Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003477.1 Kokia drynarioides strain JFW-HI SEQ_116284, 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: 35021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2506 original size:16 final size:16
Alignment explanation
Indices: 2487--2531 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2477 ATGAGCGAAT
2487 GAGTGAATGAATGGGC
1 GAGTGAATGAATGGGC
2503 GAGTGAATGAATGGGC
1 GAGTGAATGAATGGGC
*
2519 GAATGAATGAATG
1 GAGTGAATGAATG
2532 AATGAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.40, T:0.20
Consensus pattern (16 bp):
GAGTGAATGAATGGGC
Found at i:3159 original size:16 final size:16
Alignment explanation
Indices: 3138--3169 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3128 AAGCATAAAT
*
3138 ATAAATAGATATGAAA
1 ATAAATAAATATGAAA
3154 ATAAATAAATATGAAA
1 ATAAATAAATATGAAA
3170 TAAGAATAAA
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:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (16 bp):
ATAAATAAATATGAAA
Found at i:3717 original size:3 final size:3
Alignment explanation
Indices: 3709--3743 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
3699 GATCGAAAAT
* *
3709 TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3744 TTAATGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:3725 original size:12 final size:12
Alignment explanation
Indices: 3708--3745 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
3698 TGATCGAAAA
3708 TTTCTTCTTCTT
1 TTTCTTCTTCTT
3720 TTTCTTCTTCTT
1 TTTCTTCTTCTT
3732 TTTCTTCTTCTT
1 TTTCTTCTTCTT
3744 TT
1 TT
3746 AATGAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTCTTCTT
Found at i:3981 original size:152 final size:147
Alignment explanation
Indices: 3774--4128 Score: 462
Period size: 152 Copynumber: 2.4 Consensus size: 147
3764 TGATTAAAAC
* *
3774 AAAATCACTAATTTACTTTAAAAT-CAAAATATTTATTTCGAAATAGCTAAAAAAAATCAAAAAT
1 AAAATCACTAATTTACTTTAAAATCCAAACT-TTTATTTCGAAATAGTTAAAAAAAATCAAAAAT
* * * *
3838 TTGTTTAAAAATTTGAAC-TTTTCTTTAAAATCATTAAAAAATAGATTTTTATTTTTTAAAAAAA
65 TTATTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAT-GATTTTTA-TTTTT--AAAAA
* *
3902 TCTAAAATTTCTTTCTTTTTAATG
125 TCTAAAATTTCTCT-TTTTTAAAG
* *
3926 AAAATCACTACTTTACTTTAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTAATTTACTTTAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAAATT
3991 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATGATTTTTATTTTTAAAAATCTAAA
66 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATGATTTTTATTTTTAAAAATCTAAA
*
4056 CTTTCTCTTTTTTAAAG
131 ATTTCTCTTTTTTAAAG
* * * * * * * *
4073 AAAATCGCTATTTTTCTTCAAAATCAAAACTTTTATTTCAAAATTGTTTAAAAAAA
1 AAAATCACTAATTTACTTTAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAA
4129 CGAAACTTTT
Statistics
Matches: 182, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
147 56 0.31
148 17 0.09
150 5 0.03
151 8 0.04
152 76 0.42
153 20 0.11
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (147 bp):
AAAATCACTAATTTACTTTAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAAATT
TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATGATTTTTATTTTTAAAAATCTAAA
ATTTCTCTTTTTTAAAG
Found at i:5183 original size:23 final size:23
Alignment explanation
Indices: 5142--5185 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5132 AATGTTCGTT
*
5142 AACATGTTCGATTAAATTAAATG
1 AACATGTTCGATGAAATTAAATG
5165 AACATGTTCG-TGAACATTAAA
1 AACATGTTCGATGAA-ATTAAA
5186 CAAACAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (23 bp):
AACATGTTCGATGAAATTAAATG
Found at i:5191 original size:23 final size:23
Alignment explanation
Indices: 5142--5191 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5132 AATGTTCGTT
* **
5142 AACATGTTCGATTAAATTAAATG
1 AACATGTTCGATGAAATTAAACA
5165 AACATGTTCG-TGAACATTAAACA
1 AACATGTTCGATGAA-ATTAAACA
5188 AACA
1 AACA
5192 AACATGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (23 bp):
AACATGTTCGATGAAATTAAACA
Found at i:11045 original size:18 final size:16
Alignment explanation
Indices: 11022--11065 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
11012 TAAAAAAACT
11022 AAAATAAACTAAGTACTG
1 AAAATAAA-TAA-TACTG
*
11040 AAAATAAATGATACTG
1 AAAATAAATAATACTG
11056 AAAAGTAAAT
1 AAAA-TAAAT
11066 GATAAACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 7 0.29
18 8 0.33
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (16 bp):
AAAATAAATAATACTG
Found at i:11056 original size:16 final size:17
Alignment explanation
Indices: 11035--11069 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11025 ATAAACTAAG
11035 TACTGAAAA-TAAATGA
1 TACTGAAAAGTAAATGA
11051 TACTGAAAAGTAAATGA
1 TACTGAAAAGTAAATGA
11068 TA
1 TA
11070 AACTAAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (17 bp):
TACTGAAAAGTAAATGA
Found at i:11080 original size:26 final size:26
Alignment explanation
Indices: 11051--11100 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11041 AAATAAATGA
11051 TACTGAAAAGTAAATGATAAACTAAG
1 TACTGAAAAGTAAATGATAAACTAAG
* *
11077 TACTGAAAGGTAAATGGTAAACTA
1 TACTGAAAAGTAAATGATAAACTA
11101 TAAATGGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (26 bp):
TACTGAAAAGTAAATGATAAACTAAG
Found at i:14180 original size:15 final size:17
Alignment explanation
Indices: 14148--14181 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
14138 GTTTAATATA
14148 AAAATAATAATCATTGT
1 AAAATAATAATCATTGT
14165 AAAATAA-AAT-ATTGT
1 AAAATAATAATCATTGT
14180 AA
1 AA
14182 CACATCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAATAATAATCATTGT
Found at i:25473 original size:13 final size:13
Alignment explanation
Indices: 25432--25501 Score: 70
Period size: 13 Copynumber: 5.3 Consensus size: 13
25422 ATTAGTAAAG
* *
25432 TGAAATACTTAGA
1 TGAAATAGTTATA
*
25445 TGAAATAGTTACA
1 TGAAATAGTTATA
25458 TGAAAT-GTTATTA
1 TGAAATAGTTA-TA
*
25471 TGAAAGTAGATATA
1 TGAAA-TAGTTATA
*
25485 TGAAATGGTTATA
1 TGAAATAGTTATA
25498 TGAA
1 TGAA
25502 GTATTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.08
13 33 0.69
14 8 0.17
15 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (13 bp):
TGAAATAGTTATA
Found at i:25489 original size:27 final size:26
Alignment explanation
Indices: 25444--25501 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
25434 AAATACTTAG
*
25444 ATGAAATAGTTACATGAAAT-GTTATT
1 ATGAAATAGATACATGAAATGGTTA-T
*
25470 ATGAAAGTAGATATATGAAATGGTTAT
1 ATGAAA-TAGATACATGAAATGGTTAT
25497 ATGAA
1 ATGAA
25502 GTATTTATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 6 0.21
27 18 0.64
28 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (26 bp):
ATGAAATAGATACATGAAATGGTTAT
Found at i:26532 original size:42 final size:42
Alignment explanation
Indices: 26486--26590 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
26476 ATTTCGAGTA
*
26486 ATGAGTCTTCCTTTAATCATATTCTCATTATCATCCCAAAAT
1 ATGAGTCTTCCTTTAATCATATTCTCATTATCATCCCAAAAC
* * * * *
26528 ATGAGTCTTCCTTTTATCATATTCTCATTCTCATCTCGAGAC
1 ATGAGTCTTCCTTTAATCATATTCTCATTATCATCCCAAAAC
26570 ATGAGTCTTCCTTTAAT-ATAT
1 ATGAGTCTTCCTTTAATCATAT
26591 CCTGATGCTC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 4 0.07
42 52 0.93
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.43
Consensus pattern (42 bp):
ATGAGTCTTCCTTTAATCATATTCTCATTATCATCCCAAAAC
Found at i:26620 original size:41 final size:41
Alignment explanation
Indices: 26488--26663 Score: 120
Period size: 42 Copynumber: 4.2 Consensus size: 41
26478 TTCGAGTAAT
* ** * * * * *
26488 GAGTCTTCCTTTAATCATATTCTCATTATCATCCCAAAATAT
1 GAGTCTTCCTTTAAT-ATATCCTCATGCTCATCTCGAGACAC
* * * *
26530 GAGTCTTCCTTTTATCATATTCTCATTCTCATCTCGAGACAT
1 GAGTCTTCCTTTAAT-ATATCCTCATGCTCATCTCGAGACAC
* * * *
26572 GAGTCTTCCTTTAATATATCCTGATGCTCGTTTCGAGTCAC
1 GAGTCTTCCTTTAATATATCCTCATGCTCATCTCGAGACAC
* * * *
26613 GAGTCTTCCATTCATATAAATTCTCAAGCTCAATCT-GAGACAC
1 GAGTCTTCC-TTTA-ATATATCCTCATGCTC-ATCTCGAGACAC
26656 GAGTCTTC
1 GAGTCTTC
26664 GATTTATACA
Statistics
Matches: 109, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
41 28 0.26
42 53 0.49
43 26 0.24
44 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (41 bp):
GAGTCTTCCTTTAATATATCCTCATGCTCATCTCGAGACAC
Found at i:30294 original size:26 final size:26
Alignment explanation
Indices: 30264--30319 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
30254 ACTGTCTGCT
30264 GGCATCACTGAATTGACTGTAGCCAA
1 GGCATCACTGAATTGACTGTAGCCAA
30290 GGCATCACTGAATTGACTGTAGCCAA
1 GGCATCACTGAATTGACTGTAGCCAA
30316 GGCA
1 GGCA
30320 ACACGTTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.21
Consensus pattern (26 bp):
GGCATCACTGAATTGACTGTAGCCAA
Found at i:34989 original size:42 final size:42
Alignment explanation
Indices: 34935--35021 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
34925 CATTCTGAGT
*
34935 CATGAGTTTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
*
34977 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCTGAGA
1 CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
35019 CAT
1 CAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.40
Consensus pattern (42 bp):
CATGAGTCTTCCTTTAATCATATTCTCATTCTCATCCCGAGA
Done.