Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005232.1 Kokia drynarioides strain JFW-HI SEQ_119118, 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: 78316
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1574 original size:21 final size:20
Alignment explanation
Indices: 1548--1594 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1538 TTCCTAATTC
1548 ATTTATA-AATTATTTATGATT
1 ATTTATATAATT-TTTA-GATT
1569 ATTTATATAATTTTTAGATT
1 ATTTATATAATTTTTAGATT
*
1589 TTTTAT
1 ATTTAT
1595 TTTTTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 9 0.38
21 11 0.46
22 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTATATAATTTTTAGATT
Found at i:6046 original size:13 final size:13
Alignment explanation
Indices: 6030--6054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6020 AAAAGCTTCT
6030 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
6043 GAAAAAAAAAAA
1 GAAAAAAAAAAA
6055 CTTATTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:8174 original size:14 final size:15
Alignment explanation
Indices: 8157--8189 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
8147 ATTTCTCTTT
8157 ATAAATTT-TTTTTA
1 ATAAATTTATTTTTA
8171 ATAAATTTAATTTTTA
1 ATAAATTT-ATTTTTA
8187 ATA
1 ATA
8190 TTTTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAAATTTATTTTTA
Found at i:22640 original size:28 final size:29
Alignment explanation
Indices: 22583--22640 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
22573 TTAATTTTTT
* *
22583 TTTGAAATTTCGATTAATAATTAATTTAA
1 TTTGAAATTTCGAGTAATAATTAAATTAA
22612 TTTGAAA-TT-GAGTAATTAATTAAATTAA
1 TTTGAAATTTCGAGTAA-TAATTAAATTAA
22640 T
1 T
22641 AAAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 5 0.19
28 14 0.54
29 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (29 bp):
TTTGAAATTTCGAGTAATAATTAAATTAA
Found at i:23234 original size:11 final size:11
Alignment explanation
Indices: 23218--23246 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
23208 ATATAAACGT
23218 AAAAATAAAAA
1 AAAAATAAAAA
23229 AAAAATAAAAA
1 AAAAATAAAAA
23240 AAAAATA
1 AAAAATA
23247 TTAAATTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:24369 original size:28 final size:30
Alignment explanation
Indices: 24299--24379 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
24289 AAATATAAAA
*
24299 ATTATATATAAATTTTGATTTCATTAATAAT
1 ATTATATATGAATTTTGATTT-ATTAATAAT
*
24330 ATTATATATGAATTTTGATTT-TT-ATGACT
1 ATTATATATGAATTTTGATTTATTAAT-AAT
*
24359 -TTATATATGAAATTGTGATTT
1 ATTATATATG-AATTTTGATTT
24380 GATTCAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.24
29 14 0.31
31 20 0.44
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (30 bp):
ATTATATATGAATTTTGATTTATTAATAAT
Found at i:24592 original size:29 final size:31
Alignment explanation
Indices: 24524--24612 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 31
24514 GTAATTGAAT
*
24524 CAAATCAAAGTTTCATGTATATATATGA-ACTA
1 CAAATCAAAGTTTCATGTATATA-ATTATAC-A
*
24556 CAATTC-AAGTTTCATGTATATAATTATAC-
1 CAAATCAAAGTTTCATGTATATAATTATACA
24585 CAAATCAAAG-TTCATGTATCA-AATTATA
1 CAAATCAAAGTTTCATGTAT-ATAATTATA
24613 ATTAAACCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 21 0.41
30 7 0.14
31 18 0.35
32 5 0.10
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (31 bp):
CAAATCAAAGTTTCATGTATATAATTATACA
Found at i:25473 original size:21 final size:22
Alignment explanation
Indices: 25440--25482 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
25430 GTTGGATATG
25440 TTAAAAATATTTTAATTATAAT
1 TTAAAAATATTTTAATTATAAT
* *
25462 TTAAAACT-TTTTTATTATAAT
1 TTAAAAATATTTTAATTATAAT
25483 ATTTGAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATATTTTAATTATAAT
Found at i:26270 original size:14 final size:14
Alignment explanation
Indices: 26234--26273 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
26224 ACGTTTTTTT
*
26234 AAAAATAAAAATTA
1 AAAAATAATAATTA
* *
26248 AAAAATAATATTTC
1 AAAAATAATAATTA
26262 AAAAATAATAAT
1 AAAAATAATAAT
26274 ATAATCAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATAATAATTA
Found at i:29942 original size:13 final size:13
Alignment explanation
Indices: 29924--29948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29914 AGTTTCGTTG
29924 CCTTAGAGAATTT
1 CCTTAGAGAATTT
29937 CCTTAGAGAATT
1 CCTTAGAGAATT
29949 CTAACTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
CCTTAGAGAATTT
Found at i:31977 original size:43 final size:43
Alignment explanation
Indices: 31937--32018 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
31927 TCGAAGCATT
*
31937 TATACTGGCACATACAGTACATCATCAAATATATCAAAGCAAC
1 TATACTGGCACACACAGTACATCATCAAATATATCAAAGCAAC
* ** * * *
31980 TGTTTTGGCACACATAGTGCATCATCGAATATATCAAAG
1 TATACTGGCACACACAGTACATCATCAAATATATCAAAG
32019 TGATTTACCG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (43 bp):
TATACTGGCACACACAGTACATCATCAAATATATCAAAGCAAC
Found at i:33290 original size:32 final size:32
Alignment explanation
Indices: 33236--33321 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
33226 TTTTGACCCT
*
33236 CAACCTTTT-AAAAAGAGACAAATTTAACCAC
1 CAACCTTTTGAAAAAGAGTCAAATTTAACCAC
* * *
33267 CAACCTTTTGAAATAGAGTCAAATTTCACCAT
1 CAACCTTTTGAAAAAGAGTCAAATTTAACCAC
*
33299 CAATCTTTTGAAAAAGAGTCAAA
1 CAACCTTTTGAAAAAGAGTCAAA
33322 ATGATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 9 0.19
32 39 0.81
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (32 bp):
CAACCTTTTGAAAAAGAGTCAAATTTAACCAC
Found at i:44179 original size:6 final size:6
Alignment explanation
Indices: 44168--44192 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44158 ACCCAAGAAA
44168 ATAATG ATAATG ATAATG ATAATG A
1 ATAATG ATAATG ATAATG ATAATG A
44193 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATAATG
Found at i:49393 original size:53 final size:53
Alignment explanation
Indices: 49328--49501 Score: 249
Period size: 53 Copynumber: 3.3 Consensus size: 53
49318 TCTTATTTAT
* *
49328 ATAATATATTTATTACCCCCAATTATGACTGAATTATTAAATATTGGAATATA
1 ATAATATATTTATTACCCCCAATTAAGACTGAATTATTAAATATTTGAATATA
* * * *
49381 ATAATATGTTTATTTCCCCCCATTAAGACTGAATTATTAAATATTTTAATATA
1 ATAATATATTTATTACCCCCAATTAAGACTGAATTATTAAATATTTGAATATA
* * * * *
49434 ATAATATATTTATTATCCCAAATTACGACTCAATTCTTAAATATTTGAATATA
1 ATAATATATTTATTACCCCCAATTAAGACTGAATTATTAAATATTTGAATATA
49487 ATAATATATTTATTA
1 ATAATATATTTATTA
49502 ACTAATTTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 106 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (53 bp):
ATAATATATTTATTACCCCCAATTAAGACTGAATTATTAAATATTTGAATATA
Found at i:53765 original size:15 final size:15
Alignment explanation
Indices: 53712--53766 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
53702 TCCACCACCG
*
53712 GGATATCCTCCACAA
1 GGATATCCTCCTCAA
53727 GGATA---TCCTCAA
1 GGATATCCTCCTCAA
*
53739 GGTTATCCTCCTCAA
1 GGATATCCTCCTCAA
53754 GGATATCCTCCTC
1 GGATATCCTCCTC
53767 CTTACGCCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.29
15 24 0.71
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
GGATATCCTCCTCAA
Found at i:55293 original size:17 final size:18
Alignment explanation
Indices: 55271--55305 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55261 ATAATTAAAT
*
55271 AAAAATATAAAAT-ATAA
1 AAAAATAAAAAATCATAA
55288 AAAAATAAAAAATCATAA
1 AAAAATAAAAAATCATAA
55306 TTGATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATAAAAAATCATAA
Found at i:55517 original size:36 final size:36
Alignment explanation
Indices: 55477--55549 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
55467 TCAACACGAA
*
55477 TTCTCTATTACATTATATTGATTAAATCATTACTTT
1 TTCTCTATTACATTATATTGATTAAATCATTAATTT
55513 TTCTCTATTACATTATATTGATTAAATCATTAATTT
1 TTCTCTATTACATTATATTGATTAAATCATTAATTT
55549 T
1 T
55550 CGATACAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (36 bp):
TTCTCTATTACATTATATTGATTAAATCATTAATTT
Found at i:61156 original size:15 final size:16
Alignment explanation
Indices: 61120--61157 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
61110 GAGCAGTTGC
61120 AGAAGCAGAAGCTGCA
1 AGAAGCAGAAGCTGCA
*
61136 A-TAGCAGAAGCTG-A
1 AGAAGCAGAAGCTGCA
61150 AGAAGCAG
1 AGAAGCAG
61158 CAAGAGAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 16 0.84
16 1 0.05
ACGTcount: A:0.45, C:0.16, G:0.32, T:0.08
Consensus pattern (16 bp):
AGAAGCAGAAGCTGCA
Found at i:61497 original size:29 final size:29
Alignment explanation
Indices: 61453--61539 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 29
61443 TGTTGACGAT
** *
61453 TTTTGCAGCACACACCCAGTCATCATCCC
1 TTTTGCAGCAGGCACCCAGTAATCATCCC
** **
61482 TTTTGCAGCAGGCACCTGGTAATTGTCCC
1 TTTTGCAGCAGGCACCCAGTAATCATCCC
* *
61511 TATTTGTAGCAGGCACCCAGTGATCATCC
1 T-TTTGCAGCAGGCACCCAGTAATCATCC
61540 TTATTATTTG
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (29 bp):
TTTTGCAGCAGGCACCCAGTAATCATCCC
Found at i:69056 original size:31 final size:30
Alignment explanation
Indices: 68990--69058 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
68980 GTTACATTTA
*
68990 ACAAAACAGTCACTCAACTTAGAAAATGTG
1 ACAAAACAGTCACTCAACTTAGAAAATATG
69020 ACAAAACAGTCACT-AACGTTATCGAAAA-ATG
1 ACAAAACAGTCACTCAAC-TTA--GAAAATATG
69051 ACAAAACA
1 ACAAAACA
69059 ATCAACGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 3 0.09
30 17 0.49
31 10 0.29
32 5 0.14
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.17
Consensus pattern (30 bp):
ACAAAACAGTCACTCAACTTAGAAAATATG
Found at i:74561 original size:2 final size:2
Alignment explanation
Indices: 74542--74582 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
74532 AATCAGGAAA
*
74542 AT AT AT A- AT GAT AA AT 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 AT AT AT AT AT AT AT AT A
74583 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:75954 original size:26 final size:27
Alignment explanation
Indices: 75923--75978 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
75913 ACCCAATTTT
*
75923 TTTTAATCTATTC-ATAAT-AAATAATA
1 TTTTAATATATTCAATAATAAAATAA-A
75949 TTTTAATATATTCAATAATAAAATAAA
1 TTTTAATATATTCAATAATAAAATAAA
75976 TTT
1 TTT
75979 CAAATAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.44
27 9 0.33
28 6 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTTAATATATTCAATAATAAAATAAA
Found at i:75984 original size:28 final size:26
Alignment explanation
Indices: 75931--75984 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
75921 TTTTTTAATC
*
75931 TATTCATAATAAATAATATTTTAATA
1 TATTCATAATAAATAATATTTAAATA
75957 TATTCAATAATAAAATAA-ATTTCAAATA
1 TATTC-ATAAT-AAATAATATTT-AAATA
75985 AAAGAATTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 10 0.42
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (26 bp):
TATTCATAATAAATAATATTTAAATA
Done.