Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012422.1 Kokia drynarioides strain JFW-HI SEQ_127426, 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: 118594
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4607 original size:39 final size:40
Alignment explanation
Indices: 4563--4654 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 40
4553 TGGGACAAGT
*
4563 CTCTTCCAAGAGGT-AT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTGATCATCCAATATG-AAAGGATTGTGA
* * * *
4602 CTCTT-CAATAGGTGTTCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTGATCATCCAATATGAAAGGATTGTGA
*
4641 CTCTT-CAAAAGGTG
1 CTCTTCCAAGAGGTG
4655 TCCATTAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 7 0.16
39 30 0.67
40 8 0.18
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (40 bp):
CTCTTCCAAGAGGTGATCATCCAATATGAAAGGATTGTGA
Found at i:4655 original size:39 final size:40
Alignment explanation
Indices: 4580--4655 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
4570 AAGAGGTATG
*
4580 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTTCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTTCA
* *
4620 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGT
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGT
4656 CCATTAAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 25 0.76
40 8 0.24
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTTCA
Found at i:10832 original size:26 final size:26
Alignment explanation
Indices: 10783--10832 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
10773 CCAAAAGCAC
* * *
10783 CAGCGCATGAAAATATCAAGTTGCCG
1 CAGCGAATAAAAATATAAAGTTGCCG
*
10809 CAGCGAATAAAAATATAAATTTGC
1 CAGCGAATAAAAATATAAAGTTGC
10833 ATCCAGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (26 bp):
CAGCGAATAAAAATATAAAGTTGCCG
Found at i:21008 original size:17 final size:17
Alignment explanation
Indices: 20988--21026 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
20978 CTAAACAAAT
20988 AAAATGCAGA-GACAATA
1 AAAATGCA-ATGACAATA
*
21005 AAAATGCAATGACAATT
1 AAAATGCAATGACAATA
21022 AAAAT
1 AAAAT
21027 AAATGCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:21129 original size:14 final size:13
Alignment explanation
Indices: 21110--21157 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
21100 TTTTTCTTCT
21110 TCTTTGGATGCTCC
1 TCTTTGGAT-CTCC
*
21124 TCTTTGCGCTCTCC
1 TCTTTG-GATCTCC
*
21138 TCTTTGTACTCTCC
1 TCTTTGGA-TCTCC
21152 TCTTTG
1 TCTTTG
21158 TACTTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 27 0.93
15 2 0.07
ACGTcount: A:0.04, C:0.33, G:0.15, T:0.48
Consensus pattern (13 bp):
TCTTTGGATCTCC
Found at i:21158 original size:14 final size:14
Alignment explanation
Indices: 21120--21161 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
21110 TCTTTGGATG
**
21120 CTCCTCTTTGCGCT
1 CTCCTCTTTGTACT
21134 CTCCTCTTTGTACT
1 CTCCTCTTTGTACT
21148 CTCCTCTTTGTACT
1 CTCCTCTTTGTACT
21162 TCTTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.05, C:0.38, G:0.10, T:0.48
Consensus pattern (14 bp):
CTCCTCTTTGTACT
Found at i:38371 original size:16 final size:16
Alignment explanation
Indices: 38350--38381 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38340 GGTATTTTCG
38350 CAAAAAATATGAAATA
1 CAAAAAATATGAAATA
*
38366 CAAAAAATGTGAAATA
1 CAAAAAATATGAAATA
38382 AGATATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (16 bp):
CAAAAAATATGAAATA
Found at i:51233 original size:102 final size:102
Alignment explanation
Indices: 51057--51261 Score: 410
Period size: 102 Copynumber: 2.0 Consensus size: 102
51047 CAGAATTGAA
51057 GGGGAAGCACCAAGAGTTGAAGGCACAAATTTCTGAAACAATACAATCATCTGGTGGAGCTAATG
1 GGGGAAGCACCAAGAGTTGAAGGCACAAATTTCTGAAACAATACAATCATCTGGTGGAGCTAATG
51122 GAAGTTTGCAAAAGGAAACCAAGCTTGCGGAACCTAT
66 GAAGTTTGCAAAAGGAAACCAAGCTTGCGGAACCTAT
51159 GGGGAAGCACCAAGAGTTGAAGGCACAAATTTCTGAAACAATACAATCATCTGGTGGAGCTAATG
1 GGGGAAGCACCAAGAGTTGAAGGCACAAATTTCTGAAACAATACAATCATCTGGTGGAGCTAATG
51224 GAAGTTTGCAAAAGGAAACCAAGCTTGCGGAACCTAT
66 GAAGTTTGCAAAAGGAAACCAAGCTTGCGGAACCTAT
51261 G
1 G
51262 CTGGAGATGA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (102 bp):
GGGGAAGCACCAAGAGTTGAAGGCACAAATTTCTGAAACAATACAATCATCTGGTGGAGCTAATG
GAAGTTTGCAAAAGGAAACCAAGCTTGCGGAACCTAT
Found at i:57625 original size:33 final size:33
Alignment explanation
Indices: 57583--57659 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
57573 TACTATGGGG
57583 ATGCGTCGATAGAAAAGAGCTTCTCATCTGGAA
1 ATGCGTCGATAGAAAAGAGCTTCTCATCTGGAA
57616 ATGCGTCGATAGAAAAGAGCTTCTCATCTGGAA
1 ATGCGTCGATAGAAAAGAGCTTCTCATCTGGAA
*
57649 ATGCATCGATA
1 ATGCGTCGATA
57660 ATTTGTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (33 bp):
ATGCGTCGATAGAAAAGAGCTTCTCATCTGGAA
Found at i:60208 original size:18 final size:18
Alignment explanation
Indices: 60181--60227 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
60171 TGCAGTCTGC
*
60181 TGTGGCTGCATAC-AAGCA
1 TGTGACTGCAT-CTAAGCA
* *
60199 TGTGATTGCATCTGAGCA
1 TGTGACTGCATCTAAGCA
60217 TGTGACTGCAT
1 TGTGACTGCAT
60228 TTGATCATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
TGTGACTGCATCTAAGCA
Found at i:70955 original size:8 final size:8
Alignment explanation
Indices: 70932--70966 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
70922 CAATATTGTA
70932 TTTATTAGT
1 TTTATTA-T
70941 CTTTATTAT
1 -TTTATTAT
70950 TTTATTAT
1 TTTATTAT
70958 TTTATTAT
1 TTTATTAT
70966 T
1 T
70967 CCAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 1 0.04
10 7 0.28
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (8 bp):
TTTATTAT
Found at i:73866 original size:15 final size:15
Alignment explanation
Indices: 73842--73889 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
73832 TAGTTACGAT
*
73842 GATGACATCTATGAG
1 GATGACATCTATGAA
*
73857 GATGATATCTATGAA
1 GATGACATCTATGAA
73872 GATGGACA-CTATGAA
1 GAT-GACATCTATGAA
73887 GAT
1 GAT
73890 AAGGAGATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 26 0.90
16 3 0.10
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (15 bp):
GATGACATCTATGAA
Found at i:83270 original size:40 final size:40
Alignment explanation
Indices: 83225--83390 Score: 251
Period size: 40 Copynumber: 4.2 Consensus size: 40
83215 CCATAGCTTG
*
83225 GCTTGAATTTTAACACCGGCTTATAGCCTACTAAGCCGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTACTAAGCCGTA
* *
83265 GCTTGAATTTTAACACCGGCTTATAGCCTGCTAAGCCGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTACTAAGCCGTA
* * *
83305 GCTTGAATTTTAACACCGACTCATAGCCTACTAAACTGTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTACTAAGCCGTA
* * *
83345 GCTTGAATTTTAACATCGGCTCATAGCCTGCTAAGCCTTA
1 GCTTGAATTTTAACACCGGCTCATAGCCTACTAAGCCGTA
83385 GCTTGA
1 GCTTGA
83391 TTCTTTACAC
Statistics
Matches: 114, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 114 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (40 bp):
GCTTGAATTTTAACACCGGCTCATAGCCTACTAAGCCGTA
Found at i:89328 original size:23 final size:22
Alignment explanation
Indices: 89283--89328 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
89273 TTCTGGCCTT
*
89283 AATATTTGAGAAAAAAAGAGAG
1 AATATTTGAGAAAAAAACAGAG
* *
89305 AATATTTGTGCAAAAAAACTGAG
1 AATATTTGAG-AAAAAAACAGAG
89328 A
1 A
89329 GTGAAAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (22 bp):
AATATTTGAGAAAAAAACAGAG
Found at i:112093 original size:14 final size:15
Alignment explanation
Indices: 112066--112094 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
112056 CCACTATGTA
112066 TTGAGCAGCCACCAC
1 TTGAGCAGCCACCAC
112081 TTGAGCA-CCACCAC
1 TTGAGCAGCCACCAC
112095 CCAAGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.41, G:0.17, T:0.14
Consensus pattern (15 bp):
TTGAGCAGCCACCAC
Found at i:113819 original size:23 final size:22
Alignment explanation
Indices: 113762--113819 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
113752 AGTTTTAATG
* *
113762 TTTTTAGTATTTTTAAAATTTA
1 TTTTTAATATTTTGAAAATTTA
*
113784 TTTTTAATTTTTTGGAAATATTTA
1 TTTTTAATATTTT-GAAA-ATTTA
113808 -TTTTAATATTTT
1 TTTTTAATATTTT
113820 TAATATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 11 0.37
23 14 0.47
24 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTTAATATTTTGAAAATTTA
Found at i:113822 original size:9 final size:9
Alignment explanation
Indices: 113808--113832 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
113798 GAAATATTTA
113808 TTTTAATAT
1 TTTTAATAT
113817 TTTTAATAT
1 TTTTAATAT
113826 TTTTAAT
1 TTTTAAT
113833 GCATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:113830 original size:23 final size:22
Alignment explanation
Indices: 113763--113830 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
113753 GTTTTAATGT
* *
113763 TTTTAGTATTTTTAAA-ATTTA
1 TTTTAATATTTTTAAATTTTTA
*
113784 TTTTTAAT-TTTTTGGAAATATTTA
1 -TTTTAATATTTTT--AAATTTTTA
113808 TTTTAATATTTTTAATATTTTTA
1 TTTTAATATTTTTAA-ATTTTTA
113831 ATGCATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 5 0.13
22 8 0.21
23 16 0.41
24 10 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTAATATTTTTAAATTTTTA
Found at i:115071 original size:32 final size:32
Alignment explanation
Indices: 115005--115074 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
114995 TTAAAAAAAC
*
115005 ATTTTCTAATTTTGACTTTTCTCCCCCCAACAA
1 ATTTTCTAATTTTGACTTTTCTCCCACC-ACAA
115038 ATTTTC-AATTTTGACTTTTCTCGACCACC-CAA
1 ATTTTCTAATTTTGACTTTTCTC--CCACCACAA
115070 ATTTT
1 ATTTT
115075 TCTGTCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 24 0.71
33 6 0.18
34 4 0.12
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (32 bp):
ATTTTCTAATTTTGACTTTTCTCCCACCACAA
Found at i:115101 original size:12 final size:12
Alignment explanation
Indices: 115086--115117 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
115076 CTGTCATTTC
115086 TTCTTCTTCTTT
1 TTCTTCTTCTTT
*
115098 TTCTTTTTCTTT
1 TTCTTCTTCTTT
115110 TTCTTCTT
1 TTCTTCTT
115118 AATCATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:118100 original size:17 final size:17
Alignment explanation
Indices: 118072--118134 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
118062 GGCCTATTGG
118072 AAATTTAATTTATTTTT
1 AAATTTAATTTATTTTT
118089 AAA-TTAAGTTTA-TTTT
1 AAATTTAA-TTTATTTTT
*
118105 AAATTTAAATTTA-TTTG
1 AAATTT-AATTTATTTTT
118122 AAATTTAAATTTA
1 AAATTT-AATTTA
118135 CTATAAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
16 11 0.26
17 29 0.69
18 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
AAATTTAATTTATTTTT
Found at i:118119 original size:34 final size:34
Alignment explanation
Indices: 118072--118147 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
118062 GGCCTATTGG
* * * *
118072 AAATTT-AATTTATTTTTAAA-TTAAGTTTATTTT
1 AAATTTAAATTTA-TTTGAAATTTAAATTTACTAT
118105 AAATTTAAATTTATTTGAAATTTAAATTTACTAT
1 AAATTTAAATTTATTTGAAATTTAAATTTACTAT
118139 AAATTTAAA
1 AAATTTAAA
118148 AAAGTCCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 12 0.32
34 25 0.68
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAATTTAAATTTACTAT
Found at i:118142 original size:17 final size:16
Alignment explanation
Indices: 118104--118147 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 16
118094 AAGTTTATTT
*
118104 TAAATTTAAATTTATT
1 TAAATTTAAATTTATA
118120 TGAAATTTAAATTTACTA
1 T-AAATTTAAATTTA-TA
118138 TAAATTTAAA
1 TAAATTTAAA
118148 AAAGTCCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 22 0.88
18 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAATTTAAATTTATA
Found at i:118212 original size:15 final size:15
Alignment explanation
Indices: 118170--118213 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
118160 AGGTACAGAT
118170 CAAATTGGCCCAATTA
1 CAAA-TGGCCCAATTA
*
118186 CAAAACGGCCCAATTA
1 C-AAATGGCCCAATTA
118202 CAAATGGCCCAA
1 CAAATGGCCCAA
118214 ATAGGCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 12 0.48
17 3 0.12
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (15 bp):
CAAATGGCCCAATTA
Done.