Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012979.1 Kokia drynarioides strain JFW-HI SEQ_127997, 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: 5830
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:69 original size:3 final size:3
Alignment explanation
Indices: 61--114 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
51 AAAGTTTTCT
61 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
109 TAA TAA
1 TAA TAA
115 AAAATAGATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1052 original size:59 final size:58
Alignment explanation
Indices: 957--1260 Score: 289
Period size: 59 Copynumber: 5.2 Consensus size: 58
947 CCCTAAACAA
* * * *
957 TCCAAAAATTACA-TTTTACCCCCTAACTTTCCAAAATTCTATTTTTGACCTCGATTTT
1 TCCAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCTCGA-TTT
* * * *
1015 TTCAAAAATTATATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACC-CTAATTTT
1 TCCAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCTC-GA-TTT
*
1074 TCCAAAAATTATATTTTTACCC-CTAAACTTT-TCAAAATTCCATTTTTGACCTCGATTT
1 TCCAAAAATTACATTTTTACCCTC-AAACTTTCT-AAAATTCCATTTTTGACCTCGATTT
* * * * * * *
1132 TTCAAAAATTACATTTTTATCCTTAAACTTCCAAAAATTCCATTTTTTAACCCCGATTT
1 TCCAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTCCA-TTTTTGACCTCGATTT
* * * *
1191 TCCAAAAATTACCA-TTTTACCCTCGAA-TATCTAAAAATTCCA-TTATGACCTCGAACTT
1 TCCAAAAATTA-CATTTTTACCCTCAAACTTTCT-AAAATTCCATTTTTGACCTCG-ATTT
*
1249 TCCCAAAATTAC
1 TCCAAAAATTAC
1261 CATTCCCCTT
Statistics
Matches: 205, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
57 9 0.04
58 66 0.32
59 127 0.62
60 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCTCGATTT
Found at i:1139 original size:29 final size:28
Alignment explanation
Indices: 984--1244 Score: 134
Period size: 29 Copynumber: 8.9 Consensus size: 28
974 ACCCCCTAAC
* *
984 TTTCCAAAATTCTATTTTTGACCTCGATTT
1 TTTCAAAAATTCCATTTTT-ACCTCGA-TT
** **
1014 TTTCAAAAATTATATTTTTACCCTCGAAC
1 TTTCAAAAATTCCATTTTTA-CCTCGATT
* *
1043 TTTCTAAAATTCCATTTTTGACC-CTAATT
1 TTTCAAAAATTCCATTTTT-ACCTC-GATT
** ** *
1072 TTTCCAAAAATTATATTTTTACCCCTAAACT
1 TTT-CAAAAATTCCATTTTTA--CCTCGATT
1103 TTTC-AAAATTCCATTTTTGACCTCGATT
1 TTTCAAAAATTCCATTTTT-ACCTCGATT
* ** **
1131 TTTCAAAAATTACATTTTTATCCTTAAAC
1 TTTCAAAAATTCCATTTTTA-CCTCGATT
* *
1160 TTCCAAAAATTCCATTTTTTAACCCCGATT
1 TTTCAAAAATTCCA-TTTTT-ACCTCGATT
* *
1190 TTCCAAAAATTACCA-TTTTACCCTCGA-A
1 TTTCAAAAATT-CCATTTTTA-CCTCGATT
* * *
1218 TATCTAAAAATTCCATTATGACCTCGA
1 TTTC-AAAAATTCCATTTTTACCTCGA
1245 ACTTTCCCAA
Statistics
Matches: 177, Mismatches: 38, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
28 23 0.13
29 84 0.47
30 58 0.33
31 12 0.07
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (28 bp):
TTTCAAAAATTCCATTTTTACCTCGATT
Found at i:1209 original size:117 final size:116
Alignment explanation
Indices: 957--1212 Score: 345
Period size: 117 Copynumber: 2.2 Consensus size: 116
947 CCCTAAACAA
*
957 TCCAAAAATTACATTTTACCCCCTAACTTTCCAAAATTCTATTTTTGACCTCGATTTTTTCAAAA
1 TCCAAAAATTACATTTTA-CCCCTAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCAAAA
* * * * * *
1022 ATTATATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAATTTT
65 ATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAATTTT
* *
1074 TCCAAAAATTATATTTTTACCCCTAAACTTTTCAAAATTCCATTTTTGACCTCGA-TTTTTCAAA
1 TCCAAAAATTACA-TTTTACCCCT-AACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCAAA
* * *
1138 AATTACATTTTTATCCTTAAACTTCCAAAAATTCCATTTTTTAACCCCGA-TTT
64 AATTACATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTTAACCCCAATTTT
1191 TCCAAAAATTACCATTTTACCC
1 TCCAAAAATTA-CATTTTACCC
1213 TCGAATATCT
Statistics
Matches: 122, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
117 78 0.64
118 44 0.36
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.42
Consensus pattern (116 bp):
TCCAAAAATTACATTTTACCCCTAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTTCAAAAA
TTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAATTTT
Found at i:1228 original size:117 final size:116
Alignment explanation
Indices: 957--1244 Score: 325
Period size: 117 Copynumber: 2.5 Consensus size: 116
947 CCCTAAACAA
* *
957 TCCAAAAATTACATTTTACCCCCTAACTTTC-CAAAATTCTATTTTTGACCTCGATTTTTTCAAA
1 TCCAAAAATTACATTTTA-CCCCTAA-TATCTCAAAATTCCATTTTTGACCTCGATTTTTTCAAA
* * * * * *
1021 AATTATATTTTTACCCTCGAACTTTCTAAAATTCCATTTTTGACCCTAATTTT
64 AATTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAATTTT
* *
1074 TCCAAAAATTATATTTTTACCCCTAA-ACTTTTCAAAATTCCATTTTTGACCTCGA-TTTTTCAA
1 TCCAAAAATTACA-TTTTACCCCTAATA--TCTCAAAATTCCATTTTTGACCTCGATTTTTTCAA
* * *
1137 AAATTACATTTTTATCCTTAAACTTCCAAAAATTCCATTTTTTAACCCCGA-TTT
63 AAATTACATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTTAACCCCAATTTT
* * *
1191 TCCAAAAATTACCATTTTACCCTCGAATATCTAAAAATTCCA-TTATGACCTCGA
1 TCCAAAAATTA-CATTTTACCC-CTAATATCTCAAAATTCCATTTTTGACCTCGA
1245 ACTTTCCCAA
Statistics
Matches: 145, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
116 11 0.08
117 92 0.63
118 41 0.28
119 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.03, T:0.41
Consensus pattern (116 bp):
TCCAAAAATTACATTTTACCCCTAATATCTCAAAATTCCATTTTTGACCTCGATTTTTTCAAAAA
TTACATTTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCCAATTTT
Found at i:1638 original size:98 final size:98
Alignment explanation
Indices: 1525--1704 Score: 229
Period size: 98 Copynumber: 1.8 Consensus size: 98
1515 CATAAAAACT
* * * * * *
1525 TTAAAATCAAGGCAATATTAT-TTTATTTC-GAGTTTTGAAAATTTGTGCCTTAACTTACTAAGC
1 TTAAAATCAAGGCAATATT-TCTTTATCTCGGA-CTCTGAAAATTGGTACCTTAACTTACGAAGC
*
1588 GCGATTTTTCTTCAAATCGGAATAATTGAATACCC
64 GCGACTTTTCTTCAAATCGGAATAATTGAATACCC
* * * *
1623 TTAAAATCGAGGCAATGTTTCTTTATCTCGGACTCTGAAAATTGGTACCTTAACTTACGAGGTGC
1 TTAAAATCAAGGCAATATTTCTTTATCTCGGACTCTGAAAATTGGTACCTTAACTTACGAAGCGC
1688 GACTTTTCTTCAAATCG
66 GACTTTTCTTCAAATCG
1705 AGATAATCGA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
97 1 0.01
98 66 0.96
99 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (98 bp):
TTAAAATCAAGGCAATATTTCTTTATCTCGGACTCTGAAAATTGGTACCTTAACTTACGAAGCGC
GACTTTTCTTCAAATCGGAATAATTGAATACCC
Found at i:2507 original size:44 final size:44
Alignment explanation
Indices: 2444--2531 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2434 TATAAATAAA
2444 GAATTATTACAAATGACGATAAAAGTACGATGAAAACCTTATAG
1 GAATTATTACAAATGACGATAAAAGTACGATGAAAACCTTATAG
2488 GAATTATTACAAATGACGATAAAAGTACGATGAAAACCTTATAG
1 GAATTATTACAAATGACGATAAAAGTACGATGAAAACCTTATAG
2532 TAGGAGTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (44 bp):
GAATTATTACAAATGACGATAAAAGTACGATGAAAACCTTATAG
Found at i:5009 original size:4 final size:4
Alignment explanation
Indices: 5000--5034 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
4990 ACCTCAATTT
5000 CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CAT
5035 GTATTGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Done.