTAAACAT
48839 CAAGTGACTC
Statistics
Matches: 154, Mismatches: 31, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
40 22 0.14
41 31 0.20
42 27 0.18
43 58 0.38
44 16 0.10
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (43 bp):
TCATGAGTCTTCCTTTTAAACATATTCTCATGCTCATTTCGAG
Found at i:48766 original size:84 final size:84
Alignment explanation
Indices: 48678--48831 Score: 202
Period size: 84 Copynumber: 1.8 Consensus size: 84
48668 TAATCTCACA
* * * * * * ** *
48678 CTCATTTCTGAGTCATGAGTCTTCC-TTTAAACATATTCTCATTCTCATTGTGAGACATGAGTCT
1 CTCATTTC-AAGTCACGAGTCTTCCATTCAAACAAATTCTCATGCTCAATCCGAGACATGAATCT
48742 TCCTTTAATATATCCTCATG
65 TCCTTTAATATATCCTCATG
*
48762 CTCATTTCAAGTCACGAGTCTTCCATTCATACAAATTCTCATGCTCAATCCGAGACATGAATCTT
1 CTCATTTCAAGTCACGAGTCTTCCATTCAAACAAATTCTCATGCTCAATCCGAGACATGAATCTT
48827 CCTTT
66 CCTTT
48832 TATACATCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
83 14 0.24
84 45 0.76
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (84 bp):
CTCATTTCAAGTCACGAGTCTTCCATTCAAACAAATTCTCATGCTCAATCCGAGACATGAATCTT
CCTTTAATATATCCTCATG
Found at i:51152 original size:25 final size:25
Alignment explanation
Indices: 51115--51346 Score: 200
Period size: 25 Copynumber: 9.2 Consensus size: 25
51105 GAATTCTGAT
* *
51115 TCTGGCTCATAAGAGCG-TATTTTTG
1 TCTGGCTCGTAAGAGCGATA-TTCTG
*
51140 TTTGGCTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * *
51165 TCTGGCTCGTAAGAGTGAGATTTTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* *
51190 ATTCTGGCTCATAAGAGCGATATTCTA
1 --TCTGGCTCGTAAGAGCGATATTCTG
* * **
51217 TCTGGCACATAAGAGTAATATT-TAG
1 TCTGGCTCGTAAGAGCGATATTCT-G
* *
51242 TCTGGCTCGTATGAGCGATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTG
*
51267 TCTGGCTCGTATA-AGCGATATTCTA
1 TCTGGCTCGTA-AGAGCGATATTCTG
* **
51292 TTTGGCTCGTTTGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * * *
51317 TTTGACACGTATGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
51342 TCTGG
1 TCTGG
51347 GCTTGTTGGA
Statistics
Matches: 168, Mismatches: 32, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
24 1 0.01
25 144 0.86
26 3 0.02
27 20 0.12
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTCTG
Found at i:51238 original size:77 final size:77
Alignment explanation
Indices: 51107--51297 Score: 212
Period size: 77 Copynumber: 2.5 Consensus size: 77
51097 AGACGAAGGA
* * * * *
51107 ATTCTGATTCTGGCTCATAAGAGCG-TATTTTTGTTTGGCTCGTAAGAGCGATATTCT-GTCTGG
1 ATTCTGATTCTGGCTCATAAGAGCGATA-TTCTATTTGGCACATAAGAGCAATATT-TAGTCTGG
*
51170 CTCGTAAGAGTGAG
64 CTCGTAAGAGCGAG
* * *
51184 ATTTTGATTCTGGCTCATAAGAGCGATATTCTATCTGGCACATAAGAGTAATATTTAGTCTGGCT
1 ATTCTGATTCTGGCTCATAAGAGCGATATTCTATTTGGCACATAAGAGCAATATTTAGTCTGGCT
* *
51249 CGTATGAGCGAT
66 CGTAAGAGCGAG
*
51261 ATTCT-A-TCTGGCTCGTATA-AGCGATATTCTATTTGGC
1 ATTCTGATTCTGGCTCATA-AGAGCGATATTCTATTTGGC
51298 TCGTTTGAGC
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
75 27 0.28
76 3 0.03
77 65 0.67
78 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (77 bp):
ATTCTGATTCTGGCTCATAAGAGCGATATTCTATTTGGCACATAAGAGCAATATTTAGTCTGGCT
CGTAAGAGCGAG
Found at i:51313 original size:75 final size:75
Alignment explanation
Indices: 51115--51346 Score: 236
Period size: 75 Copynumber: 3.1 Consensus size: 75
51105 GAATTCTGAT
* * *
51115 TCTGGCTCATAAGAGCG-TATTTTTGTTTGGCTCGTAAGAGCGATATTCTGTCTGGCTCGTAAGA
1 TCTGGCTCATAAGAGCGATA-TTCTATTTGGCTCGTAAGAGCGATATTCTGTCTGGCTCGTATGA
* * *
51179 GTGAGATTTTGA
65 GCGATATTCT-A
* * * **
51191 TTCTGGCTCATAAGAGCGATATTCTATCTGGCACATAAGAGTAATATT-TAGTCTGGCTCGTATG
1 -TCTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATATTCT-GTCTGGCTCGTATG
51255 AGCGATATTCTA
64 AGCGATATTCTA
* ** * * *
51267 TCTGGCTCGTATA-AGCGATATTCTATTTGGCTCGTTTGAGCGATATTCTGTTTGACACGTATGA
1 TCTGGCTCATA-AGAGCGATATTCTATTTGGCTCGTAAGAGCGATATTCTGTCTGGCTCGTATGA
*
51331 GCGATATTCTG
65 GCGATATTCTA
51342 TCTGG
1 TCTGG
51347 GCTTGTTGGA
Statistics
Matches: 128, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
75 64 0.50
76 4 0.03
77 58 0.45
78 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (75 bp):
TCTGGCTCATAAGAGCGATATTCTATTTGGCTCGTAAGAGCGATATTCTGTCTGGCTCGTATGAG
CGATATTCTA
Found at i:61056 original size:6 final size:6
Alignment explanation
Indices: 61042--61081 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
61032 TGGAAACCGA
*
61042 CTCTGC CTCTAC CTCTAC CTCTAC CTCTAC CTCTAC CTCT
1 CTCTAC CTCTAC CTCTAC CTCTAC CTCTAC CTCTAC CTCT
61082 TTATTTCCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.12, C:0.50, G:0.03, T:0.35
Consensus pattern (6 bp):
CTCTAC
Found at i:76445 original size:18 final size:17
Alignment explanation
Indices: 76416--76453 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
76406 ATTTTTAATA
*
76416 TATATTTTAAATTATTT
1 TATATTTTAAATTATGT
76433 TATATTATTAAATTATGT
1 TATATT-TTAAATTATGT
76451 TAT
1 TAT
76454 CATCCTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATTTTAAATTATGT
Found at i:83596 original size:18 final size:17
Alignment explanation
Indices: 83558--83596 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
83548 CATTTTTACT
*
83558 TTATATTTTAAAATATT
1 TTATATTTTAAAATATG
*
83575 TTATATTATTAAATTATG
1 TTATATT-TTAAAATATG
83593 TTAT
1 TTAT
83597 CGTCTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTATATTTTAAAATATG
Done.