Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010094.1 Kokia drynarioides strain JFW-HI SEQ_124875, 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: 9371
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.27
Warning! 155 characters in sequence are not A, C, G, or T
Found at i:1335 original size:17 final size:17
Alignment explanation
Indices: 1311--1367 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
1301 TTGGAAATTG
1311 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
1328 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
1345 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
1362 AATTTA
1 AATTTA
1368 GAAAAGTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:2061 original size:59 final size:59
Alignment explanation
Indices: 1969--2413 Score: 606
Period size: 59 Copynumber: 7.5 Consensus size: 59
1959 GGAGATCCTT
* * *
1969 GAACCTTCCAAAAATTACTATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
2028 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTTACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACCCC
* * * * **
2088 AAACCTTCCAAAAATTACTAATTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* *
2147 GAACCTTCTTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * * * *
2206 AAACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCATTTTTGACCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
*
2265 GAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTG-CCTCC
1 GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTGACC-CC
* * * *
2325 GAACCTTTCTAAAAATCACCATTTTACCCTCGAACATCCAAAAATCCCATTTTTGACTCC
1 GAACC-TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
* * *
2385 GAACCTTC-CAAAACTACCATTTTGCCCCC
1 GAACCTTCTAAAAATTACCATTTTACCCCC
2414 CCGTGCATCC
Statistics
Matches: 341, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
58 16 0.05
59 208 0.61
60 77 0.23
61 40 0.12
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (59 bp):
GAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:2181 original size:119 final size:118
Alignment explanation
Indices: 1970--2413 Score: 606
Period size: 119 Copynumber: 3.7 Consensus size: 118
1960 GAGATCCTTG
* *
1970 AACCTTCCAAAAATTACTATTTTATCCCC-GAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
1 AACCTTCCAAAAATTACCATTTTA-CCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
*
2034 TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTTACCCCA
65 TCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTTTACCCCA
* *
2089 AACCTTCCAAAAATTACTAATTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* * *
2154 CTTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
66 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCA
** * * *
2207 AACCTTCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCATTTTTGACCCCGAACCTT
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
* * *
2272 CTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTGCCTCCG
66 CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACC-CCA
* * * * *
2326 AACCTTTCTAAAAATCACCATTTTA-CCCTCGAACATCCAAAAATCCCATTTTTGACTCCGAACC
1 AACC-TTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
2390 TTC-CAAAACTACCATTTTGCCCCC
64 TTCTAAAAATTACCATTTTACCCCC
2414 CCGTGCATCC
Statistics
Matches: 291, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
118 118 0.41
119 123 0.42
120 50 0.17
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (118 bp):
AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAACCTT
CTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCA
Found at i:2329 original size:178 final size:178
Alignment explanation
Indices: 1969--2413 Score: 655
Period size: 178 Copynumber: 2.5 Consensus size: 178
1959 GGAGATCCTT
* *
1969 GAACCTTCCAAAAATTACTATTTTATCCC-CGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 GAACCTTCTAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
2033 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCATTTTTTTACCCCAAACCTTCCA
65 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCATTTTTTGACCCCAAACCTTCCA
* *
2098 AAAATTACTAATTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCC
130 AAAATTACCAATTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
* *
2147 GAACCTTCTTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAACCT
1 GAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
* * *
2212 TCTTAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCA-TTTTTGACCCCGAACCTTCTAA
66 TCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCATTTTTTGACCCCAAACCTTCCAA
*
2276 AAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTG-CCTCC
131 AAATTACCAATTTACCCCCAAACTTCCAAAAATCCCA-TTTTTGACC-CC
* * *
2325 GAACCTTTCTAAAAATCACCATTTTACCCTCGAACATCCAAAAATCCCATTTTTGACTCCGAACC
1 GAACC-TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
2390 TTC-CAAAACTACCATTTTGCCCCC
65 TTCTAAAAATTACCATTTTACCCCC
2414 CCGTGCATCC
Statistics
Matches: 242, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
177 58 0.24
178 127 0.52
179 57 0.24
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.31
Consensus pattern (178 bp):
GAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCT
TCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAAACTCATTTTTTGACCCCAAACCTTCCAA
AAATTACCAATTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCC
Found at i:5343 original size:17 final size:17
Alignment explanation
Indices: 5319--5375 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
5309 TTGGAAATTG
5319 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
5336 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
5353 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
5370 AATTTA
1 AATTTA
5376 GAAAAGTNNN
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:7249 original size:17 final size:17
Alignment explanation
Indices: 7225--7281 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
7215 TTGGAAATTG
7225 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
7242 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
7259 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
7276 AATTTA
1 AATTTA
7282 GAAAAGTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:7967 original size:28 final size:28
Alignment explanation
Indices: 7919--7974 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
7909 AAGTGGGCGG
* *
7919 TTTTTCAAAATATTTATTAATAATAATT
1 TTTTTAAAAATATTTAATAATAATAATT
*
7947 TTTTTAAACAATA-TTAATAATATTAATT
1 TTTTTAAA-AATATTTAATAATAATAATT
7975 AATAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTAAAAATATTTAATAATAATAATT
Found at i:8211 original size:21 final size:23
Alignment explanation
Indices: 8181--8222 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
8171 GGGGAAAACC
*
8181 GTTTGGATCTAGGC-TAGATCTG
1 GTTTGGATCTAGACTTAGATCTG
8203 GTTT-GATCTAGACTTAGATC
1 GTTTGGATCTAGACTTAGATC
8223 CGTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (23 bp):
GTTTGGATCTAGACTTAGATCTG
Found at i:8227 original size:21 final size:21
Alignment explanation
Indices: 8179--8227 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
8169 AAGGGGAAAA
*
8179 CCGTTTGGATCTAGGCTAGAT
1 CCGTTTGGATCTAGACTAGAT
*
8200 CTGGTTT-GATCTAGACTTAGAT
1 C-CGTTTGGATCTAGAC-TAGAT
8222 CCGTTT
1 CCGTTT
8228 TTTTAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (21 bp):
CCGTTTGGATCTAGACTAGAT
Found at i:9070 original size:29 final size:29
Alignment explanation
Indices: 9033--9198 Score: 101
Period size: 29 Copynumber: 5.7 Consensus size: 29
9023 GTCCCTGAAC
* *
9033 CTTCTAAAAATTACTATTTTATCCCCAAA
1 CTTCCAAAAATTACCATTTTATCCCCAAA
* *
9062 CTTCCAAAAAAT-CACATTTT-TGACCCCGAAC
1 CTTCCAAAAATTAC-CATTTTAT--CCCC-AAA
*** *
9093 CTTTTGAAAATTACCATTTTA-CCCCTAA
1 CTTCCAAAAATTACCATTTTATCCCCAAA
* *
9121 CTTCCAAAAA-TCCCATTTT-TGACCCTAAA
1 CTTCCAAAAATTACCATTTTAT--CCCCAAA
* * *
9150 CCTTCTAAAAATTACCATTTTACCCCCGAA
1 -CTTCCAAAAATTACCATTTTATCCCCAAA
*
9180 CTTCCAAAAA-TCCCATTTT
1 CTTCCAAAAATTACCATTTT
9199 TTTTTACCCC
Statistics
Matches: 102, Mismatches: 23, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
27 8 0.08
28 18 0.18
29 33 0.32
30 18 0.18
31 24 0.24
32 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTATCCCCAAA
Found at i:9152 original size:58 final size:59
Alignment explanation
Indices: 9025--9222 Score: 254
Period size: 58 Copynumber: 3.3 Consensus size: 59
9015 CCTCGGAGGT
* * *
9025 CCCTGAACCTTCTAAAAATTACTATTTTATCCCCAAACTTCCAAAAAATCACATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCC-AAAAATCCCATTTTTGA
* * * *
9085 CCCCGAACCTTTTGAAAATTACCATTTTA-CCCCTAACTTCCAAAAATCCCATTTTTGA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
* * *
9143 CCCTAAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTTTTA
1 CCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA---TTTTTGA
*
9205 CCCCGAACCTTCTAAAAA
1 CCCTGAACCTTCTAAAAA
9223 AAGGTTTTAC
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
58 41 0.34
59 32 0.27
60 25 0.21
62 22 0.18
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTGAACCTTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
Found at i:9199 original size:29 final size:28
Alignment explanation
Indices: 9049--9199 Score: 108
Period size: 30 Copynumber: 5.1 Consensus size: 28
9039 AAAATTACTA
*
9049 TTTTATCCCCAAACTTCCAAAAAATCACAT
1 TTTTA-CCCCAAACTTCC-AAAAATCCCAT
* ** * *
9079 TTTTGACCCCGAACCTTTTGAAAATTACCA-
1 TTTT-ACCCC-AAAC-TTCCAAAAATCCCAT
*
9109 TTTTACCCCTAACTTCCAAAAATCCCAT
1 TTTTACCCCAAACTTCCAAAAATCCCAT
* * *
9137 TTTTGACCCTAAACCTTCTAAAAATTACCA-
1 TTTT-ACCCCAAA-CTTCCAAAAA-TCCCAT
*
9167 TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTA-CCCCAAACTTCCAAAAATCCCAT
9196 TTTT
1 TTTT
9200 TTTTACCCCG
Statistics
Matches: 92, Mismatches: 20, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
27 10 0.11
28 10 0.11
29 25 0.27
30 30 0.33
31 15 0.16
32 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
TTTTACCCCAAACTTCCAAAAATCCCAT
Done.