Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012384.1 Kokia drynarioides strain JFW-HI SEQ_127388, 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: 40627
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Warning! 83 characters in sequence are not A, C, G, or T
Found at i:60 original size:4 final size:4
Alignment explanation
Indices: 51--117 Score: 71
Period size: 4 Copynumber: 16.2 Consensus size: 4
41 AAATAAACGG
* * * *
51 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GGAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
*
101 GAAA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
118 GTAATGTGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
4 47 0.85
5 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:70 original size:13 final size:13
Alignment explanation
Indices: 52--79 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42 AATAAACGGG
52 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
65 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
78 AA
1 AA
80 GGAAGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:73 original size:17 final size:17
Alignment explanation
Indices: 51--116 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 17
41 AAATAAACGG
51 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
*
68 GAAAGAAAGAAAG-GAA
1 GAAAGAAAGAAAGAAAA
* * * *
84 GGAAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGAAAA
*
101 GAAAGAAGGAAAGAAA
1 GAAAGAAAGAAAGAAA
117 GGTAATGTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 12 0.30
17 28 0.70
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Found at i:3942 original size:14 final size:14
Alignment explanation
Indices: 3925--3971 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3915 CAAGTCTAGT
*
3925 GTTTATGGTTTAGG
1 GTTTATAGTTTAGG
3939 GTTT-TAAGTTTAGG
1 GTTTAT-AGTTTAGG
*
3953 GTTTATAATTTAGG
1 GTTTATAGTTTAGG
*
3967 TTTTA
1 GTTTA
3972 GGGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (14 bp):
GTTTATAGTTTAGG
Found at i:3968 original size:13 final size:14
Alignment explanation
Indices: 3932--3971 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3922 AGTGTTTATG
3932 GTTTAGGGTTTTAA
1 GTTTAGGGTTTTAA
3946 GTTTAGGGTTTATAA
1 GTTTAGGGTTT-TAA
3961 -TTTA-GGTTTTA
1 GTTTAGGGTTTTA
3972 GGGTTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 5 0.20
14 15 0.60
15 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (14 bp):
GTTTAGGGTTTTAA
Found at i:4223 original size:20 final size:21
Alignment explanation
Indices: 4198--4239 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4188 TAGGGTCCAT
*
4198 TTGCCC-GAAGGAGTAGAGTA
1 TTGCCCGGAAGGAATAGAGTA
*
4218 TTGCCCGGGAGGAATAGAGTA
1 TTGCCCGGAAGGAATAGAGTA
4239 T
1 T
4240 CGCGGTGGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.21
Consensus pattern (21 bp):
TTGCCCGGAAGGAATAGAGTA
Found at i:5744 original size:16 final size:16
Alignment explanation
Indices: 5725--5774 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5715 TGATGAGGAT
5725 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
5741 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
5756 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
5771 ATTA
1 ATTA
5775 ACTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:5956 original size:21 final size:21
Alignment explanation
Indices: 5923--5973 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5913 TAAAATTATT
*
5923 AATTTTACCATTAAATATTTAA
1 AATTTTA-TATTAAATATTTAA
* * *
5945 AATTTTATATTAATTTTTTAT
1 AATTTTATATTAAATATTTAA
5966 AATTTTAT
1 AATTTTAT
5974 TATATAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTATATTAAATATTTAA
Found at i:6268 original size:20 final size:21
Alignment explanation
Indices: 6243--6285 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6233 TATTTAGTAC
6243 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
6263 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
6284 TA
1 TA
6286 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:6673 original size:4 final size:4
Alignment explanation
Indices: 6666--6704 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
6656 TCCTTCTTCC
*
6666 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
6705 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:6681 original size:25 final size:24
Alignment explanation
Indices: 6623--6700 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
6613 AACATATTAC
* * *
6623 CTTTTTTTTTCCTTCTCCTTCTTCC
1 CTTTCTTTCTCCTTCTCCTTCTT-T
*
6648 CCTTC-TTCTCCTTCTTCCTTCTTT
1 CTTTCTTTCTCCTTC-TCCTTCTTT
*
6672 CTTTCTTTCT--TTCT-CTTTTTT
1 CTTTCTTTCTCCTTCTCCTTCTTT
6693 CTTTCTTT
1 CTTTCTTT
6701 TTTCCTTCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 14 0.31
22 1 0.02
23 3 0.07
24 12 0.27
25 15 0.33
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (24 bp):
CTTTCTTTCTCCTTCTCCTTCTTT
Found at i:9090 original size:10 final size:10
Alignment explanation
Indices: 9077--9103 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9067 AAATATCAAA
9077 AAAAAAAAAT
1 AAAAAAAAAT
9087 AAAAAAAAAT
1 AAAAAAAAAT
9097 AAAAAAA
1 AAAAAAA
9104 TTTGGGGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:23518 original size:21 final size:21
Alignment explanation
Indices: 23492--23537 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
23482 TTGGATTACT
23492 GGCACATAGCCTGAAAACACC
1 GGCACATAGCCTGAAAACACC
*
23513 GGCACATAGCCTGAATACACC
1 GGCACATAGCCTGAAAACACC
23534 GGCA
1 GGCA
23538 AAAAGCCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.33, G:0.22, T:0.11
Consensus pattern (21 bp):
GGCACATAGCCTGAAAACACC
Found at i:23544 original size:21 final size:21
Alignment explanation
Indices: 23499--23545 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
23489 ACTGGCACAT
* *
23499 AGCCTGAAAACACCGGCACAT
1 AGCCTGAAAACACCGGCAAAA
*
23520 AGCCTGAATACACCGGCAAAA
1 AGCCTGAAAACACCGGCAAAA
23541 AGCCT
1 AGCCT
23546 ACTAGGCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.32, G:0.19, T:0.11
Consensus pattern (21 bp):
AGCCTGAAAACACCGGCAAAA
Found at i:26263 original size:22 final size:22
Alignment explanation
Indices: 26193--26264 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
26183 GTGCATTTAC
* *
26193 TTACGATATAATTAATTTCAAG
1 TTACAATATAATTAATTTCATG
*
26215 TTAAATATATCAAATTAAAATTT--TG
1 TTACA-ATAT--AATT--AATTTCATG
26240 TTACAATATAATTAATTTCATG
1 TTACAATATAATTAATTTCATG
26262 TTA
1 TTA
26265 GAGCACATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 5 0.13
22 12 0.31
23 4 0.10
24 4 0.10
25 9 0.23
27 5 0.13
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (22 bp):
TTACAATATAATTAATTTCATG
Found at i:26453 original size:26 final size:26
Alignment explanation
Indices: 26404--26461 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
26394 TTAGAGAAGT
* *
26404 TTTTAACTTTTTATATATTATTTATAG
1 TTTTAACTTTTTATAAATTATTTA-AA
26431 TTTTAA-TTTTTATAAA-TATTTTAAA
1 TTTTAACTTTTTATAAATTA-TTTAAA
26456 TTTTAA
1 TTTTAA
26462 AAATTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.32
26 13 0.46
27 6 0.21
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTAACTTTTTATAAATTATTTAAA
Found at i:26454 original size:18 final size:19
Alignment explanation
Indices: 26431--26476 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
26421 TTATTTATAG
*
26431 TTTTAATTTTTATAAA-TA
1 TTTTAATTTTTAAAAATTA
*
26449 TTTTAAATTTTAAAAATTA
1 TTTTAATTTTTAAAAATTA
26468 TTTTGAATT
1 TTTT-AATT
26477 ATTTTGTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 14 0.61
19 6 0.26
20 3 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAATTTTTAAAAATTA
Found at i:29428 original size:19 final size:18
Alignment explanation
Indices: 29406--29468 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
29396 TAGAACTATT
*
29406 ACTCAAATACATATTGAAA
1 ACTCAAATTC-TATTGAAA
* *
29425 ACTCAACTTTGTATTGAAA
1 ACTCAA-ATTCTATTGAAA
*
29444 ACTCAAAATTCTCTTGAAA
1 ACTC-AAATTCTATTGAAA
29463 ACTCAA
1 ACTCAA
29469 CTTTATAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
18 2 0.06
19 31 0.86
20 3 0.08
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.30
Consensus pattern (18 bp):
ACTCAAATTCTATTGAAA
Found at i:31011 original size:21 final size:21
Alignment explanation
Indices: 30987--31054 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
30977 CAAAAAGCTT
30987 AAAAATCATAAGAAAAAATTG
1 AAAAATCATAAGAAAAAATTG
* *
31008 AAAAA-CCTGAGATAAATAATT-
1 AAAAATCATAAGA-AAA-AATTG
*
31029 AAAAAT-AAAAGAAAAAAAATTG
1 AAAAATCATAAG--AAAAAATTG
31051 AAAA
1 AAAA
31055 TAAATAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
20 5 0.14
21 19 0.53
22 11 0.31
23 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (21 bp):
AAAAATCATAAGAAAAAATTG
Found at i:34620 original size:33 final size:33
Alignment explanation
Indices: 34580--34647 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
34570 TTATTTCTTA
* *
34580 AAATATA-TTATAAAAATTATATATAAATTAAAT
1 AAATATATTTAT-AAAATGACATATAAATTAAAT
34613 AAATATATTTATAAAATGACATATAAATTAAAT
1 AAATATATTTATAAAATGACATATAAATTAAAT
34646 AA
1 AA
34648 GTCCTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
AAATATATTTATAAAATGACATATAAATTAAAT
Found at i:35334 original size:22 final size:23
Alignment explanation
Indices: 35313--35362 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
35303 GAATGGAAAT
*
35313 TATAT-ATTTAAGA-TAATAAAA
1 TATATAATTTAAAATTAATAAAA
35334 TATATAATTTAAAATTAATAATAA
1 TATATAATTTAAAATTAATAA-AA
35358 TATAT
1 TATAT
35363 TAAATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 7 0.28
23 6 0.24
24 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TATATAATTTAAAATTAATAAAA
Found at i:35452 original size:18 final size:17
Alignment explanation
Indices: 35418--35452 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35408 AAAACGAAAT
*
35418 TTAAAAATATAATTATA
1 TTAAAAATATAAATATA
35435 TTAAAAATACTAAATATA
1 TTAAAAATA-TAAATATA
35453 CTATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAATATAAATATA
Found at i:36390 original size:2 final size:2
Alignment explanation
Indices: 36383--36419 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36373 GTTACTAACC
36383 AT AT AT AT AT 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 A
36420 CACTTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36593 original size:19 final size:19
Alignment explanation
Indices: 36551--36594 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
36541 TATAAATATA
* * *
36551 ATAAAATAATAAATATTTT
1 ATAAAACAAAAAATAATTT
36570 A-AAAACAAAAAATAATTT
1 ATAAAACAAAAAATAATTT
36588 ATAAAAC
1 ATAAAAC
36595 TATTCCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAACAAAAAATAATTT
Found at i:39901 original size:22 final size:23
Alignment explanation
Indices: 39867--39923 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
39857 TGCTAGGAAA
* *
39867 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCACACACAGCGCAAAT
* *
39889 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGCGCAAAT
39912 CAGTAGGCACAC
1 CAGTAGGCACAC
39924 GAAGTACGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGTAGGCACACACAGCGCAAAT
Found at i:39959 original size:23 final size:21
Alignment explanation
Indices: 39840--39965 Score: 83
Period size: 23 Copynumber: 5.5 Consensus size: 21
39830 CGAAGTACTT
39840 AACAGTAAGCACACAAGTGCTAGG
1 AACAGTAAGCACACAAGTGC---G
39864 AAACAGTAAGCACACACAGTGC-
1 -AACAGTAAGCACACA-AGTGCG
* * * *
39886 AATCAGTAGGCGCACATAGCGCA
1 AA-CAGTAAGCACACA-AGTGCG
* *
39909 AATCAGTAGGCACACGAAGTACG
1 AA-CAGTAAGCACAC-AAGTGCG
39932 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGC-G
39956 AACAGTAAGC
1 AACAGTAAGC
39966 GCGCTAGCGT
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.02
22 16 0.19
23 42 0.50
24 4 0.05
25 15 0.18
26 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (21 bp):
AACAGTAAGCACACAAGTGCG
Done.