Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009661.1 Kokia drynarioides strain JFW-HI SEQ_124379, 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: 13021
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:2819 original size:40 final size:40
Alignment explanation
Indices: 2731--2825 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
2721 TTTGGAAAGA
*
2731 AAACGCCGCAAAAGGTAAAACAATAGCGACGCTTTTACAT
1 AAACGCCGCAAAAGGTAAAACAATAACGACGCTTTTACAT
* * *
2771 AAATGCCGCAAAAGGTAAAGCAATAACGGCGC-TTTACACT
1 AAACGCCGCAAAAGGTAAAACAATAACGACGCTTTTACA-T
*
2811 AAGCGCCGCTAAAAG
1 AAACGCCGC-AAAAG
2826 TCAAGTCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 6 0.13
40 36 0.77
41 5 0.11
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAACAATAACGACGCTTTTACAT
Found at i:2861 original size:41 final size:41
Alignment explanation
Indices: 2811--2950 Score: 199
Period size: 41 Copynumber: 3.4 Consensus size: 41
2801 GCTTTACACT
* ** * * *
2811 AAGCGCCGCTAAAAGTCAAGTCATTAGCGCCTCTTTCCCCC
1 AAGCGCCGCTAAAGGTCGGGTCATTAGTGGCGCTTTCCCCC
*
2852 AAGCTCCGCTAAAGGTCGGGTCATTAGTGGCGCTTTCCCCC
1 AAGCGCCGCTAAAGGTCGGGTCATTAGTGGCGCTTTCCCCC
*
2893 AAGCGCCGCTAAAGGTCGGGTCATTAGTGGGGCTTTCCCCC
1 AAGCGCCGCTAAAGGTCGGGTCATTAGTGGCGCTTTCCCCC
*
2934 AACCGCCGCTAAAGGTC
1 AAGCGCCGCTAAAGGTC
2951 TAGCTGAACA
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCGGGTCATTAGTGGCGCTTTCCCCC
Found at i:3326 original size:21 final size:19
Alignment explanation
Indices: 3288--3326 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
3278 TTATAATTTA
*
3288 ATTTTATTTATTAAATATT
1 ATTTTATTTATAAAATATT
3307 ATTTTCATTTAATAAAATAT
1 ATTTT-ATTT-ATAAAATAT
3327 CATTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTATTTATAAAATATT
Found at i:4671 original size:382 final size:385
Alignment explanation
Indices: 3955--4722 Score: 1355
Period size: 382 Copynumber: 2.0 Consensus size: 385
3945 GAGAAAAAAC
*
3955 AAAAAGTAAAATACAAAGAAAAAATTTTCAATTTTTCAAGGGTTGAATCGATCTACACTCTCTTG
1 AAAAAGAAAAATACAAAGAAAAAATTTTCAATTTTTCAAGGGTTGAATCGATCTACACTCTCTTG
* * * *
4020 TCAAAGCTTTGATCTTTTGATTTTAAAGGTAACATTTTTTCCCTCATTAACTTTAGCACCCTTAT
66 TCAAAGCCTTGATCTTTTGATTTTAAAGGTAACATTTTTTCCCTCATTAACTTCAACACCCTTAC
4085 TTTTTGGTTTTTGCCTCCCATAATTATTTCATATTTAAGGTTTTCTTTCACTCGAATTTAGGAAC
131 TTTTTGGTTTTTGCCTCCCATAATTATTTCATATTTAAGGTTTTCTTTCACTCGAATTTAGGAAC
*
4150 TTTTTTTTTTTGTTAATATTCTTTTTTTCTTATTGCTTAAATGTTTTGAATTCGATAATTTTCTC
196 TTTTTTTTTTTGTTAATATTCTTTTTTTCTTATTGCTTAAATGTTTCGAATTCGATAATTTTCTC
* ***
4215 TTGGATTATGTAATATATCTTAGCTCATTGTTTTGGACTTTTTTTGGGGTTAAGTTTTTTAAGCA
261 TTGGATTATGTAATATACCTTAGCTCACAATTTTGGACTTTTTTTGGGGTTAAGTTTTTTAAGCA
4280 TGAACCTCTGTTTTATTTAGGGGAAAAGGAGCAGCTTCAATCGGTCCATTGTTGTTGCTT
326 TGAACCTCTGTTTTATTTAGGGGAAAAGGAGCAGCTTCAATCGGTCCATTGTTGTTGCTT
4340 AAAAAGAAAAATACAAAGAAGAAAA-TTTCAATTTTTCAAGGGTTGAATCGATCTACACTCTCTT
1 AAAAAGAAAAATACAAAGAA-AAAATTTTCAATTTTTCAAGGGTTGAATCGATCTACACTCTCTT
*
4404 GTCAAAGCCTTGATCTTTTGATTTTAAAGGTAACCTTTTTT-CCTCATTAACTTCAACACCCTT-
65 GTCAAAGCCTTGATCTTTTGATTTTAAAGGTAACATTTTTTCCCTCATTAACTTCAACACCCTTA
* * *
4467 CTTTTTGGTTTTTGTCTCCCATAATTATTTCATATTTAGGGTTTTCTTTCACTCGAATTTGGGAA
130 CTTTTTGGTTTTTGCCTCCCATAATTATTTCATATTTAAGGTTTTCTTTCACTCGAATTTAGGAA
*
4532 C-TTTTTTTTTTGTTAATCTTCTTTTTTTCTTATTGCTTAAATGTTTCGAATTCGATAATTTTCT
195 CTTTTTTTTTTTGTTAATATTCTTTTTTTCTTATTGCTTAAATGTTTCGAATTCGATAATTTTCT
4596 CTTGGATTATGTAATATACCTTAGCTCACAATTTTGGACTTTTTTTGGGGTTAAGTTTTTTAAGC
260 CTTGGATTATGTAATATACCTTAGCTCACAATTTTGGACTTTTTTTGGGGTTAAGTTTTTTAAGC
*
4661 ATGAACCTCTGTTTTATTTAGGGGGAAAGGAGCAGCTTCAATCGGTCCATTGTTGTTGCTT
325 ATGAACCTCTGTTTTATTTAGGGGAAAAGGAGCAGCTTCAATCGGTCCATTGTTGTTGCTT
4722 A
1 A
4723 GTTTTATCAT
Statistics
Matches: 366, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
382 183 0.50
383 62 0.17
384 20 0.05
385 97 0.27
386 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (385 bp):
AAAAAGAAAAATACAAAGAAAAAATTTTCAATTTTTCAAGGGTTGAATCGATCTACACTCTCTTG
TCAAAGCCTTGATCTTTTGATTTTAAAGGTAACATTTTTTCCCTCATTAACTTCAACACCCTTAC
TTTTTGGTTTTTGCCTCCCATAATTATTTCATATTTAAGGTTTTCTTTCACTCGAATTTAGGAAC
TTTTTTTTTTTGTTAATATTCTTTTTTTCTTATTGCTTAAATGTTTCGAATTCGATAATTTTCTC
TTGGATTATGTAATATACCTTAGCTCACAATTTTGGACTTTTTTTGGGGTTAAGTTTTTTAAGCA
TGAACCTCTGTTTTATTTAGGGGAAAAGGAGCAGCTTCAATCGGTCCATTGTTGTTGCTT
Found at i:8892 original size:21 final size:21
Alignment explanation
Indices: 8866--8912 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8856 CTACAACTTA
8866 AAGCGGAGGCAACAGCGAGGC
1 AAGCGGAGGCAACAGCGAGGC
* **
8887 AAGCGGAGGTAGTAGCGAGGC
1 AAGCGGAGGCAACAGCGAGGC
8908 AAGCG
1 AAGCG
8913 AGGGAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.45, T:0.04
Consensus pattern (21 bp):
AAGCGGAGGCAACAGCGAGGC
Found at i:10611 original size:23 final size:24
Alignment explanation
Indices: 10568--10612 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
10558 ATTTTTAAAT
*
10568 TTGAAAAATAAAATTACTAAATTC
1 TTGAAAAATAAAAATACTAAATTC
10592 TTGAAATAA-AAAAATA-TAAAT
1 TTGAAA-AATAAAAATACTAAAT
10613 ACTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
TTGAAAAATAAAAATACTAAATTC
Done.