Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009521.1 Kokia drynarioides strain JFW-HI SEQ_124232, 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: 82009
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Warning! 70 characters in sequence are not A, C, G, or T
Found at i:1075 original size:28 final size:28
Alignment explanation
Indices: 1044--1098 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1034 AAATGAATTT
* *
1044 TAAATTTAAATTTATAATAAATTTAAAA
1 TAAACTTAAATTTAAAATAAATTTAAAA
*
1072 TAAACTTAATTTTAAAATAAATTTAAA
1 TAAACTTAAATTTAAAATAAATTTAAA
1099 TTTGTTGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAACTTAAATTTAAAATAAATTTAAAA
Found at i:1085 original size:17 final size:17
Alignment explanation
Indices: 1065--1097 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1055 TTATAATAAA
1065 TTTAAAATAAACTTAAT
1 TTTAAAATAAACTTAAT
*
1082 TTTAAAATAAATTTAA
1 TTTAAAATAAACTTAA
1098 ATTTGTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAACTTAAT
Found at i:2347 original size:5 final size:5
Alignment explanation
Indices: 2337--2361 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2327 ATTTTGTTAG
2337 GACCC GACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC
2362 ATAAACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:3898 original size:11 final size:11
Alignment explanation
Indices: 3882--3912 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3872 CCTAATGGGA
3882 TCTACTTCTTC
1 TCTACTTCTTC
3893 TCTACTTCTTC
1 TCTACTTCTTC
3904 TCTACTTCT
1 TCTACTTCT
3913 AAACCAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (11 bp):
TCTACTTCTTC
Found at i:4952 original size:15 final size:14
Alignment explanation
Indices: 4931--4968 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
4921 TAATCCTTTA
4931 AAAATTATAAAAAT
1 AAAATTATAAAAAT
*
4945 ATAAATTATTAAAAT
1 A-AAATTATAAAAAT
4960 AAAATTATA
1 AAAATTATA
4969 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATTATAAAAAT
Found at i:4996 original size:22 final size:22
Alignment explanation
Indices: 4937--4996 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
4927 TTTAAAAATT
*
4937 ATAAAAA-TATAAATTATTAAA
1 ATAAAAATTATAATTTATTAAA
* *
4958 AT-AAAATTATATTTTTATTATA
1 ATAAAAATTATA-ATTTATTAAA
*
4980 GTAAAAATTATAATTTA
1 ATAAAAATTATAATTTA
4997 ATTTCGATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.13
21 6 0.19
22 12 0.39
23 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAAAAATTATAATTTATTAAA
Found at i:5889 original size:8 final size:8
Alignment explanation
Indices: 5878--5919 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
5868 TTTAATCCTT
5878 TAAAATTA
1 TAAAATTA
*
5886 TAAAAATA
1 TAAAATTA
*
5894 T-ATATTA
1 TAAAATTA
5901 TTAAAATTA
1 -TAAAATTA
5910 TAAAATTA
1 TAAAATTA
5918 TA
1 TA
5920 TTTTAACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.14
8 19 0.68
9 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAAATTA
Found at i:5909 original size:24 final size:23
Alignment explanation
Indices: 5876--5949 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 23
5866 AATTTAATCC
5876 TTTAAAATTATAAAAATATATAT
1 TTTAAAATTATAAAAATATATAT
5899 TATTAAAATTAT-AAAAT-TATAT
1 T-TTAAAATTATAAAAATATATAT
* *
5921 TTTAACTATCATAAAAATATATAAT
1 TTTAA-AATTATAAAAATATAT-AT
5946 TTTA
1 TTTA
5950 TTCAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.09
22 10 0.23
23 11 0.25
24 13 0.30
25 6 0.14
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATTATAAAAATATATAT
Found at i:9606 original size:21 final size:20
Alignment explanation
Indices: 9553--9607 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
9543 TATTTATTCA
9553 ATTTTT-TAATAT-TAATTT
1 ATTTTTATAATATCTAATTT
* *
9571 ATTTTTATCATATCTATTTT
1 ATTTTTATAATATCTAATTT
*
9591 TTTTTATATAATATCTA
1 ATTTT-TATAATATCTA
9608 GAATTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.20
19 5 0.17
20 9 0.30
21 10 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTATAATATCTAATTT
Found at i:11258 original size:16 final size:16
Alignment explanation
Indices: 11237--11268 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11227 TCTATATTAT
11237 TTAATTGTATATATAC
1 TTAATTGTATATATAC
*
11253 TTAATTTTATATATAC
1 TTAATTGTATATATAC
11269 ATTATTATTT
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:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAATTGTATATATAC
Found at i:11329 original size:28 final size:29
Alignment explanation
Indices: 11297--11358 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
11287 CATATGCAAC
11297 TAAAATTATAAATTAAAAAAAATAATT-T
1 TAAAATTATAAATTAAAAAAAATAATTGT
* ** *
11325 TAAAATTATTAATTAATCAAAATATTTGT
1 TAAAATTATAAATTAAAAAAAATAATTGT
11354 TAAAA
1 TAAAA
11359 AAAATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAATTATAAATTAAAAAAAATAATTGT
Found at i:12163 original size:3 final size:3
Alignment explanation
Indices: 12155--12181 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12145 TGATTCTAAG
12155 GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT
12182 TGTGCAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:13190 original size:32 final size:33
Alignment explanation
Indices: 13144--13205 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
13134 TTCATGCTAT
**
13144 TTTTTTTTTGAATTTTTAT-GATTTTAAATATG
1 TTTTTTTTAAAATTTTTATAGATTTTAAATATG
*
13176 TTTTTTTTAAAATTTTTATAGTTTTTAAAT
1 TTTTTTTTAAAATTTTTATAGATTTTAAAT
13206 TATTTATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (33 bp):
TTTTTTTTAAAATTTTTATAGATTTTAAATATG
Found at i:28486 original size:20 final size:20
Alignment explanation
Indices: 28461--28508 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
28451 TTCTAGTGTT
28461 GATTTTGTTTGTGAAAATGG
1 GATTTTGTTTGTGAAAATGG
28481 GATTTTGTTTGTGAAAATGG
1 GATTTTGTTTGTGAAAATGG
*
28501 GACTTTGT
1 GATTTTGT
28509 CATGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.46
Consensus pattern (20 bp):
GATTTTGTTTGTGAAAATGG
Found at i:28516 original size:19 final size:20
Alignment explanation
Indices: 28472--28518 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28462 ATTTTGTTTG
* **
28472 TGAAAATGGGATTTTGTTTG
1 TGAAAATGGGACTTTGTTCA
28492 TGAAAATGGGACTTTG-TCA
1 TGAAAATGGGACTTTGTTCA
28511 TGAAAATG
1 TGAAAATG
28519 TGATTGTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (20 bp):
TGAAAATGGGACTTTGTTCA
Found at i:32015 original size:19 final size:19
Alignment explanation
Indices: 31991--32028 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31981 ATATAGTAGA
31991 AATAAAATTTTCATAAAAG
1 AATAAAATTTTCATAAAAG
32010 AATAAAATTTTCATAAAAG
1 AATAAAATTTTCATAAAAG
32029 TAAGTGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAAAATTTTCATAAAAG
Found at i:35319 original size:21 final size:21
Alignment explanation
Indices: 35285--35330 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
35275 CGATCTGAGG
*
35285 AAAAATAAATAAA-CAGAATT
1 AAAAATAAAGAAACCAGAATT
*
35305 AAAAATAAAAGAAACCATAATT
1 AAAAAT-AAAGAAACCAGAATT
35327 AAAA
1 AAAA
35331 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
22 10 0.45
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAAATAAAGAAACCAGAATT
Found at i:38244 original size:37 final size:38
Alignment explanation
Indices: 38159--38272 Score: 99
Period size: 40 Copynumber: 3.0 Consensus size: 38
38149 TACACCAGAA
* *
38159 TGACACCCAGTGCCTCATCGGA--TAGTCCGAAGCAATAAAG
1 TGACACCCAGTACCTCATCGAATCTAG-CCGAAG---TAAAG
**
38199 TGACACCCAGTGTCTCATCG-ATCTAGCCGAAGTAAAG
1 TGACACCCAGTACCTCATCGAATCTAGCCGAAGTAAAG
** * *
38236 TGGTACCCAGTACCTCATTGAATCTATCCGAAGTAAA
1 TGACACCCAGTACCTCATCGAATCTAGCCGAAGTAAA
38273 ATAATGACAC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
37 20 0.31
38 15 0.23
39 1 0.02
40 25 0.39
41 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (38 bp):
TGACACCCAGTACCTCATCGAATCTAGCCGAAGTAAAG
Found at i:38902 original size:32 final size:32
Alignment explanation
Indices: 38864--38928 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
38854 TTTTTTTACT
38864 AAAAATTATTTATCTTTTAGTACAGAGATCTA
1 AAAAATTATTTATCTTTTAGTACAGAGATCTA
38896 AAAAATTATTTATCTTTTAGTACAGAGATCTA
1 AAAAATTATTTATCTTTTAGTACAGAGATCTA
38928 A
1 A
38929 TAATGTTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (32 bp):
AAAAATTATTTATCTTTTAGTACAGAGATCTA
Found at i:61010 original size:25 final size:23
Alignment explanation
Indices: 60982--61028 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
60972 AGTTGGATTC
60982 AAATTAAATTCTAAAAAGATAATTA
1 AAATTAAATT-TAAAAA-ATAATTA
*
61007 AAATTAAATTTAAACAATAATT
1 AAATTAAATTTAAAAAATAATT
61029 CCCTAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATTAAATTTAAAAAATAATTA
Found at i:65345 original size:16 final size:17
Alignment explanation
Indices: 65326--65358 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65316 AGGCCAAACA
65326 AATCAAACA-AAGATTC
1 AATCAAACACAAGATTC
*
65342 AATCAAAGACAAGATTC
1 AATCAAACACAAGATTC
65359 GAGGATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (17 bp):
AATCAAACACAAGATTC
Found at i:66282 original size:27 final size:27
Alignment explanation
Indices: 66230--66283 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
66220 ATTTTGTTCC
*
66230 TATTTAATTATTTAAATCTTTGATTTT
1 TATTTAATTATTTAAATCTTTAATTTT
* *
66257 TATTTAATTTCTTTCAATC-TTAATTTT
1 TATTTAA-TTATTTAAATCTTTAATTTT
66284 GTTTGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (27 bp):
TATTTAATTATTTAAATCTTTAATTTT
Found at i:68053 original size:29 final size:29
Alignment explanation
Indices: 68020--68075 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
68010 AAAATGTAAT
* *
68020 TTTTAAATGATTAAATCAAAATTTTATCA
1 TTTTAAAGGATTAAAACAAAATTTTATCA
* *
68049 TTTTAGAGGATTAAAACATAATTTTAT
1 TTTTAAAGGATTAAAACAAAATTTTAT
68076 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (29 bp):
TTTTAAAGGATTAAAACAAAATTTTATCA
Found at i:68773 original size:31 final size:31
Alignment explanation
Indices: 68738--68797 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
68728 AAAAAAACTT
68738 AATAGTCCAATGACTTAAATAAAAACTTTCG
1 AATAGTCCAATGACTTAAATAAAAACTTTCG
***
68769 AATAGTTTGATGACTTAAATAAAAACTTT
1 AATAGTCCAATGACTTAAATAAAAACTTT
68798 AAAATTGTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
AATAGTCCAATGACTTAAATAAAAACTTTCG
Found at i:71554 original size:19 final size:20
Alignment explanation
Indices: 71530--71575 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
71520 ATTTAGGTCG
71530 AGCCAAATT-AAAAAAAATT
1 AGCCAAATTAAAAAAAAATT
71549 AGCCAAATTAAAAAAAAATT
1 AGCCAAATTAAAAAAAAATT
*
71569 ATCCAAA
1 AGCCAAA
71576 GCTTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (20 bp):
AGCCAAATTAAAAAAAAATT
Found at i:71674 original size:25 final size:25
Alignment explanation
Indices: 71646--71693 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
71636 ATTTTTATTG
71646 AAATCCTT-TCACTTTCGGAATAACC
1 AAAT-CTTCTCACTTTCGGAATAACC
71671 AAATCTTCTCACTTTCGGAATAA
1 AAATCTTCTCACTTTCGGAATAA
71694 GTATTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (25 bp):
AAATCTTCTCACTTTCGGAATAACC
Found at i:80310 original size:10 final size:10
Alignment explanation
Indices: 80295--80325 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
80285 TAATTTTTAC
80295 AGCAACAAAA
1 AGCAACAAAA
80305 AGCAACAAAA
1 AGCAACAAAA
*
80315 AACAACAAAA
1 AGCAACAAAA
80325 A
1 A
80326 AGGCTTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.19, G:0.06, T:0.00
Consensus pattern (10 bp):
AGCAACAAAA
Found at i:81959 original size:9 final size:9
Alignment explanation
Indices: 81907--81965 Score: 57
Period size: 9 Copynumber: 6.2 Consensus size: 9
81897 AAAATTATTA
*
81907 TTTTAGAAAA
1 TTTTA-AAAT
81917 TTTT-AAAT
1 TTTTAAAAT
*
81925 TTTTAAATT
1 TTTTAAAAT
81934 TATTTATAAAT
1 T-TTTA-AAAT
81945 TCTTTAAAAT
1 T-TTTAAAAT
81955 TTTTAAAAT
1 TTTTAAAAT
81964 TT
1 TT
81966 GTAATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 7 0.17
9 14 0.33
10 13 0.31
11 8 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:81976 original size:2 final size:2
Alignment explanation
Indices: 81969--82009 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
81959 AAAATTTGTA
81969 AT AT 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 AT AT A
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.