Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003360.1 Kokia drynarioides strain JFW-HI SEQ_116081, 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: 102746
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2399 original size:19 final size:20
Alignment explanation
Indices: 2361--2403 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2351 ATTTAATATA
*
2361 TAATAAAATAAATGAAATTT
1 TAATAAAATAAATAAAATTT
*
2381 TAATAAAA-AATTAAAATTT
1 TAATAAAATAAATAAAATTT
2400 TAAT
1 TAAT
2404 TAATTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAATAAAATAAATAAAATTT
Found at i:3403 original size:15 final size:15
Alignment explanation
Indices: 3383--3425 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
3373 TGGCACCAAA
3383 AGCTGAGAAGAAGCC
1 AGCTGAGAAGAAGCC
*
3398 AGCTGAGAAAAAGCC
1 AGCTGAGAAGAAGCC
* *
3413 AGCGGAGGAGAAG
1 AGCTGAGAAGAAG
3426 AAGACGGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.37, T:0.05
Consensus pattern (15 bp):
AGCTGAGAAGAAGCC
Found at i:13725 original size:23 final size:23
Alignment explanation
Indices: 13694--13819 Score: 128
Period size: 23 Copynumber: 5.4 Consensus size: 23
13684 AGCACATCTC
*
13694 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTC--TTATTAGCACTTTGT
* *
13719 GTGCTCTCTGACTAGCACTTTGT
1 GTGCTCTCTTATTAGCACTTTGT
*
13742 GTGCTCTCTTACTAGCACTTTGT
1 GTGCTCTCTTATTAGCACTTTGT
* * *
13765 GTTCTCTCTAATTAGTACTTTGT
1 GTGCTCTCTTATTAGCACTTTGT
* * *
13788 GTACTCTC-TATTTAGCAGTGTGT
1 GTGCTCTCTTA-TTAGCACTTTGT
13811 GTGCTCTCT
1 GTGCTCTCT
13820 GTTGCCCAGC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.01
23 76 0.89
25 8 0.09
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (23 bp):
GTGCTCTCTTATTAGCACTTTGT
Found at i:13804 original size:69 final size:68
Alignment explanation
Indices: 13731--13865 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 68
13721 GCTCTCTGAC
* *
13731 TAGCACTTTGTGTGCTCTC-TT-ACTAGCACTT-TGTGTTCTCTCTAATTAGTACTTTGTGTACT
1 TAGCACTGTGTGTGCTCTCGTTGACCAGCACTTATGTG--CTCTCT-ATTAGTACTTTG-GTACT
13793 CTCTATT
62 CTCTATT
* *
13800 TAGCAGTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTATTAGTACTTTGGTACTCTC
1 TAGCACTGTGTGTGCTCTC-GTTGACCAGCACTTATGTGCTCTCTATTAGTACTTTGGTACTCTC
13865 T
65 T
13866 GTTTGTTTCG
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
69 26 0.45
70 12 0.21
71 8 0.14
72 8 0.14
73 4 0.07
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (68 bp):
TAGCACTGTGTGTGCTCTCGTTGACCAGCACTTATGTGCTCTCTATTAGTACTTTGGTACTCTCT
ATT
Found at i:22321 original size:35 final size:35
Alignment explanation
Indices: 22267--22349 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
22257 TTGGGAAGTA
22267 ACTTATTA-GCTCTAATCCTCATATTTTGGTTAGGC
1 ACTT-TTAGGCTCTAATCCTCATATTTTGGTTAGGC
22302 ACTTTTAGGCTCTAATCCTCATATTTTGGTTAGGC
1 ACTTTTAGGCTCTAATCCTCATATTTTGGTTAGGC
22337 ACTTTTAGGCTCT
1 ACTTTTAGGCTCT
22350 CTAAGCTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 3 0.06
35 44 0.94
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (35 bp):
ACTTTTAGGCTCTAATCCTCATATTTTGGTTAGGC
Found at i:24371 original size:31 final size:30
Alignment explanation
Indices: 24238--24373 Score: 87
Period size: 31 Copynumber: 4.5 Consensus size: 30
24228 GAATCACTAT
*
24238 TTGGGGCCTGAACTTGGTAATTGTTCCTATA
1 TTGGGGCCTGAACTTGGTAATTGTTCCCA-A
** ** * * *
24269 TTGTAGTTTGAACTAGGCAATTGTTCTCAA
1 TTGGGGCCTGAACTTGGTAATTGTTCCCAA
* ** ** *
24299 TTGGGGCCTAAACTTTTTTTTTG-TCCAAA
1 TTGGGGCCTGAACTTGGTAATTGTTCCCAA
* *
24328 TT-AGTCCTTGAACTTGGTAATTGTTCCCACA
1 TTGGGGCC-TGAACTTGGTAATTGTTCCCA-A
24359 TTGGGGCCTGAACTT
1 TTGGGGCCTGAACTT
24374 TAAGGTTTTC
Statistics
Matches: 70, Mismatches: 31, Indels: 8
0.64 0.28 0.07
Matches are distributed among these distances:
28 3 0.04
29 16 0.23
30 17 0.24
31 31 0.44
32 3 0.04
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (30 bp):
TTGGGGCCTGAACTTGGTAATTGTTCCCAA
Found at i:26848 original size:18 final size:17
Alignment explanation
Indices: 26815--26850 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
26805 AAAGTTTAGG
26815 ATTTAAAATTTTTAATT
1 ATTTAAAATTTTTAATT
*
26832 ATTTAAATTTATTTAATT
1 ATTTAAAATT-TTTAATT
26850 A
1 A
26851 AAGATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAAATTTTTAATT
Found at i:28157 original size:24 final size:25
Alignment explanation
Indices: 28114--28163 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
28104 AAAGAAATTG
*
28114 TTAAAAAAATAATTGCTCAATTTTT
1 TTAAAAAAATAATTGCTCAAATTTT
28139 TTAAAAAAGATAA-TG-TCAAATTTT
1 TTAAAAAA-ATAATTGCTCAAATTTT
28163 T
1 T
28164 GGTTTGCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (25 bp):
TTAAAAAAATAATTGCTCAAATTTT
Found at i:34957 original size:115 final size:115
Alignment explanation
Indices: 34755--34989 Score: 380
Period size: 115 Copynumber: 2.0 Consensus size: 115
34745 TAAATAAAAT
* * *
34755 TTAATTGATTCAATAAAATATACATTAAACAACTTCAACGATACATTAAGTCTTTATTCGAAAAG
1 TTAATTGATTCAATAAAACATACATTAAACAACTTCAACGATACATTAAGTCCTTATTCGAAAAA
* * * *
34820 GAATTTATCTCGTAAATTAAAGAAAGTTTAAGGAATTATGGACATTCTCA
66 AAAATTATCTCGTAAATTAAAGAAAGTTTAAGGAATTATGAACATTCCCA
* * *
34870 TTAATTGATTCAATAAAACATACATTAAACAACTTTAACGATACATTGATTCCTTATTCGAAAAA
1 TTAATTGATTCAATAAAACATACATTAAACAACTTCAACGATACATTAAGTCCTTATTCGAAAAA
34935 AAAATTATCTCGTAAATTAAAGAAAGTTTAAGGAATTATGAACATTCCCA
66 AAAATTATCTCGTAAATTAAAGAAAGTTTAAGGAATTATGAACATTCCCA
34985 TTAAT
1 TTAAT
34990 GTATTCGTAA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (115 bp):
TTAATTGATTCAATAAAACATACATTAAACAACTTCAACGATACATTAAGTCCTTATTCGAAAAA
AAAATTATCTCGTAAATTAAAGAAAGTTTAAGGAATTATGAACATTCCCA
Found at i:35451 original size:10 final size:9
Alignment explanation
Indices: 35415--35457 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
35405 TTATTAATTT
35415 TAAATTTTGA
1 TAAATTTT-A
* *
35425 TATATTTAA
1 TAAATTTTA
35434 TAAATTTTA
1 TAAATTTTA
35443 TAAATTTT-
1 TAAATTTTA
35451 TAAATTT
1 TAAATTT
35458 ATTAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 7 0.24
9 16 0.55
10 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TAAATTTTA
Found at i:36474 original size:25 final size:25
Alignment explanation
Indices: 36426--36475 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
36416 GTCACTTTAA
* * *
36426 AAAAATAAAATTTTACGTAGTTTTT
1 AAAAATAAAAGTTCACGTACTTTTT
*
36451 AAAAATAAAAGTTCACTTACTTTTT
1 AAAAATAAAAGTTCACGTACTTTTT
36476 TTAGAAAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
AAAAATAAAAGTTCACGTACTTTTT
Found at i:39322 original size:21 final size:21
Alignment explanation
Indices: 39273--39325 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
39263 AAAATTATGA
39273 ATCTTTATTTTTTATTGTATC
1 ATCTTTATTTTTTATTGTATC
* *
39294 AT-TCTATTTTTTATTATTATC
1 ATCTTTATTTTTTATT-GTATC
39315 -TCTTTATTTTT
1 ATCTTTATTTTT
39326 AAAAACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
ATCTTTATTTTTTATTGTATC
Found at i:56172 original size:2 final size:2
Alignment explanation
Indices: 56165--56206 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
56155 CAAATCTCAT
*
56165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56207 AGGGCAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:66107 original size:2 final size:2
Alignment explanation
Indices: 66100--66135 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
66090 GTACTCTATC
66100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66136 GTGATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77949 original size:144 final size:142
Alignment explanation
Indices: 77689--77976 Score: 479
Period size: 141 Copynumber: 2.0 Consensus size: 142
77679 CCAAGATTTA
* * * *
77689 CCTGGTTCCATGTTTGGGTTCAAATTTGATCACGGCTCAGTGCCACTGCCAGTGTGTGCAAATCA
1 CCTGGTTCCATGTATGGGTTCAAATTTGATCACGGCTCAGTACCACTGCCAGTGTATACAAATCA
77754 CAACCTTGATAATGGGTCTAAAGAGAGTCCCATTGATTCATCTTCATCATCATCATCATCAGGCA
66 CAACCTTG--AATGGGTCTAAAGAGAGTCCCATTGATTCATCTTCATCATCATCATCATCAGGCA
*
77819 TGAGTTCAGATAGT
129 CGAGTTCAGATAGT
* *
77833 CCTGGTTCCATGTATGGGTTCAAATTTGATCACGGCTCAGTATCAGTGCCAGTGTATACAAATCA
1 CCTGGTTCCATGTATGGGTTCAAATTTGATCACGGCTCAGTACCACTGCCAGTGTATACAAATCA
*
77898 CAACCTTG-ATGGGTCTAAAGAGAGTCCCATTTATTCATCTTCATCATCATCATCATCAGGCACG
66 CAACCTTGAATGGGTCTAAAGAGAGTCCCATTGATTCATCTTCATCATCATCATCATCAGGCACG
77962 AGTTCAGATAGT
131 AGTTCAGATAGT
77974 CCT
1 CCT
77977 TTCCCTAATG
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
141 69 0.51
144 67 0.49
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (142 bp):
CCTGGTTCCATGTATGGGTTCAAATTTGATCACGGCTCAGTACCACTGCCAGTGTATACAAATCA
CAACCTTGAATGGGTCTAAAGAGAGTCCCATTGATTCATCTTCATCATCATCATCATCAGGCACG
AGTTCAGATAGT
Found at i:85673 original size:29 final size:31
Alignment explanation
Indices: 85605--85675 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
85595 ATAAATATTA
*
85605 AATT-TATACATAAATTTTGATTTAATGTGT
1 AATTGTATATATAAATTTTGATTTAATGTGT
*
85635 AACTTG-ATATATAAATTTTGGTTT-A-GTGT
1 AA-TTGTATATATAAATTTTGATTTAATGTGT
85664 AATTGTATATAT
1 AATTGTATATAT
85676 GAAACTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.08
29 12 0.33
30 3 0.08
31 18 0.50
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (31 bp):
AATTGTATATATAAATTTTGATTTAATGTGT
Found at i:89431 original size:59 final size:55
Alignment explanation
Indices: 89282--89498 Score: 162
Period size: 59 Copynumber: 4.0 Consensus size: 55
89272 AAAATTTGAA
* * * *
89282 TTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAA-GTAATGATCAACACCAAAATT
1 TTTTTTATCAGATAAAAAAGGTGGTGTCGGACAATG-CATGACCAACACAAAAATT
* * * *
89337 TTTTTTTTCTGAT-ACAAAGGTGGTGT-TGACTAATGCATGACCAACACAAAAAAAATAT
1 TTTTTTATCAGATAAAAAAGGTGGTGTCGGAC-AATGCATGACCAACAC---AAAAAT-T
* * * *
89395 TTTTTTATCAGATAAAAAAGGTGATGTCGGTCAATGCATGGCCAACAC-CAAA-T
1 TTTTTTATCAGATAAAAAAGGTGGTGTCGGACAATGCATGACCAACACAAAAATT
* ** * *
89448 TCTTTT-T--GATAAAAAATACTGGTGTCGGCCAATGCATGGCCAACACAAAAA
1 TTTTTTATCAGATAAAAAA-GGTGGTGTCGGACAATGCATGACCAACACAAAAA
89499 AAAAAATTTG
Statistics
Matches: 130, Mismatches: 22, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
50 9 0.07
51 25 0.19
52 4 0.03
53 8 0.06
54 24 0.18
55 15 0.12
57 5 0.04
58 12 0.09
59 26 0.20
60 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (55 bp):
TTTTTTATCAGATAAAAAAGGTGGTGTCGGACAATGCATGACCAACACAAAAATT
Done.