Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001048.1 Kokia drynarioides strain JFW-HI SEQ_112282, 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: 54905
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Found at i:1406 original size:18 final size:18
Alignment explanation
Indices: 1361--1408 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
1351 AAATACCTAA
*
1361 ACCTGTGAGCTTGACCCG
1 ACCTGTGAGCTCGACCCG
*** *
1379 ACCCACGAGCTCGACTCG
1 ACCTGTGAGCTCGACCCG
1397 ACCTGTGAGCTC
1 ACCTGTGAGCTC
1409 AACCTGAACC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (18 bp):
ACCTGTGAGCTCGACCCG
Found at i:3272 original size:197 final size:198
Alignment explanation
Indices: 2921--3298 Score: 587
Period size: 197 Copynumber: 1.9 Consensus size: 198
2911 GTGTTTTGAA
* *
2921 ATTATGCTTTGCATAGGTGACTGTAAGTAGACTTAAATGGTATATGTTATCATATTTTAAGATTC
1 ATTATGCTTTGCATAGGTGACTGTAAGTAGACTCAAATGGTATATGTTATCATATTTTAAGATGC
* * * * *
2986 TTTTGGGTGTTTTTTTAAGTTGTGGTAGATAGTGTTATGAATTGGGTTAGGCATTTAAATTAAAC
66 TTTTAGGTGATATTTTAAGTTGTGGTAGATAGTGTTATGAATTAGGTTAGGCATTTAAATCAAAC
3051 GAGTGATAGCCGAATACATTTTTAAGTATTTTTGGGCACACACAGGTTGTATATATATAAGCCTT
131 GAGTGATAGCCGAATACATTTTTAAGTATTTTTGGGCACACACAGGTTGTATATATATAAGCCTT
3116 TAT
196 TAT
* * * *
3119 ATTATGCTTTGCGTAGGTGATTGTAAGTATACTCAAATGGTATATGTTATCATATTTTAGGATGC
1 ATTATGCTTTGCATAGGTGACTGTAAGTAGACTCAAATGGTATATGTTATCATATTTTAAGATGC
* *
3184 TTTTAGGT-ATATTTTAAGTTTTGGTAGATAGTGTTATGAATTAGGTTAGGCATTTAAATCAAAT
66 TTTTAGGTGATATTTTAAGTTGTGGTAGATAGTGTTATGAATTAGGTTAGGCATTTAAATCAAAC
** * * *
3248 GAGTGATAGTTGAATACGTTTTTAAGTATTTTTGGGCACATATAGGTTGTA
131 GAGTGATAGCCGAATACATTTTTAAGTATTTTTGGGCACACACAGGTTGTA
3299 CACGGGCGTG
Statistics
Matches: 162, Mismatches: 18, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
197 96 0.59
198 66 0.41
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (198 bp):
ATTATGCTTTGCATAGGTGACTGTAAGTAGACTCAAATGGTATATGTTATCATATTTTAAGATGC
TTTTAGGTGATATTTTAAGTTGTGGTAGATAGTGTTATGAATTAGGTTAGGCATTTAAATCAAAC
GAGTGATAGCCGAATACATTTTTAAGTATTTTTGGGCACACACAGGTTGTATATATATAAGCCTT
TAT
Found at i:8987 original size:15 final size:15
Alignment explanation
Indices: 8967--9000 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
8957 GAAGTTAAAG
*
8967 ACTTTGGTTGTGTTA
1 ACTTTGGTTGTGTGA
8982 ACTTTGGTTGTGTGA
1 ACTTTGGTTGTGTGA
8997 ACTT
1 ACTT
9001 GGATTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.09, G:0.26, T:0.50
Consensus pattern (15 bp):
ACTTTGGTTGTGTGA
Found at i:9450 original size:50 final size:50
Alignment explanation
Indices: 9389--9575 Score: 225
Period size: 50 Copynumber: 3.8 Consensus size: 50
9379 TAAAGTAACA
* * * * *
9389 CATATATAAGCTGACGAGTGTAAAAGTGTGTAAATTGGCGAGCGTAAACG
1 CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGCGAGCGTAAACG
* *
9439 CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGTGAGTGTAAACG
1 CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGCGAGCGTAAACG
* * * * *
9489 CGTATATAAGCTGATGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACA
1 CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGCGAGCGTAAACG
* * *
9539 CATAT--AAGTTGACGAGCGTAAACATGTGCAAGCTGGC
1 CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGC
9576 AAACATAAGT
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
48 29 0.24
50 90 0.76
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.21
Consensus pattern (50 bp):
CATATAAAAGCTGACGAGCGTAAACGTGTGCAAACTGGCGAGCGTAAACG
Found at i:9518 original size:100 final size:98
Alignment explanation
Indices: 9391--9574 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 98
9381 AAGTAACACA
* * * *
9391 TATATAAGCTGACGAGTGTAAAAGTGTGTAAATTGGCGAGCGTAAACGCATATAAAAGCTGACGA
1 TATATAAGCTGACGAGCGTAAAAGTGTGCAAACTGGCGAGCGTAAACACATAT--AAGCTGACGA
*
9456 GCGTAAACGTGTGCAAACTGGTGAGTGTAAACGCG
64 GCGTAAACATGTGCAAACTGGTGAGTGTAAACGCG
* * * *
9491 TATATAAGCTGATGAGCGTAAACGTGTGCAAGCTGGCGAGCGTAAACACATATAAGTTGACGAGC
1 TATATAAGCTGACGAGCGTAAAAGTGTGCAAACTGGCGAGCGTAAACACATATAAGCTGACGAGC
*
9556 GTAAACATGTGCAAGCTGG
66 GTAAACATGTGCAAACTGG
9575 CAAACATAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 28 0.38
100 46 0.62
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (98 bp):
TATATAAGCTGACGAGCGTAAAAGTGTGCAAACTGGCGAGCGTAAACACATATAAGCTGACGAGC
GTAAACATGTGCAAACTGGTGAGTGTAAACGCG
Found at i:9531 original size:24 final size:24
Alignment explanation
Indices: 9396--9573 Score: 95
Period size: 24 Copynumber: 7.2 Consensus size: 24
9386 ACACATATAT
* * *
9396 AAGCTGACGAGTGTAAAAGTGTGT
1 AAGCTGACGAGCGTAAACGTGTGC
** * * **
9420 AAATTGGCGAGCGTAAACGCATATAA
1 AAGCTGACGAGCGTAAACG--TGTGC
9446 AAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* ** * * **
9470 AAACTGGTGAGTGTAAACGCGTATAT
1 AAGCTGACGAGCGTAAA--CGTGTGC
*
9496 AAGCTGATGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *** **
9520 AAGCTGGCGAGCGTAAACACATAT
1 AAGCTGACGAGCGTAAACGTGTGC
* *
9544 AAGTTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
9568 AAGCTG
1 AAGCTG
9574 GCAAACATAA
Statistics
Matches: 109, Mismatches: 41, Indels: 8
0.69 0.26 0.05
Matches are distributed among these distances:
24 73 0.67
26 36 0.33
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:18833 original size:16 final size:16
Alignment explanation
Indices: 18812--18842 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18802 GCTTAATTAA
18812 TGAAAAAGGATTAAAT
1 TGAAAAAGGATTAAAT
*
18828 TGAAAAAGGGTTAAA
1 TGAAAAAGGATTAAA
18843 AGTTAATTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (16 bp):
TGAAAAAGGATTAAAT
Found at i:20599 original size:28 final size:28
Alignment explanation
Indices: 20561--20615 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
20551 AAATGAGCAT
20561 CATGACCTTTGGGTCAACAAGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAG
20589 CATGACCTTTGGGTCAACAAGGAGTAA
1 CATGACCTTTGGGTCAACAAGGAGTAA
20616 ATCGAATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAG
Found at i:37368 original size:55 final size:55
Alignment explanation
Indices: 37284--37394 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
37274 CACTAGGGAG
37284 AGAGGTTACCTTCCAACAAACAACATTCGGGAAAGATTAGACAGAGGTGTGACAA
1 AGAGGTTACCTTCCAACAAACAACATTCGGGAAAGATTAGACAGAGGTGTGACAA
37339 AGAGGTTACCTTCCAACAAACAACATTCGGGAAAGATTAGACAGAGGTGTGACAA
1 AGAGGTTACCTTCCAACAAACAACATTCGGGAAAGATTAGACAGAGGTGTGACAA
37394 A
1 A
37395 TCAGGCATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (55 bp):
AGAGGTTACCTTCCAACAAACAACATTCGGGAAAGATTAGACAGAGGTGTGACAA
Found at i:46610 original size:38 final size:37
Alignment explanation
Indices: 46526--46610 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 37
46516 TTCATGCTTT
* *
46526 TTTTTTACTTTTTATAAATTTTTATATTTTTAATTTTGA
1 TTTTTTA--TTTTAGAAATTTTTATATTTTTAATGTTGA
46565 TTTTTTATTTTAGAATATTTTTATAATTTTTAA-GTT-A
1 TTTTTTATTTTAGAA-ATTTTTAT-ATTTTTAATGTTGA
46602 TTTGTTTAT
1 TTT-TTTAT
46611 GTGACAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
37 11 0.27
38 15 0.37
39 15 0.37
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (37 bp):
TTTTTTATTTTAGAAATTTTTATATTTTTAATGTTGA
Found at i:48506 original size:2 final size:2
Alignment explanation
Indices: 48499--48524 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48489 TCAAATATCA
48499 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
48525 CCGAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50538 original size:26 final size:26
Alignment explanation
Indices: 50480--50530 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
50470 ATCAAGTAAG
* *
50480 ATTACTTTCCACATATTTTTATGTGA
1 ATTACTTTCCAAAGATTTTTATGTGA
50506 ATTACTTTCCAAAGATTTTTATGTG
1 ATTACTTTCCAAAGATTTTTATGTG
50531 GTTTACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (26 bp):
ATTACTTTCCAAAGATTTTTATGTGA
Found at i:54348 original size:6 final size:6
Alignment explanation
Indices: 54337--54400 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
54327 ATTTGTGTAG
* *
54337 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CGAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
*
54383 -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT A
54401 TTTTCCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.08
5 9 0.19
6 31 0.65
7 4 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:54359 original size:17 final size:16
Alignment explanation
Indices: 54337--54432 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 16
54327 ATTTGTGTAG
54337 AAATTTAAATTTATATT
1 AAATTTAAATTTAT-TT
54354 AAATTTAAATTTATTT
1 AAATTTAAATTTATTT
*
54370 CGAATTTAAATTTAATTT
1 -AAATTTAAATTT-ATTT
*
54388 AAGTTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
54405 CCAAATTTAAGA-TTATTAT
1 --AAATTTAA-ATTTATT-T
54424 AAATTTAAA
1 AAATTTAAA
54433 ATAAATAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
16 4 0.06
17 46 0.68
18 6 0.09
19 11 0.16
20 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:54381 original size:34 final size:34
Alignment explanation
Indices: 54338--54403 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
54328 TTTGTGTAGA
54338 AATTTAAATTT-ATATTAAATTTAAATTTATTTCG
1 AATTTAAATTTAAT-TTAAATTTAAATTTATTTCG
*
54372 AATTTAAATTTAATTTAAGTTTAAATTTATTT
1 AATTTAAATTTAATTTAAATTTAAATTTATTT
54404 TCCAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
AATTTAAATTTAATTTAAATTTAAATTTATTTCG
Done.