Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012822.1 Kokia drynarioides strain JFW-HI SEQ_127835, 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: 59805
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:147 original size:26 final size:25
Alignment explanation
Indices: 96--162 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 25
86 CGAAGTATTA
* *
96 AACAGAGAGCACATAAGTGCTAGGC
1 AACAAAGAGCACACAAGTGCTAGGC
121 AACAAAGAGCACACACAGTGCTAGGC
1 AACAAAGAGCACACA-AGTGCTAGGC
147 AACAAAGAGCACACAA
1 AACAAAGAGCACACAA
163 AGTACTAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 14 0.36
26 25 0.64
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.07
Consensus pattern (25 bp):
AACAAAGAGCACACAAGTGCTAGGC
Found at i:228 original size:25 final size:25
Alignment explanation
Indices: 96--250 Score: 101
Period size: 23 Copynumber: 6.4 Consensus size: 25
86 CGAAGTATTA
* **
96 AACAGAGAGCACATA-AGTGCTAGGC
1 AACAGAGAGCACACACAGTGCTA-AT
* **
121 AACAAAGAGCACACACAGTGCTAGGC
1 AACAGAGAGCACACACAGTGCTA-AT
* * *
147 AACAAAGAGCACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAAT
* *
172 --CAGATAGCACACAAAGTGCTAAT
1 AACAGAGAGCACACACAGTGCTAAT
* *
195 --TAGAAAGCACACACAGTGCTAAT
1 AACAGAGAGCACACACAGTGCTAAT
*
218 AACAGAGAGCACGAGAC-GTGCT-A-
1 AACAGAGAGCAC-ACACAGTGCTAAT
241 AACAGAGAGC
1 AACAGAGAGC
251 GCGCTAGTGT
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
23 50 0.45
24 1 0.01
25 26 0.23
26 34 0.31
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (25 bp):
AACAGAGAGCACACACAGTGCTAAT
Found at i:2727 original size:20 final size:20
Alignment explanation
Indices: 2681--2719 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2671 CTACCTTGGA
*
2681 ACTTCTACCGATATAACTTC
1 ACTTCTACCGATACAACTTC
2701 ACTTCTACCGATACAACTT
1 ACTTCTACCGATACAACTT
2720 TAGTTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (20 bp):
ACTTCTACCGATACAACTTC
Found at i:4365 original size:20 final size:20
Alignment explanation
Indices: 4327--4382 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
4317 AGAAGCATAC
*
4327 TTGTATCGGT-GAAATTGAAG
1 TTGTATCGGTAG-AAGTGAAG
4347 TTGTATCGGTAGAAGTGAAG
1 TTGTATCGGTAGAAGTGAAG
* *
4367 TTCTACCGGTAGAAGT
1 TTGTATCGGTAGAAGT
4383 CCCAGGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.32
Consensus pattern (20 bp):
TTGTATCGGTAGAAGTGAAG
Found at i:11445 original size:13 final size:13
Alignment explanation
Indices: 11427--11455 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11417 TGATTCAACG
11427 AAATTATCAAACC
1 AAATTATCAAACC
11440 AAATTATCAAACC
1 AAATTATCAAACC
11453 AAA
1 AAA
11456 ATTCAATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATTATCAAACC
Found at i:13793 original size:21 final size:21
Alignment explanation
Indices: 13743--13795 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
13733 AATAGTGCAA
*
13743 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGAAACAAGT-ACT
*
13765 -CTTTTACCGAAACAAGT-CTT
1 ACTTCTACCGAAACAAGTAC-T
13785 ACTTCTACCGA
1 ACTTCTACCGA
13796 TACTAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 24 0.92
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGAAACAAGTACT
Found at i:15566 original size:6 final size:6
Alignment explanation
Indices: 15555--15593 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
15545 GCACTGCCCC
15555 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TTA
15594 ATCGGTTTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTATAA
Found at i:24459 original size:21 final size:22
Alignment explanation
Indices: 24426--24480 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
24416 GATTGGTAAC
24426 ATAATTGTTTAATAATGAT-TTT
1 ATAATT-TTTAATAATGATCTTT
24448 ATAATTTTTAATAATGATCTTT
1 ATAATTTTTAATAATGATCTTT
24470 -TAAATTTTTAA
1 AT-AATTTTTAA
24481 CATTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATTTTTAATAATGATCTTT
Found at i:28492 original size:14 final size:15
Alignment explanation
Indices: 28464--28493 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28454 TATTTTTATT
28464 TCCATTTTCTAAAAA
1 TCCATTTTCTAAAAA
28479 TCCATTTT-TAAAAA
1 TCCATTTTCTAAAAA
28493 T
1 T
28494 TTTCTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (15 bp):
TCCATTTTCTAAAAA
Found at i:35523 original size:29 final size:31
Alignment explanation
Indices: 35451--35523 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
35441 TATCATATTC
*
35451 TTATACACGTGAACTTTGATTTAATATGCAA
1 TTATACACGTGAACTTTGATATAATATGCAA
* * *
35482 TTGTACACATGAACTTT-A-AT-ATGGTGCAA
1 TTATACACGTGAACTTTGATATAAT-ATGCAA
35511 TTATACACGTGAA
1 TTATACACGTGAA
35524 ACTCTAATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
30 1 0.03
31 15 0.43
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (31 bp):
TTATACACGTGAACTTTGATATAATATGCAA
Found at i:35732 original size:30 final size:29
Alignment explanation
Indices: 35696--35761 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
35686 ATAATTTACA
35696 AAAATTAAATC-AAATCAAAATTTAATGTAT
1 AAAATTAAA-CAAAATCAAAATTT-ATGTAT
* *
35726 AAAATTACACAAAATCAAAGTTTATGTAT
1 AAAATTAAACAAAATCAAAATTTATGTAT
*
35755 ATAATTA
1 AAAATTA
35762 CACATTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAATTAAACAAAATCAAAATTTATGTAT
Found at i:35753 original size:29 final size:30
Alignment explanation
Indices: 35707--35765 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
35697 AAATTAAATC
35707 AAATCAAAATTTAATGTATAAAATTACACA
1 AAATCAAAATTTAATGTATAAAATTACACA
* *
35737 AAATCAAAGTTT-ATGTATATAATTACACA
1 AAATCAAAATTTAATGTATAAAATTACACA
35766 TTAAACCGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTAATGTATAAAATTACACA
Found at i:35827 original size:31 final size:31
Alignment explanation
Indices: 35792--35853 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
35782 GTATAGATTT
* *
35792 AATATTTATCTCAATTAAAATTAAAATTTCA
1 AATATATATCTCAATCAAAATTAAAATTTCA
* * *
35823 AATATATATTTGAATCACAATTAAAATTTCA
1 AATATATATCTCAATCAAAATTAAAATTTCA
35854 CGTATATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (31 bp):
AATATATATCTCAATCAAAATTAAAATTTCA
Found at i:36235 original size:12 final size:12
Alignment explanation
Indices: 36218--36247 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
36208 TCAATGAAAT
36218 ATATAATTATTA
1 ATATAATTATTA
36230 ATATAATTATTA
1 ATATAATTATTA
36242 ATATAA
1 ATATAA
36248 CATTATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATAATTATTA
Found at i:36336 original size:15 final size:15
Alignment explanation
Indices: 36316--36347 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
36306 TAAAAATAAA
36316 TTGATGTATTTATTT
1 TTGATGTATTTATTT
36331 TTGATGTATTTATTT
1 TTGATGTATTTATTT
36346 TT
1 TT
36348 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (15 bp):
TTGATGTATTTATTT
Found at i:38144 original size:30 final size:30
Alignment explanation
Indices: 38108--38182 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
38098 GTCTTATTAA
*
38108 TCCCAAGATCCTGAATGAAATATCAGGTCT
1 TCCCAAGATCCTAAATGAAATATCAGGTCT
* *
38138 TCCCAAGCTCCTAAATGAGATATCAGGTCT
1 TCCCAAGATCCTAAATGAAATATCAGGTCT
* *
38168 TCTCAAGTTCCTAAA
1 TCCCAAGATCCTAAA
38183 CATCCTCGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (30 bp):
TCCCAAGATCCTAAATGAAATATCAGGTCT
Found at i:48569 original size:21 final size:21
Alignment explanation
Indices: 48525--48562 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
48515 TTTGTTTCCA
48525 AGTTCATTTCAATTGTTAAAT
1 AGTTCATTTCAATTGTTAAAT
48546 AGTT-ATTTCAATT-TTAA
1 AGTTCATTTCAATTGTTAA
48563 TATTAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (21 bp):
AGTTCATTTCAATTGTTAAAT
Found at i:55252 original size:58 final size:58
Alignment explanation
Indices: 55190--55303 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
55180 ATATTGAATC
*
55190 TTTGAATCTTTGGGTTAATGAGTTTTAAAGATTCAAGCTTTGAGACATATTTGTAATT
1 TTTGAATCTTTGGATTAATGAGTTTTAAAGATTCAAGCTTTGAGACATATTTGTAATT
*
55248 TTTGAATCTTTGGATTAATGAGTTTTAAATATTCAAGCTTTGAGACATATTTGTAA
1 TTTGAATCTTTGGATTAATGAGTTTTAAAGATTCAAGCTTTGAGACATATTTGTAA
55304 CTAAAGATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.45
Consensus pattern (58 bp):
TTTGAATCTTTGGATTAATGAGTTTTAAAGATTCAAGCTTTGAGACATATTTGTAATT
Found at i:57827 original size:63 final size:63
Alignment explanation
Indices: 57728--57855 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
57718 GTTCTGTACA
57728 TGGTATGTTTAGGTGTGCAAAATATGTTAGTTGAAAACAGAGTCTCAAGAATAGTACCATTAT
1 TGGTATGTTTAGGTGTGCAAAATATGTTAGTTGAAAACAGAGTCTCAAGAATAGTACCATTAT
57791 TGGTATGTTTAGGTGTGCAAAATATGTTAGTTGAAAACAGAGTCTCAAGAATAGTACCATTAT
1 TGGTATGTTTAGGTGTGCAAAATATGTTAGTTGAAAACAGAGTCTCAAGAATAGTACCATTAT
57854 TG
1 TG
57856 AGGTTGCCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (63 bp):
TGGTATGTTTAGGTGTGCAAAATATGTTAGTTGAAAACAGAGTCTCAAGAATAGTACCATTAT
Done.