Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010687.1 Kokia drynarioides strain JFW-HI SEQ_125633, 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: 45714
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:15004 original size:30 final size:28
Alignment explanation
Indices: 14960--15023 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 28
14950 TTCTTGAACA
* *
14960 TTAAACAAACGAACATAAACACATACAATT
1 TTAAATAAACGAACATAAACA-AAAC-ATT
* *
14990 TTAAATAAATGAACATGAACAAAACATT
1 TTAAATAAACGAACATAAACAAAACATT
15018 TTAAAT
1 TTAAAT
15024 TCTTAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.30
29 3 0.10
30 18 0.60
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (28 bp):
TTAAATAAACGAACATAAACAAAACATT
Found at i:22747 original size:26 final size:27
Alignment explanation
Indices: 22718--22775 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
22708 GGAGTTGTAC
22718 AAAAACATAAAAATA-TAAAAATT-ATT
1 AAAAA-ATAAAAATACTAAAAATTAATT
* * *
22744 AAAAAATATATATACTAGAAATTAATT
1 AAAAAATAAAAATACTAAAAATTAATT
22771 AAAAA
1 AAAAA
22776 TAATAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.26
26 12 0.44
27 8 0.30
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAAATAAAAATACTAAAAATTAATT
Found at i:23075 original size:29 final size:28
Alignment explanation
Indices: 23015--23093 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
23005 TTTTTTCTAA
* * *
23015 TTTTTATGATTTTTATAAAATTT-ATGGT
1 TTTTTAT-ATTTTTATAAATTTTAACGAT
*
23043 TTTTAATTAATTTTTATAAATTTTAACGAT
1 TTTTTA-T-ATTTTTATAAATTTTAACGAT
23073 TTTTTATATATTTTATAAATT
1 TTTTTATAT-TTTTATAAATT
23094 CTTTATGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 7 0.17
29 27 0.64
30 8 0.19
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (28 bp):
TTTTTATATTTTTATAAATTTTAACGAT
Found at i:23104 original size:29 final size:28
Alignment explanation
Indices: 23054--23110 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
23044 TTTAATTAAT
23054 TTTTATAAATTTTAACGATTTTTTATATA
1 TTTTATAAATTTTAACGATTTTTT-TATA
* *
23083 TTTTATAAATTCTTTATG-TTTTTTTATA
1 TTTTATAAATT-TTAACGATTTTTTTATA
23111 ATTCTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATAAATTTTAACGATTTTTTTATA
Found at i:25093 original size:6 final size:6
Alignment explanation
Indices: 25072--25154 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
25062 TTTAAATTGG
** ***
25072 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAAA TTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTT-AAA TT-TAAA
**
25121 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
25155 TCAAATTTGA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 40 0.70
7 9 0.16
8 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:25107 original size:17 final size:18
Alignment explanation
Indices: 25072--25153 Score: 105
Period size: 17 Copynumber: 4.6 Consensus size: 18
25062 TTTAAATTGG
*
25072 TTTAAATTTATTTTTAAA
1 TTTAAATTTATCTTTAAA
25090 TTTAAATTTATC-TTAAA
1 TTTAAATTTATCTTTAAA
*
25107 TTTAAAATTATCTTTTTAAA
1 TTTAAATTTATC--TTTAAA
*
25127 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATCTTTAAA
25144 TTTAAATTTA
1 TTTAAATTTA
25154 ATCAAATTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
17 31 0.55
18 11 0.20
19 1 0.02
20 13 0.23
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATCTTTAAA
Found at i:27046 original size:29 final size:29
Alignment explanation
Indices: 27010--27193 Score: 124
Period size: 29 Copynumber: 6.2 Consensus size: 29
27000 TTAAAATTTA
* * *
27010 CATTTTTAACCTCGAACTTCCTAAAATTT
1 CATTTTTAACCTCAAACTTCCAAAAATTC
* * * *
27039 CATTTTTAACCCTAAAACTTTCAAAAAATA
1 CATTTTTAA-CCTCAAACTTCCAAAAATTC
*
27069 CATTTTT-ACCCCTAAACTTCCAAAAATTC
1 CATTTTTAACCTC-AAACTTCCAAAAATTC
*
27098 CA-TTTTGACCTCGAAACTTCCAAAAAATTC
1 CATTTTTAACCTC-AAACTTCC-AAAAATTC
* * * *
27128 CATTTTTACCCCCGAA-TGTCTAAAAATTC
1 CATTTTTAACCTCAAACT-TCCAAAAATTC
* * *
27157 TATTTTAAACCCCAAACTTTCTC-AAAATTAC
1 CATTTTTAACCTCAAAC-TTC-CAAAAATT-C
27188 CATTTT
1 CATTTT
27194 GCCCTCGAGA
Statistics
Matches: 121, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
28 6 0.05
29 58 0.48
30 43 0.36
31 14 0.12
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CATTTTTAACCTCAAACTTCCAAAAATTC
Found at i:27174 original size:59 final size:57
Alignment explanation
Indices: 27010--27193 Score: 147
Period size: 59 Copynumber: 3.1 Consensus size: 57
27000 TTAAAATTTA
* * * * *
27010 CATTTTTAACCTCGAACTTCCTAAAATTTCATTTTTAACCCTAAAACTTTCAAAAAA-TA
1 CATTTTTACCCCCAAACTT-CTAAAAATTCA-TTTTAACCC-AAAACTTTCAAAAAATTC
* * * * *
27069 CATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAAATTC
1 CATTTTTACCCCCAAACTTCTAAAAATT-CATTTTAACC-CAAAACTTTCAAAAAATTC
* * **
27128 CATTTTTACCCCCGAA-TGTCTAAAAATTCTATTTTAAACCCCAAACTTTCTCAAAATTAC
1 CATTTTTACCCCCAAACT-TCTAAAAATTC-ATTTT-AACCCAAAACTTTCAAAAAATT-C
27188 CATTTT
1 CATTTT
27194 GCCCTCGAGA
Statistics
Matches: 100, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
58 29 0.29
59 61 0.61
60 10 0.10
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (57 bp):
CATTTTTACCCCCAAACTTCTAAAAATTCATTTTAACCCAAAACTTTCAAAAAATTC
Found at i:27235 original size:28 final size:28
Alignment explanation
Indices: 27179--27240 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
27169 CAAACTTTCT
* * *
27179 CAAAATTACCATTTTGCCCTCGAGAATC
1 CAAAATTACCATTTTACCCCCGACAATC
*
27207 CAAAATTACCATTTTACCCCCGACTATC
1 CAAAATTACCATTTTACCCCCGACAATC
27235 CGAAAA
1 C-AAAA
27241 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.26
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCCCGACAATC
Found at i:41554 original size:261 final size:261
Alignment explanation
Indices: 41090--41612 Score: 1019
Period size: 261 Copynumber: 2.0 Consensus size: 261
41080 GCTTGGTCTT
41090 CTTTAAAATAAAAATTTTCAGTTTTATCCTATTAAAAGTTTATGAAATTTTAAGTAAATATATGA
1 CTTTAAAATAAAAATTTTCAGTTTTATCCTATTAAAAGTTTATGAAATTTTAAGTAAATATATGA
*
41155 TAAAATTATAGCTTAATCCCTAAAAATGATGCATTTTGATTTGACCTTTCTAAAAACTATAAAAA
66 TAAAATTATAGCCTAATCCCTAAAAATGATGCATTTTGATTTGACCTTTCTAAAAACTATAAAAA
*
41220 TGTCAATAAATTGGTGAAATTATATTTTATTTCTCATAAAAATATATAACTTAATCTTAATCTCC
131 TGTCAATAAATTGGTGAAATTATATTTTATTTCTCATAAAAATATATAACTTAATCTTAATCCCC
41285 GAAAAAGTTTTCAGCTTCGCCCTTGAATCTATATTTTGAAATCTGAAAGGGGGAAACAATGAGAA
196 GAAAAAGTTTTCAGCTTCGCCCTTGAATCTATATTTTGAAATCTGAAAGGGGGAAACAATGAGAA
41350 C
261 C
41351 CTTTAAAATAAAAATTTTCAGTTTTATCCTATTAAAAGTTTATGAAATTTTAAGTAAATATATGA
1 CTTTAAAATAAAAATTTTCAGTTTTATCCTATTAAAAGTTTATGAAATTTTAAGTAAATATATGA
41416 TAAAATTATAGCCTAATCCCTAAAAATGATGCATTTTGATTTGACCTTTCTAAAAACTATAAAAA
66 TAAAATTATAGCCTAATCCCTAAAAATGATGCATTTTGATTTGACCTTTCTAAAAACTATAAAAA
*
41481 TGTCAATAAATTGGTGAAATTGTATTTTATTTCTCATAAAAATATATAACTTAATCTTAATCCCC
131 TGTCAATAAATTGGTGAAATTATATTTTATTTCTCATAAAAATATATAACTTAATCTTAATCCCC
41546 GAAAAAGTTTTCAGCTTCGCCCTTGAATCTATATTTTGAAATCTGAAAGGGGGAAACAATGAGAA
196 GAAAAAGTTTTCAGCTTCGCCCTTGAATCTATATTTTGAAATCTGAAAGGGGGAAACAATGAGAA
41611 C
261 C
41612 C
1 C
41613 CATTTTGTAA
Statistics
Matches: 259, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 259 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (261 bp):
CTTTAAAATAAAAATTTTCAGTTTTATCCTATTAAAAGTTTATGAAATTTTAAGTAAATATATGA
TAAAATTATAGCCTAATCCCTAAAAATGATGCATTTTGATTTGACCTTTCTAAAAACTATAAAAA
TGTCAATAAATTGGTGAAATTATATTTTATTTCTCATAAAAATATATAACTTAATCTTAATCCCC
GAAAAAGTTTTCAGCTTCGCCCTTGAATCTATATTTTGAAATCTGAAAGGGGGAAACAATGAGAA
C
Done.