Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012835.1 Kokia drynarioides strain JFW-HI SEQ_127848, 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: 47924
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4565 original size:35 final size:35
Alignment explanation
Indices: 4501--4568 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
4491 AGAATATTAT
**
4501 TTAATTGTATTCTAAAAAAAATAGTATATAATAAA
1 TTAATTGTATTCTAAAAAAAATAACATATAATAAA
*
4536 TTAATATGTATTCT-AAAAGAATAACATATAATA
1 TTAAT-TGTATTCTAAAAAAAATAACATATAATA
4569 TAAATTAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.72
36 8 0.28
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (35 bp):
TTAATTGTATTCTAAAAAAAATAACATATAATAAA
Found at i:20136 original size:23 final size:23
Alignment explanation
Indices: 20106--20232 Score: 148
Period size: 23 Copynumber: 5.4 Consensus size: 23
20096 AGTGTTGGGC
*
20106 AACAGAGAGCACACACAGTGTTA
1 AACAGAGAGCACACACAGTGCTA
* *
20129 AACAGAGAGTC-CACAAAGTACTA
1 AACAGAGAG-CACACACAGTGCTA
** *
20152 GTCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
20175 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
20199 TAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACACACAGTGCTA
*
20223 ATCAGAGAGC
1 AACAGAGAGC
20233 GCGTTAGTGT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
22 1 0.01
23 65 0.72
24 3 0.03
25 21 0.23
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:20212 original size:48 final size:47
Alignment explanation
Indices: 20106--20232 Score: 168
Period size: 46 Copynumber: 2.7 Consensus size: 47
20096 AGTGTTGGGC
* * *
20106 AACAGAGAGCACACACAGTGTTAAACAGAGAGTCCACAAAGTACTAGT
1 AACAGAGAGCACACACAGTGCTAATCAGAGAG-CCACAAAGTACTAAT
* * *
20154 --CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAAT
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGC-CACAAAGTACTAAT
20200 AACAGAGAGCACACACAGTGCTAATCAGAGAGC
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGC
20233 GCGTTAGTGT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.01
46 38 0.55
48 30 0.43
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (47 bp):
AACAGAGAGCACACACAGTGCTAATCAGAGAGCCACAAAGTACTAAT
Found at i:25279 original size:22 final size:23
Alignment explanation
Indices: 25253--25302 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
25243 CACAAATCAC
25253 TAAGCACACGAAGTGCG-AACAG
1 TAAGCACACGAAGTGCGAAACAG
25275 TAAGCACACGAAGTGCGAAACAG
1 TAAGCACACGAAGTGCGAAACAG
25298 TAAGC
1 TAAGC
25303 GCATTAGCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (23 bp):
TAAGCACACGAAGTGCGAAACAG
Found at i:27087 original size:548 final size:546
Alignment explanation
Indices: 26085--27099 Score: 1605
Period size: 548 Copynumber: 1.9 Consensus size: 546
26075 ACTATAATTC
*
26085 AAAACTCTTGTAGTACTTACAACAAAAAGGCTGAATTTCCTCTTTTTTACCTCTTACTCTATTCT
1 AAAACTCTTGTAGTACTTACAACAAAAAGGCTGAATTTCCTCTTTTTCACCTCTTACTCTATTCT
* * *
26150 TTTCCTTTGTTTTCAATTTGATCCTTGCCTCTCTTCTTTTTCTCTTCAATTTCACATAAACACAT
66 TTTCCTTTCTCTTCAATTTGATCCTTGCCTCTCTTCTCTTTCTCTTCAATTTCACATAAACACAT
26215 ATAAGCTATAAGCTATAATTCAATAATTTTCATGCTAAATAACAGTAAAATACATGTATATAATG
131 ATAAGCTATAAGCTATAATTCAATAATTTTCATGCTAAATAACAGTAAAATACATGTATATAATG
* * * * * * *
26280 AGAATTTAACCATTTTTTTCCTTAACCCTTGAATTCAAATTTTCTCGATTTAGTCATTTATCTCT
196 AGAATTTAACCATTTCTTACCTTAAACATTGAATTCAAAATTTCTCAATTTAGTCATTTAGCTCT
* *
26345 CTAACACCTCAAAATAAATTCTATAAGAAGTTTGAGGTGTCTACTAACCCCTTTCTATACTTTTC
261 CTAACACCTCAAAATAAATTCTATAAGAAGTTTGAGGTGTCTAATAACCCATTTCTATACTTTTC
*
26410 TTTCAGAAATTTCAAAGAAAATAGGAGATTTTGGAGCTTGGAGGGCTTAAAAATGATGGAAGGAC
326 TTTCAGAAATTTCAAAGAAAATAGGAGATTTTGGAGCTTGGAGGACTTAAAAATGATGGAAGGAC
* * **
26475 CTATTTGGAATAAAATCAAAAGTTGGATGGAAGAGAGAATGGCATGAACGGTTACACTATGAAAA
391 CTATTTGGAATAAAAGCAAAAGTTGGATGGAAGAGAGAAGGGCATGAACGACTACACTATGAAAA
*
26540 GAGCTGATATTTTTTACTTTTAATTGATTTTTAACCTTTCTCAATTTCCATGCTAATAATTCAAA
456 -AGATGATATTTTTTACTTTTAATTGATTTTTAACCTTTCTCAATTTCCATGCTAATAATTCAAA
26605 TATATTATGAAATGTAGACTATAAACT
520 TATATTATGAAATGTAGACTATAAACT
* * *
26632 AAAATTCTTGTAGTGCTTACAACAAAAAGGCTG-ATTTCCTTCTCTTTTCA-CTCTTTGCTCT-T
1 AAAACTCTTGTAGTACTTACAACAAAAAGGCTGAATTTCC-TCT-TTTTCACCTC-TTACTCTAT
*
26694 CTCTTTTCCTTTCTCTTCRATTTGATCCTTGCCTCTCTTCTCTTTCTCTTCAATTTCACATAAAC
63 -TCTTTTCCTTTCTCTTCAATTTGATCCTTGCCTCTCTTCTCTTTCTCTTCAATTTCACATAAAC
26759 ACATATAAGCTATAAGCTATAATTCAATAATTTTCATGCTAAATAACAGTAAAATACATGTATAT
127 ACATATAAGCTATAAGCTATAATTCAATAATTTTCATGCTAAATAACAGTAAAATACATGTATAT
* * *
26824 CATGAGAATTTAACCATTTCTTACCTTAAACATTGAATTTAAAATTTCTCAATTTAGTGCCTTT-
192 AATGAGAATTTAACCATTTCTTACCTTAAACATTGAATTCAAAATTTCTCAATTTAGT-CATTTA
* *
26888 GCTCTCTGACACCTCAAAATGAATTCTATAAGAAGTTTGAGGTGTCTAATAACCTCATTT-TATA
256 GCTCTCTAACACCTCAAAATAAATTCTATAAGAAGTTTGAGGTGTCTAATAACC-CATTTCTATA
*
26952 TTTTTCTTTCAGAAATTTCAAAGAAAATAGGAGATTTTGGAGCTTGGAGGACTTAAAAATGATGG
320 CTTTTCTTTCAGAAATTTCAAAGAAAATAGGAGATTTTGGAGCTTGGAGGACTTAAAAATGATGG
* *
27017 AAGGACCTATTTGGAATAAAAGCAAAAGTTGGAAATGGAAGA-A-AAGGGCATGGACGACTAC-T
385 AAGGACCTATTTGGAATAAAAGCAAAAGTTGG--ATGGAAGAGAGAAGGGCATGAACGACTACAC
27079 TAATGAAAAAGATGATATTTT
448 T-ATGAAAAAGATGATATTTT
27100 CATCTTTTTA
Statistics
Matches: 428, Mismatches: 31, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
546 6 0.01
547 50 0.12
548 355 0.83
549 9 0.02
550 8 0.02
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (546 bp):
AAAACTCTTGTAGTACTTACAACAAAAAGGCTGAATTTCCTCTTTTTCACCTCTTACTCTATTCT
TTTCCTTTCTCTTCAATTTGATCCTTGCCTCTCTTCTCTTTCTCTTCAATTTCACATAAACACAT
ATAAGCTATAAGCTATAATTCAATAATTTTCATGCTAAATAACAGTAAAATACATGTATATAATG
AGAATTTAACCATTTCTTACCTTAAACATTGAATTCAAAATTTCTCAATTTAGTCATTTAGCTCT
CTAACACCTCAAAATAAATTCTATAAGAAGTTTGAGGTGTCTAATAACCCATTTCTATACTTTTC
TTTCAGAAATTTCAAAGAAAATAGGAGATTTTGGAGCTTGGAGGACTTAAAAATGATGGAAGGAC
CTATTTGGAATAAAAGCAAAAGTTGGATGGAAGAGAGAAGGGCATGAACGACTACACTATGAAAA
AGATGATATTTTTTACTTTTAATTGATTTTTAACCTTTCTCAATTTCCATGCTAATAATTCAAAT
ATATTATGAAATGTAGACTATAAACT
Found at i:32987 original size:22 final size:23
Alignment explanation
Indices: 32953--33009 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
32943 GCTGGGTAAA
*
32953 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGCGCAAAT
* * *
32975 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGCGCAAAT
32998 CAGTAAGCACAC
1 CAGTAAGCACAC
33010 GAAGTGCGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.39, C:0.28, G:0.21, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACACAGCGCAAAT
Found at i:37728 original size:15 final size:15
Alignment explanation
Indices: 37690--37764 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
37680 ATAAAAATAG
* *
37690 TTATTTTTATTTT-T
1 TTATTTATATTTTAA
*
37704 TTAATTATATTTTAA
1 TTATTTATATTTTAA
*
37719 TTATTTATATTTGAA
1 TTATTTATATTTTAA
*
37734 --ATGTTA-AGTATTAA
1 TTAT-TTATA-TTTTAA
*
37748 TTATTTATATTATAA
1 TTATTTATATTTTAA
37763 TT
1 TT
37765 TTATTATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
13 3 0.07
14 18 0.39
15 22 0.48
16 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
TTATTTATATTTTAA
Found at i:38688 original size:3 final size:3
Alignment explanation
Indices: 38680--38704 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38670 ATTTTCGCTC
38680 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
38705 ACGCTCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:45116 original size:31 final size:33
Alignment explanation
Indices: 45081--45158 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
45071 AAGCCCGTCC
* *
45081 ATATTTTTT-TTTAAAATTTTTTAGAATTTT-T
1 ATATTTTTTATTTAAAATATTTAAGAATTTTAT
* *
45112 ATATTGTTTTATTT-TAATATTTAATAATTTTAT
1 ATATT-TTTTATTTAAAATATTTAAGAATTTTAT
45145 ATATTTTTTATTTA
1 ATATTTTTTATTTA
45159 TTGAAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 5 0.13
32 25 0.64
33 9 0.23
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (33 bp):
ATATTTTTTATTTAAAATATTTAAGAATTTTAT
Found at i:45157 original size:16 final size:16
Alignment explanation
Indices: 45106--45157 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
45096 ATTTTTTAGA
45106 ATTTT-TATATTGTTTT
1 ATTTTATATATT-TTTT
* *
45122 ATTTTA-ATATTTAATA
1 ATTTTATATATTT-TTT
45138 ATTTTATATATTTTTT
1 ATTTTATATATTTTTT
45154 ATTT
1 ATTT
45158 ATTGAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 22 0.76
17 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTATATATTTTTT
Done.