Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000330.1 Kokia drynarioides strain JFW-HI SEQ_111100, 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: 106399
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 237 characters in sequence are not A, C, G, or T
Found at i:223 original size:21 final size:21
Alignment explanation
Indices: 199--241 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
189 AAGGGGAGAA
199 AGTGAAATACCCGTTCAACCC
1 AGTGAAATACCCGTTCAACCC
220 AGTGAAATACCCGTTCAACCC
1 AGTGAAATACCCGTTCAACCC
241 A
1 A
242 TTGACGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.33, G:0.14, T:0.19
Consensus pattern (21 bp):
AGTGAAATACCCGTTCAACCC
Found at i:1303 original size:2 final size:2
Alignment explanation
Indices: 1285--1341 Score: 89
Period size: 2 Copynumber: 28.5 Consensus size: 2
1275 TTTTTGCTAA
*
1285 AT AT AT CAT AT -T TT AT 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 AT AT AT AT AT AT AT AT
1327 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1342 GAGTGAATTA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.94
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5614 original size:15 final size:15
Alignment explanation
Indices: 5594--5623 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5584 TTCAATATAA
*
5594 AAAAATAATAAAAAG
1 AAAAATAAAAAAAAG
5609 AAAAATAAAAAAAAG
1 AAAAATAAAAAAAAG
5624 CGCACGTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAAATAAAAAAAAG
Found at i:22561 original size:2 final size:2
Alignment explanation
Indices: 22554--22583 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22544 GTACTTTCAG
22554 AT AT 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 AT AT
22584 TATGTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23301 original size:2 final size:2
Alignment explanation
Indices: 23294--23322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23284 GTACAACTAT
23294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23323 GTGTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32074 original size:23 final size:23
Alignment explanation
Indices: 32045--32148 Score: 93
Period size: 25 Copynumber: 4.3 Consensus size: 23
32035 ACTAGCGCGT
*
32045 CCTCTGTTTAGCAC-GTTTCGTGC
1 CCTCTGTTTAGCACTGTGT-GTGC
*
32068 TCTCTGTTTAGCACTGTGTGTGC
1 CCTCTGTTTAGCACTGTGTGTGC
* *
32091 CCTCTGTTATTAGGACTTTGTGTGC
1 CCTCTG-T-TTAGCACTGTGTGTGC
* * *
32116 CCTCTGTTATTAGGACTTTATGTGC
1 CCTCTG-T-TTAGCACTGTGTGTGC
32141 CCTCTGTT
1 CCTCTGTT
32149 AAGTACTTCG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 23 0.32
24 5 0.07
25 44 0.61
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
CCTCTGTTTAGCACTGTGTGTGC
Found at i:32103 original size:25 final size:25
Alignment explanation
Indices: 32075--32149 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
32065 TGCTCTCTGT
* *
32075 TTAGCACTGTGTGTGCCCTCTGTTA
1 TTAGGACTTTGTGTGCCCTCTGTTA
32100 TTAGGACTTTGTGTGCCCTCTGTTA
1 TTAGGACTTTGTGTGCCCTCTGTTA
*
32125 TTAGGACTTTATGTGCCCTCTGTTA
1 TTAGGACTTTGTGTGCCCTCTGTTA
32150 AGTACTTCGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (25 bp):
TTAGGACTTTGTGTGCCCTCTGTTA
Found at i:32993 original size:22 final size:23
Alignment explanation
Indices: 32908--32993 Score: 63
Period size: 26 Copynumber: 3.7 Consensus size: 23
32898 ATCATACATG
*
32908 AATTAAGAGTTA-TTTTTAACTCCAA
1 AATTAAGAGTTATTTTTTTA-T--AA
*
32933 GAATTAAGAGTTATTTTTTTATAT
1 -AATTAAGAGTTATTTTTTTATAA
***
32957 AATT-ACCTTTA-TTTTTT-TAA
1 AATTAAGAGTTATTTTTTTATAA
32977 AATTAAGAGTTATTTTT
1 AATTAAGAGTTATTTTT
32994 AATTCCATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
20 6 0.12
21 10 0.21
22 8 0.17
23 4 0.08
24 1 0.02
26 13 0.27
27 6 0.12
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (23 bp):
AATTAAGAGTTATTTTTTTATAA
Found at i:47879 original size:22 final size:23
Alignment explanation
Indices: 47824--47880 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
47814 TAACTCTTTA
*
47824 AAAATTATAAAATTATAGATTATT
1 AAAATCATAAAATTATA-ATTATT
* *
47848 AAAATGATAAAATTAT-ATTTTT
1 AAAATCATAAAATTATAATTATT
*
47870 AATATCATAAA
1 AAAATCATAAA
47881 TATATACAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 14 0.48
24 15 0.52
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
AAAATCATAAAATTATAATTATT
Found at i:48254 original size:2 final size:2
Alignment explanation
Indices: 48237--48274 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
48227 AGGTTACTGC
* *
48237 AT AT AC AT AA AT 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 AT AT AT AT AT AT
48275 GCATCATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:69365 original size:35 final size:35
Alignment explanation
Indices: 69317--69417 Score: 175
Period size: 35 Copynumber: 2.9 Consensus size: 35
69307 GAAAAAGTCC
*
69317 AGCACTGGTATTTCTTGTTTGAGTCAAACTAGACA
1 AGCACTGGCATTTCTTGTTTGAGTCAAACTAGACA
69352 AGCACTGGCATTTCTTGTTTGAGTCAAACTAGACA
1 AGCACTGGCATTTCTTGTTTGAGTCAAACTAGACA
* *
69387 AGCACTGACATTTCTTGTTTGAGTCGAACTA
1 AGCACTGGCATTTCTTGTTTGAGTCAAACTA
69418 TACTGGTTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (35 bp):
AGCACTGGCATTTCTTGTTTGAGTCAAACTAGACA
Found at i:81581 original size:82 final size:81
Alignment explanation
Indices: 81435--81585 Score: 196
Period size: 82 Copynumber: 1.8 Consensus size: 81
81425 AGCTTGCTTG
* * * *
81435 CTGATTCCTACATGTTAGCAAGGTTTGGCATGACGTTGTCTACCATAAAAATTGGATTATCTTGA
1 CTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAG-CTACCATAAAAATTAGATTACCTTGA
81500 AATCGCCCTCTTGCGTA
65 AATCGCCCTCTTGCGTA
* ** *
81517 CTGATTCCTACATGTTAGCCAGGTTTGGCATGACATAG-TACTGTGACAAATTAGATTTACCTTG
1 CTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAGCTACCAT-AAAAATTAGA-TTACCTTG
81581 AAATC
64 AAATC
81586 AGTCCAAATA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 4 0.07
81 8 0.14
82 47 0.80
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (81 bp):
CTGATTCCTACATGTTAGCAAGGTTTGGCATGACATAGCTACCATAAAAATTAGATTACCTTGAA
ATCGCCCTCTTGCGTA
Found at i:99457 original size:39 final size:39
Alignment explanation
Indices: 99414--99494 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
99404 CATGTGGGGA
99414 TCTCATTGTGGATGATCTTATTTGTAGTTTCCCATTTCT
1 TCTCATTGTGGATGATCTTATTTGTAGTTTCCCATTTCT
99453 TCTCATTGTGGATGATCTTATTTGTAGTTTCCCATTTCT
1 TCTCATTGTGGATGATCTTATTTGTAGTTTCCCATTTCT
99492 TCT
1 TCT
99495 TTTAGTAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (39 bp):
TCTCATTGTGGATGATCTTATTTGTAGTTTCCCATTTCT
Done.