Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002027.1 Kokia drynarioides strain JFW-HI SEQ_113908, 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: 2241
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Found at i:1207 original size:85 final size:85
Alignment explanation
Indices: 1063--1220 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
1053 GAATTGGTCT
* * * **
1063 ACTTCTCAGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGATTCACTTCTCTGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGATGAATACTTCATTGCTTCGACCCACTTCTCTGTATCTCAT
1128 CAGGAAGACGGATTTGGCTC
66 CAGGAAGACGGATTTGGCTC
* * * *
1148 ACTTCTCTGTATCTCGTTC-GGAAGATGAATACTTTATTGCTTCGACCCACTTCTTTGTATCTCA
1 ACTTCTCAGTATCTC-ATCAGGAAGATGAATACTTCATTGCTTCGACCCACTTCTCTGTATCTCA
1212 TCAGGAAGA
65 TCAGGAAGA
1221 TAGGGTTTGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 61 0.97
86 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (85 bp):
ACTTCTCAGTATCTCATCAGGAAGATGAATACTTCATTGCTTCGACCCACTTCTCTGTATCTCAT
CAGGAAGACGGATTTGGCTC
Found at i:1350 original size:207 final size:208
Alignment explanation
Indices: 851--1852 Score: 1393
Period size: 207 Copynumber: 4.8 Consensus size: 208
841 TCATATTTCA
* * * *
851 GTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTA-TTTAATCTACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * *
915 TCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCCGGAAGATGAACAATTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* * *
980 TCGACCTACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTTTAGTTTC
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACA-TTGAGTTTC
1045 ACTTCATTGAATTG
195 ACTTCATTGAATTG
** * *
1059 GTCTACTTCTCAGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGATTCACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * * *
1124 TCATCAGGAAGACGGATTTGGCTCACTTCTCTGTATCTCGTTCGGAAGATGAATACTTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* *
1189 TCGACCCACTTCTTTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAG-TTCA
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCA
1253 CTTCATTGAATTG
196 CTTCATTGAATTG
* * * *
1266 GTCTACTTCTCAGTATCTCATTAGAAAGATGACCGCTTCATTGTTTTGATCCACTTCTCTGTATG
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * *
1331 TCATTAGGAAGATGGATTTGGTTCACTTCTCTGCATCTCGTCCGAAAGATGAACACTTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* * *
1396 TCGACCTACTTCTTTGTATCTCATCGGGAAGATGGGGTTTGAAGTTTCACTCACATTGAG-TTCA
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCA
1460 CTTCATTGAATTG
196 CTTCATTGAATTG
*
1473 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCACTTCATTATTTTGATCCACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* ** * * * *
1538 TCATCAAGAAGATAGATTTGATTCACTTCTTTGCATCTCG-CCTAGAAGATGAACACTTTATTAC
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCC-GGAAGATGAACACTTTATTGC
* * *
1602 TTCGACTCACTTCTCTATATCTCATCAGGAATATGGGGTTTGAAGTTTCACTCACATTGAGTTTC
130 TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTC
*
1667 AATTCATTGAATTG
195 ACTTCATTGAATTG
* * ** * *
1681 GCCTACTTCTCAGTATCTCATCAGGAAGATGATCGCTTTTTTATTTTGTTCCACTTCTCTATATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * * * ** * *
1746 TTAAT-AAGAAGACGGATTTGGTTCACTTCTATACATCTCGTTTGGAAGATGAACACTCTCTTGC
66 -TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGC
* * * * *
1810 TTCAAACCACTTCTCAGTATCTCATTAGGAAGATGGAGTTTGA
130 TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGA
1853 TCTGTCCCTT
Statistics
Matches: 706, Mismatches: 83, Indels: 10
0.88 0.10 0.01
Matches are distributed among these distances:
206 2 0.00
207 376 0.53
208 198 0.28
209 130 0.18
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCA
CTTCATTGAATTG
Found at i:1585 original size:37 final size:37
Alignment explanation
Indices: 1517--1587 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
1507 ACTTCATTAT
* *
1517 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGA
1 TTTGATCCACTTCTCTGCATCTCACCAAGAAGATAGA
* * * *
1554 TTTGATTCACTTCTTTGCATCTCGCCTAGAAGAT
1 TTTGATCCACTTCTCTGCATCTCACCAAGAAGAT
1588 GAACACTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (37 bp):
TTTGATCCACTTCTCTGCATCTCACCAAGAAGATAGA
Found at i:1964 original size:47 final size:47
Alignment explanation
Indices: 1867--2025 Score: 225
Period size: 47 Copynumber: 3.4 Consensus size: 47
1857 TCCCTTTCGA
* * * *
1867 TTAGGGGTAAAAGATCGAAAT-ATGG-CTTCAATCTGCCCCTCTT-ATT
1 TTAGGGGTAAAAGATTG-GATGATGGTCTTTAATCTGCCCCTCTTGA-C
*
1913 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATTTGCCCCTCTTGAC
1 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGCCCCTCTTGAC
*
1960 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGTCCCTCTTGAC
1 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGCCCCTCTTGAC
2007 TTAGGGGTAAAAGATTGGA
1 TTAGGGGTAAAAGATTGGA
2026 ATCTTCAATC
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
45 2 0.02
46 20 0.19
47 80 0.78
48 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.34
Consensus pattern (47 bp):
TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGCCCCTCTTGAC
Found at i:2056 original size:41 final size:41
Alignment explanation
Indices: 1892--2236 Score: 298
Period size: 41 Copynumber: 8.0 Consensus size: 41
1882 CGAAATATGG
* *
1892 CTTCAATCTGCCCCTCTT-ATTTTAGGGGTAAAAGATTGGATGATGGT
1 CTTCAATCTGCCCTTCTTGA--TTAAGGGTAAAAGATTGGA--A---T
* * * *
1939 CTTTAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGT
1 CTTCAATCTGCCCTTCTTGA-TTAAGGGTAAAAGATTGGA--A---T
* *
1986 CTTTAATCTGTCCC-TCTTGACTTAGGGGTAAAAGATTGGAAT
1 CTTCAATCTG-CCCTTCTTGA-TTAAGGGTAAAAGATTGGAAT
* * *
2028 CTTCAATCTACCCTTTTTGATTAAGGGTAAGAGATTGGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
* * * * * *
2069 CTTTAATCTGCCCTTCTTTATTAAAGGTAAGAGACTAGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
* *
2110 CTTCAATCTGCCCTTCTTGATTAAGGGTAAGAGACTGGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
2151 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAATGT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAA--T
* * * *
2194 AGCTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGAAT
1 --CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
2237 GTGTT
Statistics
Matches: 265, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
41 131 0.49
42 14 0.05
43 2 0.01
45 37 0.14
47 77 0.29
48 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
Done.