Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000911.1 Kokia drynarioides strain JFW-HI SEQ_112048, 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: 3612
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:38 original size:30 final size:30
Alignment explanation
Indices: 4--233 Score: 195
Period size: 29 Copynumber: 7.8 Consensus size: 30
1 CCC
*
4 TAAACTTTTCAAAAAATACATTTTAACCCT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* ** *
34 TAAAC-TTCCAAATTTTACATTTTGACCCT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* *
63 TAAACTTCTCAAAAATTATATTTTAACCCT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* *
93 TAAA-ATTT-ATAAAATATACATTTTAACCCC
1 TAAACTTTTCA-AAAAT-TACATTTTAACCCT
*
123 TAAACTTCTT-AAAATTTACATTTT-ACCCT
1 TAAACTT-TTCAAAAATTACATTTTAACCCT
* * * * *
152 TGAAC-TTCCAAAAATCACATTTTTACCCC
1 TAAACTTTTCAAAAATTACATTTTAACCCT
* *
181 TAAA-TTTTCAAAAATTATATTTTTACCCT
1 TAAACTTTTCAAAAATTACATTTTAACCCT
** * *
210 CGAACTTCTCAAAAATTACTTTTT
1 TAAACTTTTCAAAAATTACATTTT
234 TTCCCCCGAA
Statistics
Matches: 158, Mismatches: 33, Indels: 18
0.76 0.16 0.09
Matches are distributed among these distances:
27 1 0.01
28 14 0.09
29 68 0.43
30 67 0.42
31 5 0.03
32 3 0.02
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (30 bp):
TAAACTTTTCAAAAATTACATTTTAACCCT
Found at i:96 original size:59 final size:59
Alignment explanation
Indices: 1--233 Score: 227
Period size: 59 Copynumber: 3.9 Consensus size: 59
* * * *
1 CCCTAAACTTTTCAAAAAATACATTTTAACCCTTAAACTTCCAAATTTTACATTTTGAC
1 CCCTAAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCCAAAATTTACATTTTAAC
* * * ** *
60 CCTTAAACTTCTCAAAAATTATATTTTAACCCTTAAAATTTATAAAATATACATTTTAAC
1 CCCTAAACTTCTCAAAAATTACATTTTAACCCTT-AAACTTCCAAAATTTACATTTTAAC
* * * * * *
120 CCCTAAACTTCTTAAAATTTACATTTT-ACCCTTGAACTTCCAAAAATCACATTTTTAC
1 CCCTAAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCCAAAATTTACATTTTAAC
* * * ** * *
178 CCCTAAA-TTTTCAAAAATTATATTTTTACCCTCGAACTTCTCAAAAATTACTTTTT
1 CCCTAAACTTCTCAAAAATTACATTTTAACCCTTAAACTTC-CAAAATTTACATTTT
234 TTCCCCCGAA
Statistics
Matches: 142, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
57 15 0.11
58 36 0.25
59 49 0.35
60 42 0.30
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (59 bp):
CCCTAAACTTCTCAAAAATTACATTTTAACCCTTAAACTTCCAAAATTTACATTTTAAC
Found at i:176 original size:89 final size:89
Alignment explanation
Indices: 14--184 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 89
4 TAAACTTTTC
* *
14 AAAAAATACATTTTAACCCTTAAACTTCCAAATTTTACATTTTGACCCTTAAACTTCTCAAAAAT
1 AAAAAATACATTTTAACCCCTAAACTTCCAAAATTTACATTTTGACCCTTAAACTTCTCAAAAAT
* *
79 TATATTTTAACCCTTAAAATTTAT
66 CACATTTTAACCCTTAAAATTTAT
* * *
103 AAAATATACATTTTAACCCCTAAACTTCTTAAAATTTACATTTT-ACCCTTGAACTTC-CAAAAA
1 AAAAAATACATTTTAACCCCTAAACTTC-CAAAATTTACATTTTGACCCTTAAACTTCTCAAAAA
* *
166 TCACATTTTTACCCCTAAA
65 TCACATTTTAACCCTTAAA
185 TTTTCAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
88 21 0.29
89 38 0.53
90 13 0.18
ACGTcount: A:0.40, C:0.22, G:0.01, T:0.37
Consensus pattern (89 bp):
AAAAAATACATTTTAACCCCTAAACTTCCAAAATTTACATTTTGACCCTTAAACTTCTCAAAAAT
CACATTTTAACCCTTAAAATTTAT
Found at i:234 original size:30 final size:30
Alignment explanation
Indices: 125--254 Score: 117
Period size: 29 Copynumber: 4.5 Consensus size: 30
115 TTAACCCCTA
* * * *
125 AACTTCTTAAAATTTAC-ATTTTACCCTTG
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
* * *
154 AACTTC-CAAAAATCACATTTTTACCC-CT
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
* *
182 AAATTTTCAAAAATTA-TATTTTTACCCTCG
1 AACTTCTCAAAAATTACT-TTTTTACCCTCG
* *
212 AACTTCTCAAAAATTACTTTTTTTCCCCCG
1 AACTTCTCAAAAATTACTTTTTTACCCTCG
242 AAC-TCTCAAAAAT
1 AACTTCTCAAAAAT
255 CACCATTTTG
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
28 11 0.14
29 41 0.51
30 28 0.35
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTCTCAAAAATTACTTTTTTACCCTCG
Found at i:248 original size:29 final size:30
Alignment explanation
Indices: 65--254 Score: 115
Period size: 30 Copynumber: 6.5 Consensus size: 30
55 TTGACCCTTA
* ***
65 AACTTCTCAAAAATTATATTTTAACCCTTA
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * * **
95 AAATT-T-ATAAAATATACATTTTAACCCCTA
1 AACTTCTCA-AAAAT-TATATTTTTACCCCCG
* * * **
125 AACTTCTTAAAATTTACA-TTTTACCCTTG
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * *
154 AACTTC-CAAAAATCACATTTTTA-CCCCT
1 AACTTCTCAAAAATTATATTTTTACCCCCG
* * *
182 AAATTTTCAAAAATTATATTTTTACCCTCG
1 AACTTCTCAAAAATTATATTTTTACCCCCG
*
212 AACTTCTCAAAAATTACT-TTTTTTCCCCCG
1 AACTTCTCAAAAATTA-TATTTTTACCCCCG
242 AAC-TCTCAAAAAT
1 AACTTCTCAAAAAT
255 CACCATTTTG
Statistics
Matches: 128, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.12
29 50 0.39
30 56 0.44
31 6 0.05
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
AACTTCTCAAAAATTATATTTTTACCCCCG
Found at i:310 original size:30 final size:30
Alignment explanation
Indices: 141--310 Score: 113
Period size: 29 Copynumber: 5.8 Consensus size: 30
131 TTAAAATTTA
*
141 CATTTTACCCTTGAAC-TTCCAAAAATCA-
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
* * * *
169 CATTTTTACCC-CTAAATTTTCAAAAATTA-
1 CA-TTTTACCCTCGAACTTTCCAAAAATCAC
* *
198 TATTTTTACCCTCGAAC-TTCTCAAAAATTAC
1 CA-TTTTACCCTCGAACTTTC-CAAAAATCAC
** * * *
229 TTTTTTTCCCCCGAACTCT-CAAAAATCAC
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
* * *
258 CATTTT-GCCTCG-AGTATCCAAAAATCAC
1 CATTTTACCCTCGAACTTTCCAAAAATCAC
*
286 CATTTTACCCTCAAACTTTCCAAAA
1 CATTTTACCCTCGAACTTTCCAAAA
311 GTTTGATTTT
Statistics
Matches: 109, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.03
28 24 0.22
29 47 0.43
30 33 0.30
31 2 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (30 bp):
CATTTTACCCTCGAACTTTCCAAAAATCAC
Done.