Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010534.1 Kokia drynarioides strain JFW-HI SEQ_125451, 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: 22620
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Warning! 162 characters in sequence are not A, C, G, or T
Found at i:586 original size:59 final size:58
Alignment explanation
Indices: 512--717 Score: 313
Period size: 59 Copynumber: 3.5 Consensus size: 58
502 GAGGTCCCTA
* * *
512 AACTTCCAAAAATCCCATTTTTAACCTCGAACATTCCAAAAATTACCATTTTACCACCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACC-CCG
571 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCC-CG
* *
630 AACTTTCAAAAATCCCAATTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTA-CCCCG
* *
689 AACTTCCAAGAACTCCCATTTTTGACCCC
1 AACTTCCAA-AAATCCCATTTTTAACCCC
718 NNNNNNNNNN
Statistics
Matches: 135, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
58 1 0.01
59 115 0.85
60 19 0.14
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.28
Consensus pattern (58 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCCG
Found at i:707 original size:29 final size:28
Alignment explanation
Indices: 512--710 Score: 195
Period size: 30 Copynumber: 6.8 Consensus size: 28
502 GAGGTCCCTA
*
512 AACTTCCAAAAATCCCATTTTTAACCTCG
1 AACTTCCAAAAATCCCA-TTTTAACCCCG
*
541 AACATTCCAAAAATTACCATTTT-ACCACCG
1 AAC-TTCCAAAAA-TCCCATTTTAACC-CCG
*
571 AACTTCCAAAAATCCCATTTTTAACCCCA
1 AACTTCCAAAAATCCCA-TTTTAACCCCG
*
600 AACCTTCCAAAAATTACCATTTT-ACCCTCG
1 AA-CTTCCAAAAA-TCCCATTTTAACCC-CG
* *
630 AACTTTCAAAAATCCCAATTTTAACCCCA
1 AACTTCCAAAAATCCC-ATTTTAACCCCG
* *
659 AACCTTCCAAAAATTACCATTTTACCCCCG
1 AA-CTTCCAAAAA-TCCCATTTTAACCCCG
*
689 AACTTCCAAGAACTCCCATTTT
1 AACTTCCAA-AAATCCCATTTT
711 TGACCCCNNN
Statistics
Matches: 142, Mismatches: 15, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
28 7 0.05
29 59 0.42
30 65 0.46
31 11 0.08
ACGTcount: A:0.36, C:0.33, G:0.03, T:0.29
Consensus pattern (28 bp):
AACTTCCAAAAATCCCATTTTAACCCCG
Found at i:919 original size:60 final size:59
Alignment explanation
Indices: 821--958 Score: 222
Period size: 60 Copynumber: 2.3 Consensus size: 59
811 NNNNNNNNNC
* * *
821 AAAAATCCCAATTTTAACCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCA
1 AAAAATCCCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCGAACTT-CA
* *
881 AGAACTCCCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCGAACTTCA
1 AAAAATCCCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCGAACTTCA
940 AAAAATCCCATTTTTGACC
1 AAAAATCCCATTTTTGACC
959 TACATGTTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 19 0.27
60 52 0.73
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.27
Consensus pattern (59 bp):
AAAAATCCCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCGAACTTCA
Found at i:954 original size:29 final size:29
Alignment explanation
Indices: 821--953 Score: 126
Period size: 30 Copynumber: 4.5 Consensus size: 29
811 NNNNNNNNNC
*
821 AAAAATCCCAATTTTAACCCCAAACCTTCCA
1 AAAAATCCC-ATTTTACCCCCAAA-CTTCCA
* * *
852 AAAATTACCATTTTACCCCCGAACTTCCA
1 AAAAATCCCATTTTACCCCCAAACTTCCA
* *
881 AGAACTCCCATTTTTGA-CCCCAAACATTCCA
1 AAAAATCCCA-TTTT-ACCCCCAAAC-TTCCA
* * *
912 AAAATTACCATTTTACCCCCGAACTT-CA
1 AAAAATCCCATTTTACCCCCAAACTTCCA
940 AAAAATCCCATTTT
1 AAAAATCCCATTTT
954 TGACCTACAT
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
28 14 0.17
29 16 0.19
30 34 0.40
31 20 0.24
ACGTcount: A:0.37, C:0.33, G:0.03, T:0.27
Consensus pattern (29 bp):
AAAAATCCCATTTTACCCCCAAACTTCCA
Found at i:11439 original size:28 final size:28
Alignment explanation
Indices: 11405--11458 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
11395 TCAATTAATG
*
11405 ATTGTTTCCTTTGATCCTCTTTTTAAAT
1 ATTGTTTCCTTCGATCCTCTTTTTAAAT
11433 ATTGTTTCCTTCGATCCTCTTTTTAA
1 ATTGTTTCCTTCGATCCTCTTTTTAA
11459 TAAGAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTGTTTCCTTCGATCCTCTTTTTAAAT
Found at i:20826 original size:28 final size:28
Alignment explanation
Indices: 20792--20845 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
20782 TCAATTAATG
*
20792 ATTGTTTCCTTTGATCCTCTTTTTAAAT
1 ATTGTTTCCTTCGATCCTCTTTTTAAAT
20820 ATTGTTTCCTTCGATCCTCTTTTTAA
1 ATTGTTTCCTTCGATCCTCTTTTTAA
20846 TAAGAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTGTTTCCTTCGATCCTCTTTTTAAAT
Found at i:22034 original size:49 final size:49
Alignment explanation
Indices: 21980--22244 Score: 256
Period size: 49 Copynumber: 5.4 Consensus size: 49
21970 CGGACCACAG
*
21980 CTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTCCGA
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGA
* * * * *
22029 CTTAAACCTTTCCCTT-GTGTCT-TCATGGTACT-GGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTCTCTGA-GGTACTAGG-TTCGCCATTGCGA
*
22077 CTTAAATCCTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGA
1 CTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGA
* * * *
22126 CTTAAAACTTTCCCTTTATG-CTTTTTAGGTAC-ACGGTTCGCCATTGCGA
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTA-GGTTCGCCATTGCGA
* * * * * * *
22175 CTTAAACCTTTCCCTCCATATCTTCT-CGGTA-TTGGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGG-TTCGCCATTGCGA
*
22224 CTTAAATCTTGCCCTTCATGT
1 CTTAAATCTTTCCCTTCATGT
22245 TTCGTGGTAC
Statistics
Matches: 176, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
47 4 0.02
48 39 0.22
49 125 0.71
50 8 0.05
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGA
Found at i:22561 original size:17 final size:17
Alignment explanation
Indices: 22539--22617 Score: 88
Period size: 17 Copynumber: 4.5 Consensus size: 17
22529 CAAATTCACT
22539 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
*
22556 TTAAATTT-GTTTAAAA
1 TTAAATTTATTTTAAAA
*
22572 TTTTAAATTTATTTTTAAAT
1 --TTAAATTTA-TTTTAAAA
* *
22592 TTAAATTTATTTTGAAT
1 TTAAATTTATTTTAAAA
22609 TTAAATTTA
1 TTAAATTTA
22618 ATT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.13
17 24 0.44
18 17 0.31
20 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:22577 original size:35 final size:35
Alignment explanation
Indices: 22538--22617 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
22528 CCAAATTCAC
*
22538 TTTAAATTTA-TTTTAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTTAAAATTAAATTTATTTAAAA
* **
22572 TTTTAAATTTATTTTTAAATTTAAATTTATTTTGAA
1 -TTTAAATTTATTTTTAAAATTAAATTTATTTAAAA
22608 TTTAAATTTA
1 TTTAAATTTA
22618 ATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.50
36 20 0.50
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAAATTAAATTTATTTAAAA
Found at i:22579 original size:18 final size:18
Alignment explanation
Indices: 22538--22617 Score: 103
Period size: 18 Copynumber: 4.6 Consensus size: 18
22528 CCAAATTCAC
22538 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
*
22556 -TTAAATTT-GTTTAAAA
1 TTTAAATTTATTTTAAAA
*
22572 TTTTAAATTTATTTTTAAA
1 -TTTAAATTTATTTTAAAA
*
22591 TTTAAATTTATTTT-GAA
1 TTTAAATTTATTTTAAAA
22608 TTTAAATTTA
1 TTTAAATTTA
22618 ATT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.13
17 20 0.36
18 22 0.40
19 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:22594 original size:6 final size:6
Alignment explanation
Indices: 22538--22618 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
22528 CCAAATTCAC
* * * **
22538 TTTAAA TTT-AT TTTAAA ATTAAA TTT--G TTTAAAA TTTTAAA TTTATT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA -TTTAAA TTTAAA
* *
22585 TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
22619 TT
Statistics
Matches: 56, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
4 3 0.05
5 8 0.14
6 39 0.70
7 3 0.05
8 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Done.