Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004622.1 Kokia drynarioides strain JFW-HI SEQ_118136, 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: 23607
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1184 original size:36 final size:36
Alignment explanation
Indices: 1074--1229 Score: 180
Period size: 36 Copynumber: 4.5 Consensus size: 36
1064 CTCCTTACTA
1074 TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
1 TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
* * * **
1110 TTATAAGTCACCACCTCCTCC-A-CCATAC-TA---
1 TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
* *
1140 TTACAAGTCCCCGCCACCACCAAGCCCCACTTATGT
1 TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
* * *
1176 TTATAAGTCACCACCACCACCAAGCCCTACCTATGT
1 TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
1212 TTACAAGTCACCACCACC
1 TTACAAGTCACCACCACC
1230 TCCACCATAC
Statistics
Matches: 96, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
30 16 0.17
31 1 0.01
32 4 0.04
33 4 0.04
34 4 0.04
35 1 0.01
36 66 0.69
ACGTcount: A:0.29, C:0.42, G:0.08, T:0.21
Consensus pattern (36 bp):
TTACAAGTCACCACCACCACCAAGCCCCACTTATGT
Found at i:1262 original size:102 final size:102
Alignment explanation
Indices: 1078--1263 Score: 291
Period size: 102 Copynumber: 1.8 Consensus size: 102
1068 TTACTATTAC
* * * *
1078 AAGTCACCACCACCACCAAGCCCCACTTATGTTTATAAGTCACCACCTCCTCCACCATACTATTA
1 AAGTCACCACCACCACCAAGCCCCACCTATGTTTACAAGTCACCACCACCTCCACCATACTACTA
* *
1143 CAAGTCCCCGCCACCACCAAGCCCCACTTATGTTTAT
66 CAAATCCCCACCACCACCAAGCCCCACTTATGTTTAT
*
1180 AAGTCACCACCACCACCAAGCCCTACCTATGTTTACAAGTCACCACCACCTCCACCATACTACTA
1 AAGTCACCACCACCACCAAGCCCCACCTATGTTTACAAGTCACCACCACCTCCACCATACTACTA
* *
1245 CAAATCTCCACCGCCACCA
66 CAAATCCCCACCACCACCA
1264 GTCCACTCTC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
102 75 1.00
ACGTcount: A:0.30, C:0.43, G:0.07, T:0.20
Consensus pattern (102 bp):
AAGTCACCACCACCACCAAGCCCCACCTATGTTTACAAGTCACCACCACCTCCACCATACTACTA
CAAATCCCCACCACCACCAAGCCCCACTTATGTTTAT
Found at i:1277 original size:48 final size:48
Alignment explanation
Indices: 1225--1730 Score: 383
Period size: 48 Copynumber: 10.7 Consensus size: 48
1215 CAAGTCACCA
* * *
1225 CCACCTCCACCATACTACTACAAATCTCCACCGCCACCAGTCCACTCT
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * *
1273 CCACCCCCACCATACTATTACAAATCTCCACCACCACCAGTCCACTCT
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * * * * *
1321 CCACCCCCACCATACTATTACAAGTCTCCACCACCACC-TTCTC-CTTCA
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTC-CAC-TCT
* * * * * *
1369 CCACCTCCACCATACTACTACAAATCACCTCCGCCTCC--TTCACCATCT
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCA-C-TCT
* * * * * * ** ** *
1417 CCTCCGCCACCATACTACTACAAATCACCGCCACCTCCAATGAAGGCC
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * * * *
1465 CCAGCACCAACC-TACCACTACAACTCCCCTCCTCCACCA-T-CACCATCT
1 CCACCACC-ACCATACTACTACAAATCCCCACCACCACCAGTCCA-C-TCT
* * * * * * * *
1513 CCTCCTCCTCCTTACTATTACAAATCCCCACCACCTCCATCTCCA-TCA
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCA-GTCCACTCT
* * *
1561 CCACCACCTCCATACTACTACAAATCCCCACCACCACCAGTTCACTCA
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* *
1609 CCACCACCACC--ACCA-TAC---NCCCCACCACCACCAGTCCACTCT
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
*
1651 CCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACTCT
1 CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * *
1699 CCACCACCGCCCTACTACTACAAGTCCCCACC
1 CCACCACCACCATACTACTACAAATCCCCACC
1731 TCCTCCTCCC
Statistics
Matches: 370, Mismatches: 68, Indels: 40
0.77 0.14 0.08
Matches are distributed among these distances:
42 32 0.09
44 3 0.01
45 6 0.02
46 5 0.01
47 10 0.03
48 306 0.83
49 3 0.01
50 3 0.01
51 2 0.01
ACGTcount: A:0.27, C:0.51, G:0.03, T:0.18
Consensus pattern (48 bp):
CCACCACCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
Found at i:1373 original size:144 final size:139
Alignment explanation
Indices: 1223--1730 Score: 425
Period size: 144 Copynumber: 3.6 Consensus size: 139
1213 TACAAGTCAC
* *
1223 CACCACCTCCACCATACTACTACAAATCTCCACCGCCACCAGTCCACTCTCCACCCCCACCATAC
1 CACCACCTCCACCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCACCATAC
* * * * *
1288 TATTACAAATCTCCACCACCACCAGTCCACTCTCCACCCCCACCATACTATTACAAGTCTCCACC
66 TACTACAAATCCCCACCACCACCAGTCCACTCACCACCCCCACC-TACCA-TACAA-TCCCCACC
*
1353 ACCACCTTCTCCTT
128 ACCACCATC-CC-T
* * * * * * *
1367 CACCACCTCCACCATACTACTACAAATCACCTCCGCCTCC--TTCACCATCTCCTCCGCCACCAT
1 CACCACCTCCACCATACTACTACAAATCTCCACCACCACCAGTCCA-C-TCTCCACCACCACCAT
* * * * ** ** * * * *
1430 ACTACTACAAATCACCGCCACCTCCAATGAAGGCCCCAGCACCAACCTACCACTACAACTCCCCT
64 ACTACTACAAATCCCCACCACCACCAGTCCACTCACCA-CCCCCACCTACCA-TACAA-TCCCCA
*
1495 CCTCCACCATCACCAT
126 CCACCACCATC-CC-T
* * * * * * * * * *
1511 CTCCTCCTCCTCCTTACTATTACAAATCCCCACCACCTCCATCTCCA-TCACCACCACCTCCATA
1 CACCACCTCCACCATACTACTACAAATCTCCACCACCACCA-GTCCACTCTCCACCACCACCATA
* * *
1575 CTACTACAAATCCCCACCACCACCAGTTCACTCACCACCACCACC-ACCATAC--NCCCCACCAC
65 CTACTACAAATCCCCACCACCACCAGTCCACTCACCACCCCCACCTACCATACAATCCCCACCAC
1637 CACCAGTCCACT
130 CACCA-TCC-CT
* * * *
1649 CTCCACCACCACCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCGCCCTAC
1 CACCACCTCCACCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCACCATAC
*
1714 TACTACAAGTCCCCACC
66 TACTACAAATCCCCACC
1731 TCCTCCTCCC
Statistics
Matches: 288, Mismatches: 67, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
137 4 0.01
138 79 0.27
139 3 0.01
141 3 0.01
142 7 0.02
143 6 0.02
144 177 0.61
145 6 0.02
147 3 0.01
ACGTcount: A:0.27, C:0.51, G:0.03, T:0.18
Consensus pattern (139 bp):
CACCACCTCCACCATACTACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCACCATAC
TACTACAAATCCCCACCACCACCAGTCCACTCACCACCCCCACCTACCATACAATCCCCACCACC
ACCATCCCT
Found at i:1633 original size:18 final size:18
Alignment explanation
Indices: 1612--1666 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1602 TCACTCACCA
*
1612 CCACCACCACCATACNCC
1 CCACCACCACCATACTCC
*
1630 CCACCACCACCAGTCCACTCT
1 CCACCACCACCA-T--ACTCC
1651 CCACCACCACCATACT
1 CCACCACCACCATACT
1667 ACTACAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.47
19 1 0.03
20 1 0.03
21 15 0.47
ACGTcount: A:0.27, C:0.58, G:0.02, T:0.11
Consensus pattern (18 bp):
CCACCACCACCATACTCC
Found at i:1664 original size:90 final size:89
Alignment explanation
Indices: 1538--1706 Score: 250
Period size: 90 Copynumber: 1.9 Consensus size: 89
1528 TATTACAAAT
* * *
1538 CCCCACCACCTCCATCTCCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACCAGTT
1 CCCCACCACCACCATCTCCATCACCACCACCACCATACTACTACAAATCCCCACCACCACCAGTC
1603 CACTCACCACCACCACCACCATAC
66 CACTCACCACCACCACCACCATAC
* * *
1627 NCCCCACCACCACCA-GTCCACTCTCCACCACCACCATACTACTACAAATCTCCACCACCACCAG
1 -CCCCACCACCACCATCTCCA-TCACCACCACCACCATACTACTACAAATCCCCACCACCACCAG
*
1691 TCCACTCTCCACCACC
64 TCCACTCACCACCACC
1707 GCCCTACTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
89 4 0.06
90 67 0.94
ACGTcount: A:0.28, C:0.55, G:0.02, T:0.14
Consensus pattern (89 bp):
CCCCACCACCACCATCTCCATCACCACCACCACCATACTACTACAAATCCCCACCACCACCAGTC
CACTCACCACCACCACCACCATAC
Found at i:1699 original size:21 final size:21
Alignment explanation
Indices: 1588--1706 Score: 100
Period size: 21 Copynumber: 5.4 Consensus size: 21
1578 CTACAAATCC
* *
1588 CCACCACCACCAGTTCACTCA
1 CCACCACCACCAGTCCACTCT
* *
1609 CCACCACCACCA--CCATACNCC
1 CCACCACCACCAGTCC--ACTCT
1630 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
1651 CCACCACCACCA-TACTACTACAAATCT
1 CCACCACCACCAGT-C--C-AC---TCT
1678 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
1699 CCACCACC
1 CCACCACC
1707 GCCCTACTAC
Statistics
Matches: 81, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 54 0.67
23 3 0.04
24 4 0.05
25 1 0.01
27 16 0.20
28 1 0.01
ACGTcount: A:0.29, C:0.55, G:0.03, T:0.13
Consensus pattern (21 bp):
CCACCACCACCAGTCCACTCT
Found at i:18183 original size:49 final size:49
Alignment explanation
Indices: 18130--18248 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
18120 AATATATAAG
* * * *
18130 GTTAAAAAACCTTATTCTAATCACTGTCAAATATAAAAAACGTAGTAAA
1 GTTAAAAAACCTTATTCTAATCAATATCAAATAGAAAAAACGTAGGAAA
* * ** *
18179 GTTAAAAAACCTTATTCTAATCAATATGAAGTAGAAAAAGTGTAGGAAG
1 GTTAAAAAACCTTATTCTAATCAATATCAAATAGAAAAAACGTAGGAAA
*
18228 GTTGAAAAACCTTATTCTAAT
1 GTTAAAAAACCTTATTCTAAT
18249 TGATGTCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (49 bp):
GTTAAAAAACCTTATTCTAATCAATATCAAATAGAAAAAACGTAGGAAA
Found at i:18888 original size:23 final size:23
Alignment explanation
Indices: 18864--18969 Score: 176
Period size: 23 Copynumber: 4.6 Consensus size: 23
18854 TGTTGGGTAA
* *
18864 CAGAGAGCACACATAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAT
* *
18887 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
18910 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
18933 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
18956 CAGAGAGCACACAA
1 CAGAGAGCACACAA
18970 TAACAGAGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:18937 original size:69 final size:70
Alignment explanation
Indices: 18814--18969 Score: 194
Period size: 69 Copynumber: 2.3 Consensus size: 70
18804 ATATACGGAA
* * ** * *
18814 TAAATAGAGAGTAC-CAAAGTACTAACAGAGAGCACATAGGTGTTGGGTAACAGAGAGCACACAT
1 TAAACAGAGAGTACACAAAGTACTAACAGAGAGCACACAGAAGTTGGCTAACAGAGAGCACACAA
18878 AGTGC
66 AGTGC
18883 TAAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACA-AAG-T-GCTAATCAGAGAGCACAC
1 TAAACAGAGAGTACACAAAGTACTAA-CAGAGAGCACACAGAAGTTGGCTAA-CAGAGAGCACAC
18945 AAAGTGC
64 AAAGTGC
* *
18952 TAATCAGAGAGCACACAA
1 TAAACAGAGAGTACACAA
18970 TAACAGAGAG
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
68 4 0.05
69 48 0.63
70 12 0.16
71 12 0.16
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (70 bp):
TAAACAGAGAGTACACAAAGTACTAACAGAGAGCACACAGAAGTTGGCTAACAGAGAGCACACAA
AGTGC
Done.