Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008561.1 Kokia drynarioides strain JFW-HI SEQ_123239, 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: 6890
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1352 original size:147 final size:144
Alignment explanation
Indices: 1154--1508 Score: 390
Period size: 147 Copynumber: 2.4 Consensus size: 144
1144 TTTTCTCTTG
*
1154 TTTAAAACAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAA-A
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAATA
* * * * ***
1218 TCAAACTTTGTTCGAAAATTCAAACTTTTTCTTTTAAAATGCCTAAAAAACATTTTTTTTTATTT
66 -AAAAATTTGTTCAAAAATTCAAACTTTTT-TTTT-AAATGAC-AAAAAA-ATAGATTTTTATTT
1283 TTAAAAATCTAAACTTTCC
126 TTAAAAATCTAAACTTTCC
* * * **
1302 TTTAAAA-AAATTCACTACTTTAGTTAAAAATCCAAACTTTTATTTTGAAATAGTTAAAAAAATA
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAATA
* *
1366 AAAAATTTGTTTAAAAATTTAAACTTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAA
66 AAAAATTTGTTCAAAAATTCAAACTTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAA
* *
1431 AATCTAAATTTTCTATT
131 AATCTAAACTTTC---C
* * * * * ** * *
1448 TTTAAAAGAAAATAACTATTTTTCTTAAAAATAAAAAAATTTATTTCGAAATAGTTGAAAA
1 TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAA
1509 GATCAAAACT
Statistics
Matches: 174, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
143 28 0.16
144 6 0.03
145 6 0.03
146 11 0.06
147 115 0.66
148 8 0.05
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.41
Consensus pattern (144 bp):
TTTAAAACAAAATCACTACTTTACTTAAAAATCAAAACTTTTATTCCGAAATAGTTAAAAAAATA
AAAAATTTGTTCAAAAATTCAAACTTTTTTTTTAAATGACAAAAAAATAGATTTTTATTTTTAAA
AATCTAAACTTTCC
Found at i:1432 original size:23 final size:23
Alignment explanation
Indices: 1406--1454 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1396 TTTAAATGAC
*
1406 AAAAAAATAGATTTT-TATTTTT
1 AAAAAAATAAATTTTCTATTTTT
**
1428 AAAAATCTAAATTTTCTATTTTT
1 AAAAAAATAAATTTTCTATTTTT
1451 AAAA
1 AAAA
1455 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:1960 original size:15 final size:15
Alignment explanation
Indices: 1940--1978 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1930 ATTTAATAAC
1940 AATAATAATAATGAT
1 AATAATAATAATGAT
* * *
1955 AGTAATAGTATTGAT
1 AATAATAATAATGAT
1970 AATAATAAT
1 AATAATAAT
1979 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:2210 original size:42 final size:42
Alignment explanation
Indices: 2151--2666 Score: 712
Period size: 42 Copynumber: 12.3 Consensus size: 42
2141 CTCAATTACG
* * * *
2151 CTAAATGCAATGAAAAGTAAATGGACCTTCATACTTCGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2193 CTAAATGCGATGAAAAGTAAATGAACATCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2235 CTAAATGCGATGAAAAGTAAATGAACCTCCACAC-TAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * * * *
2276 CTAAATGCAATGAAAACTGAATGGACCTTCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* *
2318 CTAAATGTGATGAAAAGTATATGGACCTCCACACTTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* *
2360 CTAAATGCGATGAAAA-TATATGGACCTCCACACTTGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2401 CTAAATCCGATGAAAAGTAAATGGACCTCCACACATGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * *
2443 CTAAATGAGATGAAAATTAAATGGACCTCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
* * * *
2485 CTAAATGTGATGAAAAGTAAATGGACCTCCATACATGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2527 CTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
**
2569 CTAAATGTAATGAAAAGTAAATGGACCTCCACACTTAGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
** *
2611 CTAAATGTAATGAAAAGTAAATGGACCTCCACACTTGGGCCT
1 CTAAATGCGATGAAAAGTAAATGGACCTCCACACTTAGGCCT
*
2653 CTAAATGCAATGAA
1 CTAAATGCGATGAA
2667 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:2358 original size:125 final size:126
Alignment explanation
Indices: 2151--2666 Score: 757
Period size: 125 Copynumber: 4.1 Consensus size: 126
2141 CTCAATTACG
* * * * *
2151 CTAAATGCAATGAAAAGTAAATGGACCTTCATACTTCGGCCTCTAAATGCGATGAAAAGTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* * * *
2216 AACATCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGAACCTCCACAC-TAGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* * * *
2276 CTAAATGCAATGAAAACTGAATGGACCTTCACACCTAGGCCTCTAAATGTGATGAAAAGTATATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* *
2341 GACCTCCACACTTAGGCCTCTAAATGCGATGAAAA-TATATGGACCTCCACACTTGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* * * * * *
2401 CTAAATCCGATGAAAAGTAAATGGACCTCCACACATGGGCCTCTAAATGAGATGAAAATTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* * *
2466 GACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATGGACCTCCATACATGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
* *
2527 CTAAATGCGATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTAATGAAAAGTAAATG
1 CTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTCTAAATGTGATGAAAAGTAAATG
* **
2592 GACCTCCACACTTAGGCCTCTAAATGTAATGAAAAGTAAATGGACCTCCACACTTGGGCCT
66 GACCTCCACACCTAGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCCACACTTGGGCCT
2653 CTAAATGCAATGAA
1 CTAAATGCAATGAA
2667 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:5929 original size:27 final size:27
Alignment explanation
Indices: 5883--5957 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 27
5873 CGATGAAGAT
* *
5883 ATTCTGATTCTAGCTCGTAATAGCGTA
1 ATTCTGATTCTAGCTCGTAAGAGCATA
* *
5910 ATTCTGATTCTAGTTGGTAAGAGCATA
1 ATTCTGATTCTAGCTCGTAAGAGCATA
* *
5937 ATTTTG--TCTGGCTCGTAAGAG
1 ATTCTGATTCTAGCTCGTAAGAG
5958 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:5956 original size:25 final size:25
Alignment explanation
Indices: 5926--5984 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
5916 ATTCTAGTTG
*
5926 GTAAGAGCATAATTTTGTCT-GGCTC
1 GTAAGAGCAT-ATTTTATCTAGGCTC
* *
5951 GTAAGAGTGATATTTTATTTAGGCTC
1 GTAAGAG-CATATTTTATCTAGGCTC
5977 GTAAGAGC
1 GTAAGAGC
5985 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.