Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004416.1 Kokia drynarioides strain JFW-HI SEQ_117797, 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: 5262
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Found at i:1144 original size:85 final size:85
Alignment explanation
Indices: 1000--1157 Score: 219
Period size: 85 Copynumber: 1.9 Consensus size: 85
990 GAATTGGTCT
* * * **
1000 ACTTCTCAGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGATTCACTTCTCTGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGATGAATACTTCATTGCTTCGACCCACTTCTCTGTATCTCAT
1065 CAGGAAGACGGATTTGGCTC
66 CAGGAAGACGGATTTGGCTC
* * * *
1085 ACTTCTCTGTATCTCGTTC-GGAAGATGAATACTTTATTGCTTCGACCCACTTCTTTGTATCTCA
1 ACTTCTCAGTATCTC-ATCAGGAAGATGAATACTTCATTGCTTCGACCCACTTCTCTGTATCTCA
1149 TCAGGAAGA
65 TCAGGAAGA
1158 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:1287 original size:207 final size:208
Alignment explanation
Indices: 788--1789 Score: 1393
Period size: 207 Copynumber: 4.8 Consensus size: 208
778 TCATATTTCA
* * * *
788 GTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTA-TTTAATCTACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * *
852 TCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCCGGAAGATGAACAATTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* * *
917 TCGACCTACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTTTAGTTTC
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACA-TTGAGTTTC
982 ACTTCATTGAATTG
195 ACTTCATTGAATTG
** * *
996 GTCTACTTCTCAGTATCTCATCAGGAAGATGACTACTTCATTGTTTTGATTCACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * * *
1061 TCATCAGGAAGACGGATTTGGCTCACTTCTCTGTATCTCGTTCGGAAGATGAATACTTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* *
1126 TCGACCCACTTCTTTGTATCTCATCAGGAAGATAGGGTTTGAAGTTTCACTCACATTGAG-TTCA
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCA
1190 CTTCATTGAATTG
196 CTTCATTGAATTG
* * * *
1203 GTCTACTTCTCAGTATCTCATTAGAAAGATGACCGCTTCATTGTTTTGATCCACTTCTCTGTATG
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * *
1268 TCATTAGGAAGATGGATTTGGTTCACTTCTCTGCATCTCGTCCGAAAGATGAACACTTTATTGCT
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGCT
* * *
1333 TCGACCTACTTCTTTGTATCTCATCGGGAAGATGGGGTTTGAAGTTTCACTCACATTGAG-TTCA
131 TCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCA
1397 CTTCATTGAATTG
196 CTTCATTGAATTG
*
1410 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCACTTCATTATTTTGATCCACTTCTCTGTATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* ** * * * *
1475 TCATCAAGAAGATAGATTTGATTCACTTCTTTGCATCTCG-CCTAGAAGATGAACACTTTATTAC
66 TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCC-GGAAGATGAACACTTTATTGC
* * *
1539 TTCGACTCACTTCTCTATATCTCATCAGGAATATGGGGTTTGAAGTTTCACTCACATTGAGTTTC
130 TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTC
*
1604 AATTCATTGAATTG
195 ACTTCATTGAATTG
* * ** * *
1618 GCCTACTTCTCAGTATCTCATCAGGAAGATGATCGCTTTTTTATTTTGTTCCACTTCTCTATATC
1 GTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCTTCATTATTTTGATCCACTTCTCTGTATC
* * * * ** * *
1683 TTAAT-AAGAAGACGGATTTGGTTCACTTCTATACATCTCGTTTGGAAGATGAACACTCTCTTGC
66 -TCATCAGGAAGACGGATTTGGTTCACTTCTCTGCATCTCGTCCGGAAGATGAACACTTTATTGC
* * * * *
1747 TTCAAACCACTTCTCAGTATCTCATTAGGAAGATGGAGTTTGA
130 TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGA
1790 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:1522 original size:37 final size:37
Alignment explanation
Indices: 1454--1524 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
1444 ACTTCATTAT
* *
1454 TTTGATCCACTTCTCTGTATCTCATCAAGAAGATAGA
1 TTTGATCCACTTCTCTGCATCTCACCAAGAAGATAGA
* * * *
1491 TTTGATTCACTTCTTTGCATCTCGCCTAGAAGAT
1 TTTGATCCACTTCTCTGCATCTCACCAAGAAGAT
1525 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:1901 original size:47 final size:47
Alignment explanation
Indices: 1804--1962 Score: 225
Period size: 47 Copynumber: 3.4 Consensus size: 47
1794 TCCCTTTCGA
* * * *
1804 TTAGGGGTAAAAGATCGAAAT-ATGG-CTTCAATCTGCCCCTCTT-ATT
1 TTAGGGGTAAAAGATTG-GATGATGGTCTTTAATCTGCCCCTCTTGA-C
*
1850 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATTTGCCCCTCTTGAC
1 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGCCCCTCTTGAC
*
1897 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGTCCCTCTTGAC
1 TTAGGGGTAAAAGATTGGATGATGGTCTTTAATCTGCCCCTCTTGAC
1944 TTAGGGGTAAAAGATTGGA
1 TTAGGGGTAAAAGATTGGA
1963 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:1993 original size:41 final size:41
Alignment explanation
Indices: 1829--2173 Score: 298
Period size: 41 Copynumber: 8.0 Consensus size: 41
1819 CGAAATATGG
* *
1829 CTTCAATCTGCCCCTCTT-ATTTTAGGGGTAAAAGATTGGATGATGGT
1 CTTCAATCTGCCCTTCTTGA--TTAAGGGTAAAAGATTGGA--A---T
* * * *
1876 CTTTAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGGT
1 CTTCAATCTGCCCTTCTTGA-TTAAGGGTAAAAGATTGGA--A---T
* *
1923 CTTTAATCTGTCCC-TCTTGACTTAGGGGTAAAAGATTGGAAT
1 CTTCAATCTG-CCCTTCTTGA-TTAAGGGTAAAAGATTGGAAT
* * *
1965 CTTCAATCTACCCTTTTTGATTAAGGGTAAGAGATTGGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
* * * * * *
2006 CTTTAATCTGCCCTTCTTTATTAAAGGTAAGAGACTAGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
* *
2047 CTTCAATCTGCCCTTCTTGATTAAGGGTAAGAGACTGGAAT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
2088 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAATGT
1 CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAA--T
* * * *
2131 AGCTTCAATTTGCCCCTCTAGATTAGGGGTAAAAGATTGGAAT
1 --CTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGATTGGAAT
2174 GTGTTCAGTC
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
Found at i:2266 original size:49 final size:47
Alignment explanation
Indices: 2177--2323 Score: 134
Period size: 48 Copynumber: 3.0 Consensus size: 47
2167 TTGGAATGTG
* * * **
2177 TTCAGTCTTTCATGGTACCAGATTCGTCGTTGCGGTCTCAATCCTT-CC
1 TTCAATCTTT-ATGGTACCGGGTTCGTCGTTGCGACCTCAA-CCTTCCC
*
2225 TATCACATCTTTATGGTACCGGGTTCGCCGTTGCGACCTCAACCTTTCCC
1 T-TCA-ATCTTTATGGTACCGGGTTCGTCGTTGCGACCTCAACC-TTCCC
* * ** * *
2275 TTCAATCTTCATGGCATTGAGTTCGTCGTTGCGACCTCAACCTTTCC
1 TTCAATCTTTATGGTACCGGGTTCGTCGTTGCGACCTCAACCTTCCC
2322 TT
1 TT
2324 TAAAATCTTC
Statistics
Matches: 82, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
47 6 0.07
48 35 0.43
49 33 0.40
50 8 0.10
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.36
Consensus pattern (47 bp):
TTCAATCTTTATGGTACCGGGTTCGTCGTTGCGACCTCAACCTTCCC
Found at i:2765 original size:32 final size:32
Alignment explanation
Indices: 2724--2789 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2714 AATCCTTTCA
2724 TCCCTCGTATCGTTAAACCACTAATCGTTATT
1 TCCCTCGTATCGTTAAACCACTAATCGTTATT
2756 TCCCTCGTATCGTTAAACCACTAATCGTTATT
1 TCCCTCGTATCGTTAAACCACTAATCGTTATT
2788 TC
1 TC
2790 AAAAGTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (32 bp):
TCCCTCGTATCGTTAAACCACTAATCGTTATT
Found at i:3299 original size:15 final size:16
Alignment explanation
Indices: 3279--3308 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3269 CCTATTGTTT
3279 CTTTTTTTT-TTTTTG
1 CTTTTTTTTCTTTTTG
3294 CTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTT
3309 TCAAGATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (16 bp):
CTTTTTTTTCTTTTTG
Done.