Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005669.1 Kokia drynarioides strain JFW-HI SEQ_119844, 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: 49285
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:918 original size:21 final size:21
Alignment explanation
Indices: 893--946 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
883 CTTGTGCTAG
893 ATCTACCGATACAAGT-ATGAT
1 ATCTACCGATACAAGTCATG-T
*
914 TTCTACCGATACAAGTCATGT
1 ATCTACCGATACAAGTCATGT
935 ATCTACCGATAC
1 ATCTACCGATAC
947 CAAAAACTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (21 bp):
ATCTACCGATACAAGTCATGT
Found at i:2528 original size:3 final size:3
Alignment explanation
Indices: 2520--2549 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2510 TTGGTCGTGT
2520 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2550 AATATGTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12847 original size:19 final size:17
Alignment explanation
Indices: 12812--12850 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
12802 GAGTGTAGAG
12812 GAAGAGGAGGAAGAAGA
1 GAAGAGGAGGAAGAAGA
12829 GAAGAGAGAGGAAGCAAGA
1 GAAGAG-GAGGAAG-AAGA
12848 GAA
1 GAA
12851 ATAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 7 0.35
19 7 0.35
ACGTcount: A:0.54, C:0.03, G:0.44, T:0.00
Consensus pattern (17 bp):
GAAGAGGAGGAAGAAGA
Found at i:13937 original size:13 final size:13
Alignment explanation
Indices: 13919--13966 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
13909 AGAAAGAAAG
13919 AAAAAAATTTGAT
1 AAAAAAATTTGAT
*
13932 AAAAAAATACAT-AT
1 AAAAAAAT--TTGAT
*
13946 ATAAAAATTTGAT
1 AAAAAAATTTGAT
13959 AAAAAAAT
1 AAAAAAAT
13967 ACATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 1 0.04
13 17 0.61
14 9 0.32
15 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (13 bp):
AAAAAAATTTGAT
Found at i:13959 original size:27 final size:27
Alignment explanation
Indices: 13921--13975 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13911 AAAGAAAGAA
13921 AAAAATTTGATAAAAAAATACATATAT
1 AAAAATTTGATAAAAAAATACATATAT
13948 AAAAATTTGATAAAAAAATACATATAT
1 AAAAATTTGATAAAAAAATACATATAT
13975 A
1 A
13976 TGTGTATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (27 bp):
AAAAATTTGATAAAAAAATACATATAT
Found at i:27298 original size:63 final size:63
Alignment explanation
Indices: 27225--27348 Score: 239
Period size: 63 Copynumber: 2.0 Consensus size: 63
27215 GATGATGGGT
27225 CGAAGGAAGAAGCATGCATTTGTACAAATGAAGAAGAAGATGTTAAGTAAGATTTCGAGTTCC
1 CGAAGGAAGAAGCATGCATTTGTACAAATGAAGAAGAAGATGTTAAGTAAGATTTCGAGTTCC
*
27288 CGAAGGAAGAAGCATGCATTTGTACAAATGAAGGAGAAGATGTTAAGTAAGATTTCGAGTT
1 CGAAGGAAGAAGCATGCATTTGTACAAATGAAGAAGAAGATGTTAAGTAAGATTTCGAGTT
27349 GGAGTATGCG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.24
Consensus pattern (63 bp):
CGAAGGAAGAAGCATGCATTTGTACAAATGAAGAAGAAGATGTTAAGTAAGATTTCGAGTTCC
Found at i:32177 original size:113 final size:113
Alignment explanation
Indices: 31988--32198 Score: 309
Period size: 113 Copynumber: 1.9 Consensus size: 113
31978 TCAAGAAAAA
*
31988 TTTCAAAACATTTCTCAGCCATTTTTTCTACCAAGGCTGGTTCTTCTTCTCTCTTCTCTGAAAAA
1 TTTCAAAACATTTCTCAGCCATTTTTTCTACCAAGGCTGGATCTTCTTCTCTCTTCTCTGAAAAA
* * *
32053 TAGTCTGGTTCAAGGCTTCATTCTTTCTCCAAACCTCTTCAAGAGACT
66 TAATCTAGTTCAAGGCTCCATTCTTTCTCCAAACCTCTTCAAGAGACT
* * *
32101 TTTCAAATCATTTCTCAGCC-TTTTCTTCTACCAAGGTTGGATGTTCTTCTCTCTTCTCT-AATA
1 TTTCAAAACATTTCTCAGCCATTTT-TTCTACCAAGGCTGGATCTTCTTCTCTCTTCTCTGAA-A
**
32164 CTTAATCTAGTTCAAGGCTCCATTCTTTCTCCAAA
64 AATAATCTAGTTCAAGGCTCCATTCTTTCTCCAAA
32199 TCCTTTCGAG
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
112 6 0.07
113 81 0.93
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (113 bp):
TTTCAAAACATTTCTCAGCCATTTTTTCTACCAAGGCTGGATCTTCTTCTCTCTTCTCTGAAAAA
TAATCTAGTTCAAGGCTCCATTCTTTCTCCAAACCTCTTCAAGAGACT
Found at i:38425 original size:18 final size:19
Alignment explanation
Indices: 38404--38449 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
38394 TTTAATTTTA
38404 TTGTTTAATATAA-TTGAT
1 TTGTTTAATATAATTTGAT
* *
38422 TTG-TTATTATAATTTTAT
1 TTGTTTAATATAATTTGAT
38440 TTGTTTAATA
1 TTGTTTAATA
38450 GGTTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (19 bp):
TTGTTTAATATAATTTGAT
Found at i:38723 original size:4 final size:5
Alignment explanation
Indices: 38706--38739 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
38696 ACTTTGATTA
*
38706 AATTT AATTT AA-TT AATTT AATTT TATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
38740 GTTAGTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
AATTT
Found at i:38814 original size:7 final size:7
Alignment explanation
Indices: 38802--38841 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
38792 ATAAATTAAT
38802 TTAAATA
1 TTAAATA
38809 TTAAATA
1 TTAAATA
38816 TTAAATA
1 TTAAATA
38823 TTAAATA
1 TTAAATA
38830 TTAAATA
1 TTAAATA
38837 TTAAA
1 TTAAA
38842 ATAGGTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATA
Found at i:39025 original size:154 final size:155
Alignment explanation
Indices: 38862--39182 Score: 513
Period size: 154 Copynumber: 2.1 Consensus size: 155
38852 TACCAAAATA
*
38862 GTACAAAATAAATATTTATACATTAAATTGATATATCCACCACATTTTCGTAATTAATGGTGTGT
1 GTACAAAATAAATATTTATACATTAAATTGATATATCCACCACATTTTCGTAATTAAT--AGTGT
* * *
38927 GGATACTATTTC-GTATATAAATATTTATTTTGTATCATTTTAGTAAATAA-C-TCATTTTGGTA
64 GGATACCATTTCGGTATATAAATATTTATTCTGTACCATTTTAGTAAATAACCTTCATTTTGGTA
* *
38989 TTTAATTATTATTTTTGTATTATATTT
129 TTCAATTATTATTTTTGTATTATATTG
* *
39016 GTACAAAATAAATATTTATATATTAAATTGATATATCCACTACATTTTCGTAATTAATAGTGTGG
1 GTACAAAATAAATATTTATACATTAAATTGATATATCCACCACATTTTCGTAATTAATAGTGTGG
39081 ATACCATTTCGGTATATAAATATTTATTCTGTACCATTTTAGTAAATAACCCTTCATTTTGGTAT
66 ATACCATTTCGGTATATAAATATTTATTCTGTACCATTTTAGTAAATAA-CCTTCATTTTGGTAT
39146 TCAATTATTATTTTTGTATTATATTG
130 TCAATTATTATTTTTGTATTATATTG
*
39172 GTAAAAAATAA
1 GTACAAAATAA
39183 TAAAAATTAT
Statistics
Matches: 154, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
152 15 0.10
153 36 0.23
154 56 0.36
155 1 0.01
156 46 0.30
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (155 bp):
GTACAAAATAAATATTTATACATTAAATTGATATATCCACCACATTTTCGTAATTAATAGTGTGG
ATACCATTTCGGTATATAAATATTTATTCTGTACCATTTTAGTAAATAACCTTCATTTTGGTATT
CAATTATTATTTTTGTATTATATTG
Found at i:40395 original size:43 final size:42
Alignment explanation
Indices: 40313--40405 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
40303 ATTAACATGT
* * *
40313 TAAATTATATTGCTTGACTCGTGTTAATATGGTTGCATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTA
*
40355 CTAAATTATATTACTTGACTCTTATTAATAT-ATTGACATGTTA
1 -TAAATTATATTACTTGACTCGTATTAATATGATTG-CATGTTA
*
40398 TTAATTAT
1 TAAATTAT
40406 GCAGTTCATC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 10 0.23
43 34 0.77
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (42 bp):
TAAATTATATTACTTGACTCGTATTAATATGATTGCATGTTA
Found at i:41016 original size:21 final size:21
Alignment explanation
Indices: 40990--41035 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40980 ACAAGCCACC
40990 GCAATACTATACTCCTCTC-GG
1 GCAATACTATACTCCTC-CAGG
*
41011 GCAATACTTTACTCCTCCAGG
1 GCAATACTATACTCCTCCAGG
41032 GCAA
1 GCAA
41036 ATGGACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (21 bp):
GCAATACTATACTCCTCCAGG
Found at i:41282 original size:14 final size:14
Alignment explanation
Indices: 41263--41315 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
41253 TTCATACTTA
41263 TAAACCCTAAACCT
1 TAAACCCTAAACCT
*
41277 TAAACCCTAAA-TT
1 TAAACCCTAAACCT
* *
41290 TAAAACCATAAACCA
1 T-AAACCCTAAACCT
*
41305 TAAACCTTAAA
1 TAAACCCTAAA
41316 TCATTAACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.06
14 29 0.91
15 1 0.03
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:41295 original size:21 final size:21
Alignment explanation
Indices: 41271--41350 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
41261 TATAAACCCT
41271 AAACCTTAAACCCTAAATTTA
1 AAACCTTAAACCCTAAATTTA
* * *
41292 AAACCATAAACCATAAACCTTA
1 AAACCTTAAACCCTAAA-TTTA
* * * *
41314 AATCATT-AACCTTAAATTCA
1 AAACCTTAAACCCTAAATTTA
* *
41334 AAACCCTAAACACTAAA
1 AAACCTTAAACCCTAAA
41351 CCTTAAAAAT
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 6 0.14
21 30 0.70
22 7 0.16
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (21 bp):
AAACCTTAAACCCTAAATTTA
Found at i:41367 original size:30 final size:29
Alignment explanation
Indices: 41323--41402 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
41313 AAATCATTAA
* *
41323 CCTTAAATTCAAAACCCTAAACACTAAA-
1 CCTTAAATTTAAAACCCTAAACACAAAAC
* * **
41351 CCTTAAAAATTTAAAACCTTTAATTCAAAAC
1 CCTT--AAATTTAAAACCCTAAACACAAAAC
41382 CCTTAAATTTAAAACCCTAAA
1 CCTTAAATTTAAAACCCTAAA
41403 ATTAAAAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 4 0.10
29 15 0.37
30 18 0.44
31 4 0.10
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (29 bp):
CCTTAAATTTAAAACCCTAAACACAAAAC
Found at i:41375 original size:14 final size:14
Alignment explanation
Indices: 41278--41409 Score: 65
Period size: 14 Copynumber: 9.2 Consensus size: 14
41268 CCTAAACCTT
*
41278 AAACCCTAAATTTA
1 AAACCTTAAATTTA
* **
41292 AAACCATAAA-CCA
1 AAACCTTAAATTTA
41305 TAAACCTTAAATCATT-
1 -AAACCTTAAAT--TTA
*
41321 -AACCTTAAATTCA
1 AAACCTTAAATTTA
* **
41334 AAACCCTAAACACT-
1 AAACCTTAAA-TTTA
41348 AAACCTTAAAAATTTA
1 AAACCTT--AAATTTA
* *
41364 AAACCTTTAATTCA
1 AAACCTTAAATTTA
41378 AAACCCTTAAATTTA
1 AAA-CCTTAAATTTA
* *
41393 AAACCCTAAAATTA
1 AAACCTTAAATTTA
41407 AAA
1 AAA
41410 ACACTAAACC
Statistics
Matches: 87, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
12 1 0.01
13 1 0.01
14 62 0.71
15 13 0.15
16 10 0.11
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACCTTAAATTTA
Found at i:41390 original size:15 final size:15
Alignment explanation
Indices: 41323--41411 Score: 67
Period size: 15 Copynumber: 6.0 Consensus size: 15
41313 AAATCATTAA
41323 CCTTAAATTCAAAAC
1 CCTTAAATTCAAAAC
** *
41338 CC-TAAACACTAAA-
1 CCTTAAATTCAAAAC
*
41351 CCTTAAAAATTTAAAA-
1 CCTT--AAATTCAAAAC
*
41367 CCTTTAATTCAAAAC
1 CCTTAAATTCAAAAC
*
41382 CCTTAAATTTAAAAC
1 CCTTAAATTCAAAAC
* *
41397 CCTAAAATTAAAAAC
1 CCTTAAATTCAAAAC
41412 ACTAAACCCT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.30
15 28 0.49
16 10 0.18
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTAAATTCAAAAC
Found at i:41404 original size:44 final size:44
Alignment explanation
Indices: 41321--41411 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
41311 TTAAATCATT
* *
41321 AACCTTAAATTCAAAACCCTAAACACTAAACCTTAAAAATTTAA
1 AACCTTAAATTCAAAACCCTAAACACTAAACCCTAAAAATTAAA
* **
41365 AACCTTTAATTCAAAACCCTTAAA-TTTAAAACCCT-AAAATTAAA
1 AACCTTAAATTCAAAACCC-TAAACACT-AAACCCTAAAAATTAAA
41409 AAC
1 AAC
41412 ACTAAACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 30 0.75
45 10 0.25
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (44 bp):
AACCTTAAATTCAAAACCCTAAACACTAAACCCTAAAAATTAAA
Found at i:41416 original size:15 final size:15
Alignment explanation
Indices: 41372--41417 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
41362 TAAAACCTTT
* *
41372 AATTCAAAACCCTTA
1 AATTAAAAACCCTAA
*
41387 AATTTAAAACCCTAA
1 AATTAAAAACCCTAA
*
41402 AATTAAAAACACTAA
1 AATTAAAAACCCTAA
41417 A
1 A
41418 CCCTTAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTAAAAACCCTAA
Found at i:45452 original size:2 final size:2
Alignment explanation
Indices: 45445--45477 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45435 AATATCATTA
45445 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 A
45478 GACTTGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45848 original size:28 final size:28
Alignment explanation
Indices: 45805--45858 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
45795 TTGTTTAGTA
*
45805 ATGTTTTTATCTCAAAAACACTTTTGGG
1 ATGTTTTTATCCCAAAAACACTTTTGGG
**
45833 ATGTTTTTATCCCAAAAGTACTTTTG
1 ATGTTTTTATCCCAAAAACACTTTTG
45859 AGAAGCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (28 bp):
ATGTTTTTATCCCAAAAACACTTTTGGG
Found at i:46549 original size:14 final size:14
Alignment explanation
Indices: 46520--46557 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
46510 CATAATAGTT
46520 AATTTT-AATTTAA
1 AATTTTAAATTTAA
*
46533 AATTTTAAATTTTA
1 AATTTTAAATTTAA
*
46547 AATTTAAAATT
1 AATTTTAAATT
46558 GAATTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTAAATTTAA
Done.