Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010822.1 Kokia drynarioides strain JFW-HI SEQ_125789, 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: 54704
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:949 original size:39 final size:39
Alignment explanation
Indices: 878--1090 Score: 189
Period size: 39 Copynumber: 5.4 Consensus size: 39
868 ATGCTTTAGT
* * * *
878 AGTGTTTATAGTGTCATTACTA-TTGCAATATAGTCTTGC
1 AGTGTTTACAGTGTCATCACTAGTT-CAGTATAGTATTGC
* * *
917 AATGTTTACAGTGTCATCACCAGTTCAGTATAGTATTTC
1 AGTGTTTACAGTGTCATCACTAGTTCAGTATAGTATTGC
* *
956 AGTGTTTACAGTGTCA-CTACCAGTTCAGTATAGTATTGT
1 AGTGTTTACAGTGTCATC-ACTAGTTCAGTATAGTATTGC
** * *
995 AGTGTTTACAGTGTCATTGCTAGTTCAGTATAATATCGC
1 AGTGTTTACAGTGTCATCACTAGTTCAGTATAGTATTGC
* * * * * *
1034 AGTGTTTATAGTGTCA-CTGCTAGTTCAATATAGGTGTCGT
1 AGTGTTTACAGTGTCATC-ACTAGTTCAGTATA-GTATTGC
*
1074 AATGTTTACAGTGTCAT
1 AGTGTTTACAGTGTCAT
1091 TGCCAATCCG
Statistics
Matches: 144, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
38 1 0.01
39 123 0.85
40 20 0.14
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (39 bp):
AGTGTTTACAGTGTCATCACTAGTTCAGTATAGTATTGC
Found at i:988 original size:78 final size:78
Alignment explanation
Indices: 878--1090 Score: 257
Period size: 78 Copynumber: 2.7 Consensus size: 78
868 ATGCTTTAGT
* * *
878 AGTGTTTATAGTGTCATTACTA-TTGCAATATAGTCTTGCAATGTTTACAGTGTCATCACCAGTT
1 AGTGTTTATAGTGTCACTACTAGTT-CAATATAGTATTGTAATGTTTACAGTGTCATCACCAGTT
* **
942 CAGTATAGTATTTC
65 CAGTATAATATCGC
* * * * ** *
956 AGTGTTTACAGTGTCACTACCAGTTCAGTATAGTATTGTAGTGTTTACAGTGTCATTGCTAGTTC
1 AGTGTTTATAGTGTCACTACTAGTTCAATATAGTATTGTAATGTTTACAGTGTCATCACCAGTTC
1021 AGTATAATATCGC
66 AGTATAATATCGC
* * *
1034 AGTGTTTATAGTGTCACTGCTAGTTCAATATAGGTGTCGTAATGTTTACAGTGTCAT
1 AGTGTTTATAGTGTCACTACTAGTTCAATATA-GTATTGTAATGTTTACAGTGTCAT
1091 TGCCAATCCG
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
78 90 0.80
79 23 0.20
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (78 bp):
AGTGTTTATAGTGTCACTACTAGTTCAATATAGTATTGTAATGTTTACAGTGTCATCACCAGTTC
AGTATAATATCGC
Found at i:1481 original size:73 final size:73
Alignment explanation
Indices: 1356--1544 Score: 236
Period size: 73 Copynumber: 2.6 Consensus size: 73
1346 CGGCTATACT
* * * ** *
1356 CACGTCCGTGTGTCTAGCCCGTGTAACTCACTATTTCCAATTCCACAAAATAGAATAT-CCACAC
1 CACGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTTATTTCACAAAATAGAAT-TCCCACAC
1420 GATCTAGCA
65 GATCTAGCA
* * ** *
1429 CACGCCCGTATGTCCAGCCTGTGTAACTCACTGTTTCTTATTTCACCGAATAGAATTCCCACATG
1 CACGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTTATTTCACAAAATAGAATTCCCACACG
*
1494 GTCTAGCA
66 ATCTAGCA
* *
1502 CACGCCCGTGTGCCCAGCCCGTGTAACTCATTGTTTCTTATTT
1 CACGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTTATTT
1545 ATATGGCACA
Statistics
Matches: 99, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
72 1 0.01
73 98 0.99
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (73 bp):
CACGCCCGTGTGTCCAGCCCGTGTAACTCACTGTTTCTTATTTCACAAAATAGAATTCCCACACG
ATCTAGCA
Found at i:2796 original size:15 final size:15
Alignment explanation
Indices: 2776--2805 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2766 GAAATAGGAT
2776 TTGTATGGAATAGAG
1 TTGTATGGAATAGAG
2791 TTGTATGGAATAGAG
1 TTGTATGGAATAGAG
2806 CTCTGATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (15 bp):
TTGTATGGAATAGAG
Found at i:4096 original size:42 final size:43
Alignment explanation
Indices: 4049--4161 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 43
4039 GTTGGTATTT
*
4049 AATTTATTTTTTAAAATTTAAAAAATT-TAAAAAAAA-ATTATA
1 AATTTA-TTTTTAAAATTTAAAAAATTATAAAAAAAATATTAAA
* *
4091 AATTTATTTTTAAAAATT-AAAATTTATAAAAAAAATATTAAA
1 AATTTATTTTTAAAATTTAAAAAATTATAAAAAAAATATTAAA
**
4133 AAAATATTTTTAAATATTTTAAAAAATTA
1 AATTTATTTTTAAA-A-TTTAAAAAATTA
4162 ATTAAATACT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
40 6 0.10
41 20 0.34
42 23 0.39
43 1 0.02
44 2 0.03
45 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (43 bp):
AATTTATTTTTAAAATTTAAAAAATTATAAAAAAAATATTAAA
Found at i:4124 original size:19 final size:19
Alignment explanation
Indices: 4070--4126 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
4060 TAAAATTTAA
4070 AAAATTTA-AAAAAAAATT
1 AAAATTTATAAAAAAAATT
***
4088 ATAAATTTATTTTTAAAAATT
1 A-AAATTTA-TAAAAAAAATT
4109 AAAATTTATAAAAAAAAT
1 AAAATTTATAAAAAAAAT
4127 ATTAAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 7 0.23
21 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTATAAAAAAAATT
Found at i:4132 original size:21 final size:20
Alignment explanation
Indices: 4076--4133 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
4066 TTAAAAAATT
4076 TAAAAAAAAATTATAAATTTA
1 TAAAAAAAAATTA-AAATTTA
****
4097 TTTTTAAAAATTAAAATTTA
1 TAAAAAAAAATTAAAATTTA
4117 TAAAAAAAATATTAAAA
1 TAAAAAAAA-ATTAAAA
4134 AAATATTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAAAAAATTAAAATTTA
Found at i:4648 original size:24 final size:24
Alignment explanation
Indices: 4621--4673 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
4611 TTTTTAGAAG
* *
4621 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAATATAATAT
*
4645 ATTTAGCATTTATTAATATAATTT
1 ATTTAGCATTTATTAATATAATAT
4669 ATTTA
1 ATTTA
4674 ACTTAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
ATTTAGCATTTATTAATATAATAT
Found at i:4787 original size:24 final size:24
Alignment explanation
Indices: 4760--4809 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4750 TTTTTGAAGA
*
4760 TTTTTGTATTT-ACATTTTAAGGGT
1 TTTTTGT-TTTAAAATTTTAAGGGT
*
4784 TTTTTGTTTTAAAATTTTTAGGGT
1 TTTTTGTTTTAAAATTTTAAGGGT
4808 TT
1 TT
4810 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (24 bp):
TTTTTGTTTTAAAATTTTAAGGGT
Found at i:7559 original size:2 final size:2
Alignment explanation
Indices: 7554--7581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7544 AGATATACTA
7554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7582 TCTTAAGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10130 original size:6 final size:6
Alignment explanation
Indices: 10119--10145 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10109 AAATTCAAAG
10119 CCTCCA CCTCCA CCTCCA CCTCCA CCT
1 CCTCCA CCTCCA CCTCCA CCTCCA CCT
10146 TCACTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.67, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:30465 original size:187 final size:189
Alignment explanation
Indices: 30146--30531 Score: 569
Period size: 187 Copynumber: 2.0 Consensus size: 189
30136 TTCATACATA
* * * * *
30146 TGGTCTAAAACCCAGTGGGTAGGGGTACAATGTGAGTATATTTGATTGTTTCTAATCGTATGCTT
1 TGGTCTAAAACCCACTGGGTAAGGGTACAATGTGAGTATATTTGATTATTTCTAACCCTATGC--
*
30211 TTTATTTTGTTTGCAAGTTCGATTGACGATTCGTTTTCTGGAGTAATCTATTATTGAATCATCAA
64 TTTATTTTGTTTGCAAGTTCGATTGACGATTCGTTTTCTGGAGTAATCTATTATTAAATCATCAA
* *
30276 AGGTTAGTCATAAGTTCATTTGTATTTTCTGAAAATGTTGGAATATGTTGATATTATACTG
129 AGGTAAGTCATAAGTTCATTTGTATTTCCTGAAAATGTTGGAATATGTTGATATTATACTG
* * *
30337 TGGTCTAAAACCTACTGGGTAAGGGTAGAATGTGAGTATATTTGATTATTTCTACCCCTATGC-T
1 TGGTCTAAAACCCACTGGGTAAGGGTACAATGTGAGTATATTTGATTATTTCTAACCCTATGCTT
* * * * * *
30401 T-TTTTGTTTGCAGGTTGGGTTGATGGTTCGTTTTCTGGAGTAATCTATTGTTAAATCATCAAAG
66 TATTTTGTTTGCAAGTTCGATTGACGATTCGTTTTCTGGAGTAATCTATTATTAAATCATCAAAG
* *
30465 GTAAGTCATCAGTTCATTTGTATTTCCTGAAAATGTTGGAATATGTTGATATTATATTG
131 GTAAGTCATAAGTTCATTTGTATTTCCTGAAAATGTTGGAATATGTTGATATTATACTG
30524 TGGTCTAA
1 TGGTCTAA
30532 CTGTCTGGGT
Statistics
Matches: 176, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
187 119 0.68
188 2 0.01
191 55 0.31
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.42
Consensus pattern (189 bp):
TGGTCTAAAACCCACTGGGTAAGGGTACAATGTGAGTATATTTGATTATTTCTAACCCTATGCTT
TATTTTGTTTGCAAGTTCGATTGACGATTCGTTTTCTGGAGTAATCTATTATTAAATCATCAAAG
GTAAGTCATAAGTTCATTTGTATTTCCTGAAAATGTTGGAATATGTTGATATTATACTG
Found at i:31669 original size:14 final size:15
Alignment explanation
Indices: 31650--31690 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
31640 GTGTTAAAAT
*
31650 ATTAAAAAAT-TTAG
1 ATTAAAAAATAATAG
31664 ATTAAAAAATAATAG
1 ATTAAAAAATAATAG
31679 -TTAAAAAATAAT
1 ATTAAAAAATAAT
31691 GTAAATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.88
15 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATTAAAAAATAATAG
Found at i:32098 original size:17 final size:19
Alignment explanation
Indices: 32052--32098 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
32042 TAGTGTCAGT
32052 AGGGTTTAGTATTTGAGACC
1 AGGGTTTAGTATTTGAGA-C
* *
32072 AGGGTGTAGT-TTTGAG-G
1 AGGGTTTAGTATTTGAGAC
32089 AGGGTTTAGT
1 AGGGTTTAGT
32099 CAGGTGTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.36
Consensus pattern (19 bp):
AGGGTTTAGTATTTGAGAC
Found at i:32414 original size:27 final size:27
Alignment explanation
Indices: 32381--32487 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 27
32371 TCGAGAGGGA
32381 AGGGAGGAAGTTGTTCCAGAGGGAGAT
1 AGGGAGGAAGTTGTTCCAGAGGGAGAT
*
32408 AGGGAGGAAGCTGTTCCAGAGGGAGAT
1 AGGGAGGAAGTTGTTCCAGAGGGAGAT
* * *
32435 AGAGAGGAAGATAG----GGAGGGAGAT
1 AGGGAGGAAG-TTGTTCCAGAGGGAGAT
* *
32459 AGGGAGGAAGTTGTTTCAGAGGAAGAT
1 AGGGAGGAAGTTGTTCCAGAGGGAGAT
32486 AG
1 AG
32488 TGATAGTGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
23 2 0.03
24 18 0.27
27 45 0.68
28 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.45, T:0.16
Consensus pattern (27 bp):
AGGGAGGAAGTTGTTCCAGAGGGAGAT
Found at i:32446 original size:12 final size:12
Alignment explanation
Indices: 32425--32468 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
32415 AAGCTGTTCC
*
32425 AGAGGGAGATAG
1 AGAGGAAGATAG
32437 AGAGGAAGATAG
1 AGAGGAAGATAG
* *
32449 GGAGGGAGATAG
1 AGAGGAAGATAG
*
32461 GGAGGAAG
1 AGAGGAAG
32469 TTGTTTCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.52, T:0.07
Consensus pattern (12 bp):
AGAGGAAGATAG
Found at i:32494 original size:6 final size:6
Alignment explanation
Indices: 32483--32515 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
32473 TTCAGAGGAA
*
32483 GATAGT GATAGT GATAGT GATAGT GACAGT GAT
1 GATAGT GATAGT GATAGT GATAGT GATAGT GAT
32516 CCTCTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (6 bp):
GATAGT
Found at i:36722 original size:14 final size:14
Alignment explanation
Indices: 36703--36730 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36693 ATAAAAAGAG
36703 AAAAAAAATTATCA
1 AAAAAAAATTATCA
36717 AAAAAAAATTATCA
1 AAAAAAAATTATCA
36731 GACCTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAAAATTATCA
Found at i:46982 original size:20 final size:20
Alignment explanation
Indices: 46950--46987 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46940 GGGGTTGACA
*
46950 AAAATTTATAAAAGTATAAT
1 AAAATTTATAAAAATATAAT
46970 AAAATATTA-AAAAATATA
1 AAAAT-TTATAAAAATATA
46988 TTTAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATTTATAAAAATATAAT
Found at i:48122 original size:27 final size:24
Alignment explanation
Indices: 48083--48141 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 24
48073 TGGTTAACGT
48083 TAAAAAAACAAATAAATTCAATATATA
1 TAAAAAAACAAAT--ATTCAATAT-TA
** *
48110 TAAAAAATTAAATATTCATTATTA
1 TAAAAAAACAAATATTCAATATTA
48134 TAAAAAAA
1 TAAAAAAA
48142 ACTAGCCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 9 0.32
25 8 0.29
27 11 0.39
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAAAAACAAATATTCAATATTA
Done.