Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008560.1 Kokia drynarioides strain JFW-HI SEQ_123238, 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: 6841
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1392 original size:147 final size:143
Alignment explanation
Indices: 1154--1507 Score: 397
Period size: 147 Copynumber: 2.4 Consensus size: 143
1144 TTTTCTCTTG
*
1154 TTTAAAACAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAAAT
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAAAT
* * * * **
1219 CAAACTTTGTTTGAAAATTCAAACTTTTTCTTTTAAAATGCCTAAAAAACATATTTTTTTATTTT
66 AAAAATTTGTTTAAAAATTCAAAC-TTTT-TTTT-AAATGAC-AAAAAA-ATAGATTTTTATTTT
1284 TAAAAATCTAAACTTTCC
126 TAAAAATCTAAACTTTCC
* * * **
1302 TTTAAAA-AAATTCACTACTTTAGTTAAAAATCCAAACTTTTATTTTGAAATAGTT-AAAAAAAT
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAAAT
*
1365 AAAAAATTTGTTTAAAAATTTAAACTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAA
66 -AAAAATTTGTTTAAAAATTCAAACTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAA
* *
1430 AATCTAAATTTTCTATT
130 AATCTAAACTTTC---C
* * * * * ** * *
1447 TTTAAAAGAAAATAACTATTTTTCTTAAAAATAAAAAAATTTATTTCGAAATAGTTGAAAA
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAA
1508 GATCAAAACT
Statistics
Matches: 175, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
142 29 0.17
143 6 0.03
144 6 0.03
145 11 0.06
146 50 0.29
147 66 0.38
148 7 0.04
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.40
Consensus pattern (143 bp):
TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAAAT
AAAAATTTGTTTAAAAATTCAAACTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAAA
ATCTAAACTTTCC
Found at i:1431 original size:23 final size:23
Alignment explanation
Indices: 1405--1453 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1395 TTTAAATGAC
*
1405 AAAAAAATAGATTTT-TATTTTT
1 AAAAAAATAAATTTTCTATTTTT
**
1427 AAAAATCTAAATTTTCTATTTTT
1 AAAAAAATAAATTTTCTATTTTT
1450 AAAA
1 AAAA
1454 GAAAATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAAAAATAAATTTTCTATTTTT
Found at i:1911 original size:15 final size:15
Alignment explanation
Indices: 1891--1929 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1881 ATTTAATAAC
1891 AATAATAATAATGAT
1 AATAATAATAATGAT
* * *
1906 AGTAATAGTATTGAT
1 AATAATAATAATGAT
1921 AATAATAAT
1 AATAATAAT
1930 TTGGGCCCTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (15 bp):
AATAATAATAATGAT
Found at i:2161 original size:42 final size:42
Alignment explanation
Indices: 2102--2617 Score: 712
Period size: 42 Copynumber: 12.3 Consensus size: 42
2092 CTCAATTACG
* * * *
2102 CTAAATGCAATGAAAAGTAAATGGACCTTCATACTTCGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2144 CTAAATGCGATGAAAAGTAAATGAACATCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2186 CTAAATGCGATGAAAAGTAAATGAACCTCCACAC-TAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * * * *
2227 CTAAATGCAATGAAAACTGAATGGACCTTCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* *
2269 CTAAATGTGATGAAAAGTATATGGACCTCCACACTTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* *
2311 CTAAATGCGATGAAAA-TATATGGACCTCCACACTTGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2352 CTAAATCCGATGAAAAGTAAATGGACCTCCACACATGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2394 CTAAATGAGATGAAAATTAAATGGACCTCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * * *
2436 CTAAATGTGATGAAAAGTAAATGGACCTCCATACATGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2478 CTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
**
2520 CTAAATGTAATGAAAAGTAAATGGACCTCCACACTTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
** *
2562 CTAAATGTAATGAAAAGTAAATGGACCTCCACACTTGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2604 CTAAATGCAATGAA
1 CTAAATGCGATGAA
2618 TGCTTTCCTT
Statistics
Matches: 428, Mismatches: 44, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
41 75 0.18
42 353 0.82
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
Found at i:2309 original size:125 final size:126
Alignment explanation
Indices: 2102--2617 Score: 757
Period size: 125 Copynumber: 4.1 Consensus size: 126
2092 CTCAATTACG
* * * * *
2102 CTAAATGCAATGAAAAGTAAATGGACCTTCATACTTCGGCCTCTAAATGCGATGAAAAGTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* * * *
2167 AACATCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCACAC-TAGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* * * *
2227 CTAAATGCAATGAAAACTGAATGGACCTTCACACCTAGGCCTCTAAATGTGATGAAAAGTATATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* *
2292 GACCTCCACACTTAGGCCTCTAAATGCGATGAAAA-TATATGGACCTCCACACTTGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* * * * * *
2352 CTAAATCCGATGAAAAGTAAATGGACCTCCACACATGGGCCTCTAAATGAGATGAAAATTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* * *
2417 GACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATGGACCTCCATACATGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* *
2478 CTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTAATGAAAAGTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* **
2543 GACCTCCACACTTAGGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCACACTTGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
2604 CTAAATGCAATGAA
1 CTAAATGCAATGAA
2618 TGCTTTCCTT
Statistics
Matches: 350, Mismatches: 39, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
124 15 0.04
125 184 0.53
126 151 0.43
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (126 bp):
CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
Found at i:5880 original size:27 final size:27
Alignment explanation
Indices: 5834--5908 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
5824 CGATGAAGAT
* *
5834 ATTCTGATTCTAGCTCGTAATAGCGTA
1 ATTCTGATTCTAGCTCGTAAGAGCATA
* *
5861 ATTCTGATTCTAGTTGGTAAGAGCATA
1 ATTCTGATTCTAGCTCGTAAGAGCATA
* *
5888 ATTTTG--TCTGGCTCGTAAGAG
1 ATTCTGATTCTAGCTCGTAAGAG
5909 TGATATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 12 0.30
27 28 0.70
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (27 bp):
ATTCTGATTCTAGCTCGTAAGAGCATA
Found at i:5907 original size:25 final size:25
Alignment explanation
Indices: 5877--5935 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5867 ATTCTAGTTG
*
5877 GTAAGAGCATAATTTTGTCT-GGCTC
1 GTAAGAGCAT-ATTTTATCTAGGCTC
* *
5902 GTAAGAGTGATATTTTATTTAGGCTC
1 GTAAGAG-CATATTTTATCTAGGCTC
5928 GTAAGAGC
1 GTAAGAGC
5936 TAAACTCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (25 bp):
GTAAGAGCATATTTTATCTAGGCTC
Done.