Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012221.1 Kokia drynarioides strain JFW-HI SEQ_127222, 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: 10675
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:2198 original size:17 final size:18
Alignment explanation
Indices: 2176--2209 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2166 GTAAAGATTA
2176 GCAAATA-AAGAATAAAT
1 GCAAATATAAGAATAAAT
2193 GCAAATATAAGAATAAA
1 GCAAATATAAGAATAAA
2210 CATCAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (18 bp):
GCAAATATAAGAATAAAT
Found at i:4170 original size:20 final size:20
Alignment explanation
Indices: 4145--4187 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
4135 ATTACATTAC
*
4145 AATCAATTCCAACTTTCAGA
1 AATCAATTCCAACTTTCAAA
*
4165 AATCAATTCCAATTTTCAAA
1 AATCAATTCCAACTTTCAAA
4185 AAT
1 AAT
4188 TGGAGTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (20 bp):
AATCAATTCCAACTTTCAAA
Found at i:7620 original size:16 final size:18
Alignment explanation
Indices: 7599--7637 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
7589 TACGGGAATA
7599 TAAATAGC-ATAAA-AAC
1 TAAATAGCAATAAATAAC
7615 TAAATAGCAAATAAATAAC
1 TAAATAGC-AATAAATAAC
7634 TAAA
1 TAAA
7638 GGGATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (18 bp):
TAAATAGCAATAAATAAC
Found at i:7984 original size:6 final size:6
Alignment explanation
Indices: 7973--8038 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
7963 TAAAATCTAT
* **
7973 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
8020 ATT--A TTCTAAA TTTAAA TT
1 TTTAAA TT-TAAA TTTAAA TT
8039 GATAATGTCC
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 37 0.77
7 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:7993 original size:17 final size:17
Alignment explanation
Indices: 7973--8038 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
7963 TAAAATCTAT
7973 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
* *
7990 TTTAAGTTTAAATTTATT
1 TTTAAATTTAAATTTA-A
*
8008 TTTAAATTTAAAATT-A
1 TTTAAATTTAAATTTAA
8024 TTCTAAATTTAAATT
1 TT-TAAATTTAAATT
8039 GATAATGTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
16 2 0.05
17 26 0.63
18 13 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:8011 original size:35 final size:35
Alignment explanation
Indices: 7972--8038 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
7962 TTAAAATCTA
* *
7972 TTTTAAATTTAAATTTAATT-TAAGTTTAAATTTAT
1 TTTTAAATTTAAAATT-ATTCTAAATTTAAATTTAT
8007 TTTTAAATTTAAAATTATTCTAAATTTAAATT
1 TTTTAAATTTAAAATTATTCTAAATTTAAATT
8039 GATAATGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTTAAATTTAAAATTATTCTAAATTTAAATTTAT
Found at i:9928 original size:86 final size:85
Alignment explanation
Indices: 9721--10032 Score: 312
Period size: 86 Copynumber: 3.6 Consensus size: 85
9711 CCTTAAAATT
* * * *
9721 TTCCAAAATCACATTTTGACCCTCAAACTTCTAAAAAATTACA-TTTTGCCCTCAAACTTCCAAA
1 TTCCAAAATCACATTTTTACCCTCGAACTTC-CAAAAATTACATTTTTACCCTC-AACTT-CAAA
9785 AAATACATTTTTG-TCTCTAAAC
63 AAATACATTTTTGCTCTCTAAAC
* * *
9807 TTTCAAAAAATTACATTTTTACCC-CTGAACTTCCAAAAATAACATTTTTACCCTCGAACTTCAA
1 -TTC-CAAAATCACATTTTTACCCTC-GAACTTCCAAAAATTACATTTTTACCCTC-AACTTCAA
* *
9871 AAAATCACATTTTTGCTTTC-GAAC
62 AAAAT-ACATTTTTGCTCTCTAAAC
* * * *
9895 TTCCCAAATTACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACCCTCAATTTTCCAAAA
1 TTCCAAAATCACATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCTCAA-CTT-CAAAA
** *
9960 TTTACATTTTTGC-CCCTAAAC
64 AATACATTTTTGCTCTCTAAAC
* *
9981 TTCCAAAAATCACATTTTTATCCT-GAACTCTCCTAAAATTACATTTTTACCC
1 TTCC-AAAATCACATTTTTACCCTCGAACT-TCCAAAAATTACATTTTTACCC
10033 CTAAAACTTT
Statistics
Matches: 190, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
85 3 0.02
86 69 0.36
87 67 0.35
88 48 0.25
89 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (85 bp):
TTCCAAAATCACATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCTCAACTTCAAAAAA
TACATTTTTGCTCTCTAAAC
Found at i:10018 original size:29 final size:28
Alignment explanation
Indices: 9721--10032 Score: 252
Period size: 29 Copynumber: 10.8 Consensus size: 28
9711 CCTTAAAATT
* * *
9721 TTCC-AAAATCACATTTTGACCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCT-GAAC
* * *
9749 TTCTAAAAAATTACA-TTTTGCCCTCAAAC
1 TTC-CAAAAATTACATTTTTACCCT-GAAC
* * * *
9778 TTCCAAAAAATACATTTTTGTCTCTAAAC
1 TTCCAAAAATTACATTTTT-ACCCTGAAC
*
9807 TTTCAAAAAATTACATTTTTACCCCTGAAC
1 -TTCCAAAAATTACATTTTTA-CCCTGAAC
*
9837 TTCCAAAAATAACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCT-GAAC
* * * **
9866 TTCAAAAAATCACATTTTTGCTTTCGAAC
1 TTCCAAAAATTACATTTTTACCCT-GAAC
*
9895 TTCC-CAAATTACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCT-GAAC
* * *
9923 TTCCAAAAATCACATTTTTACCCTCAATT
1 TTCCAAAAATTACATTTTTACCCTGAA-C
* * *
9952 TTCCAAAATTTACATTTTTGCCCCTAAAC
1 TTCCAAAAATTACATTTTT-ACCCTGAAC
* *
9981 TTCCAAAAATCACATTTTTATCCTGAAC
1 TTCCAAAAATTACATTTTTACCCTGAAC
*
10009 TCTCCTAAAATTACATTTTTACCC
1 T-TCCAAAAATTACATTTTTACCC
10033 CTAAAACTTT
Statistics
Matches: 230, Mismatches: 43, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
28 48 0.21
29 142 0.62
30 40 0.17
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTTACCCTGAAC
Found at i:10452 original size:97 final size:97
Alignment explanation
Indices: 10340--10533 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
10330 AAAATATTTA
* * * * *
10340 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGGCTTAACTTACTAGGCACGAT
1 AAATCGAGGCAATATTCCTTTATCTCGAGTTTTGAAAATTTATGCCTTAACTTACTAGGCACAAT
10405 TTTTCTTCAAATCGGGATAATCGAATACCCTT
66 TTTTCTTCAAATCGGGATAATCGAATACCCTT
* **
10437 AAATCGAGGCAATATTCTTTTATCTCGAGTTTTGAAAATTTATGCCTTAACTTACTAGGCGTAAT
1 AAATCGAGGCAATATTCCTTTATCTCGAGTTTTGAAAATTTATGCCTTAACTTACTAGGCACAAT
10502 TTTTCTTCAAATCGGGATAATCGAATACCCTT
66 TTTTCTTCAAATCGGGATAATCGAATACCCTT
10534 TTTCAAGGTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATCTCGAGTTTTGAAAATTTATGCCTTAACTTACTAGGCACAAT
TTTTCTTCAAATCGGGATAATCGAATACCCTT
Done.