Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011700.1 Kokia drynarioides strain JFW-HI SEQ_126694, 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: 364021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:345237 original size:56 final size:55
Alignment explanation
Indices: 345092--345244 Score: 222
Period size: 56 Copynumber: 2.8 Consensus size: 55
345082 ACACCCTAAA
*
345092 ACTGAAGAGGGAA-AGATTGAAGCCACAACGGTGAATCTTACACCCTAAAAAAAT
1 ACTGAAGAGGGAATAGATTGAAGCCACAACGGTGAATCTTACACCATAAAAAAAT
*
345146 --TGAAGAGGGAATAGATTGAAGCCACAACGGCGAATCTTACACCATATAAAAAAT
1 ACTGAAGAGGGAATAGATTGAAGCCACAACGGTGAATCTTACACCATA-AAAAAAT
** * *
345200 ACTGAAGAGGGAATAGATTGAAGCTGCAAAGGTGAATCGTACACC
1 ACTGAAGAGGGAATAGATTGAAGCCACAACGGTGAATCTTACACC
345245 TGAAAACTGT
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 11 0.12
53 32 0.36
54 7 0.08
56 38 0.43
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (55 bp):
ACTGAAGAGGGAATAGATTGAAGCCACAACGGTGAATCTTACACCATAAAAAAAT
Found at i:346850 original size:37 final size:35
Alignment explanation
Indices: 346787--346859 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 35
346777 TAATATTTTA
*
346787 TTTATTTATTTAATTTATGATTTTAATTATTTATT
1 TTTATTTATTTAATTTATGATATTAATTATTTATT
* *
346822 TTTATTTGTTTGATTTGCATGATATTAATTATTTATT
1 TTTATTTATTTAATTT--ATGATATTAATTATTTATT
346859 T
1 T
346860 GTTACTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 14 0.42
37 19 0.58
ACGTcount: A:0.26, C:0.01, G:0.07, T:0.66
Consensus pattern (35 bp):
TTTATTTATTTAATTTATGATATTAATTATTTATT
Found at i:352492 original size:17 final size:18
Alignment explanation
Indices: 352464--352498 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
352454 TTCAATATCT
352464 CAAAATTAAAATTTAAAC
1 CAAAATTAAAATTTAAAC
352482 CAAAA-TAAAATTTAAAC
1 CAAAATTAAAATTTAAAC
352499 ATCTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
CAAAATTAAAATTTAAAC
Found at i:354128 original size:123 final size:123
Alignment explanation
Indices: 354001--354241 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 123
353991 AAAAACGCTA
* * * * *
354001 CAAAAGATAAGAGCATTAGCGGTGTTTATTAGAAAACGCCACAAAAGGTATAAGCATTAGTGGTG
1 CAAAAGATAAGAGCACTAGCGGTGTTTATGAAAAAACGCCACAAAAGGTATAAGCATTAGCGGCG
* * * *
354066 TTAATGAGAAAACG-TCGCAAAAGGTACGAGCATTAGCGGCGTTTATGAGAAAATGCCG
66 TTAAGGAGAAAACGCT-GCAAAAGATAAGAGCATTAGCGACGTTTATGAGAAAATGCCG
* * * * * *
354124 CAAAAGGTATGAGCACTAGCGGTTTTTATGAAAAAAGGCCGCAAAAGGTATTAGCATTAGCGGCG
1 CAAAAGATAAGAGCACTAGCGGTGTTTATGAAAAAACGCCACAAAAGGTATAAGCATTAGCGGCG
* *
354189 TTTAGGAGAAAACGCTGCAAAAGATAAGAGCATTAGCGACGTTTATGGGAAAA
66 TTAAGGAGAAAACGCTGCAAAAGATAAGAGCATTAGCGACGTTTATGAGAAAA
354242 ACGCGCTAGA
Statistics
Matches: 100, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
123 99 0.99
124 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (123 bp):
CAAAAGATAAGAGCACTAGCGGTGTTTATGAAAAAACGCCACAAAAGGTATAAGCATTAGCGGCG
TTAAGGAGAAAACGCTGCAAAAGATAAGAGCATTAGCGACGTTTATGAGAAAATGCCG
Found at i:354232 original size:41 final size:41
Alignment explanation
Indices: 353952--354272 Score: 283
Period size: 41 Copynumber: 7.9 Consensus size: 41
353942 ATTTTTTCAC
* * *
353952 AAACGCCACAAAAGGTAA-AGCAATAGCGTCGTTTAT-AGGAA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGA-G-A
** * * *
353993 AAACGCTACAAAAGATAAGAGCATTAGCGGTGTTTATTAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * *
354034 AAACGCCACAAAAGGTATA-AGCATTAGTGGTGTTAATGAGA
1 AAACGCCGCAAAAGGTA-AGAGCATTAGCGGCGTTTATGAGA
* *
354075 AAACGTCGCAAAAGGTACGAGCATTAGCGGCGTTTATGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * ** *
354116 AAATGCCGCAAAAGGTATGAGCACTAGCGGTTTTTATGAAA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* ** *
354157 AAAGGCCGCAAAAGGTATTAGCATTAGCGGCGTTTAGGAGA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
* * * *
354198 AAACGCTGCAAAAGATAAGAGCATTAGCGACGTTTATGGGAA
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAG-A
* * * *
354240 AAACG-CGCTAGAGGTTA-AGCAATAGCGGCGTTT
1 AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTT
354273 TCCCTATAAA
Statistics
Matches: 230, Mismatches: 45, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
40 14 0.06
41 192 0.83
42 23 0.10
43 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (41 bp):
AAACGCCGCAAAAGGTAAGAGCATTAGCGGCGTTTATGAGA
Found at i:355747 original size:41 final size:41
Alignment explanation
Indices: 355702--355924 Score: 180
Period size: 41 Copynumber: 5.4 Consensus size: 41
355692 AAAAAATTAG
* * * *
355702 AGGTAAAGTAATAGTGACGTTTATGGGAAAAACGCTGCAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAA
* *** *
355743 AGGTAAAGCAATAGTGGCGTTT-TCTCATAAACGCCGCAAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGGAAAAACGCCGC-AAA
* * ** * *
355784 AGGTCAATCAATAGCGGCGTTTATGCAAAAAATGCCACAAA
1 AGGTAAAGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAA
355825 AGGTAAAGACCAATAGCGGCGTTTATGGG-AAAACGCCGCAAA
1 AGGTAAAG--CAATAGCGGCGTTTATGGGAAAAACGCCGCAAA
* ** * * *
355867 AGGTTAAGAGCACTAGCAACGTTTATTGGAAAAACACCGCTAA
1 AGG-TAA-AGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAA
* *
355910 AGGTTAAGAAATAGC
1 AGGTAAAGCAATAGC
355925 AGTGTTTTCT
Statistics
Matches: 144, Mismatches: 31, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
40 10 0.07
41 58 0.40
42 40 0.28
43 34 0.24
44 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AGGTAAAGCAATAGCGGCGTTTATGGGAAAAACGCCGCAAA
Found at i:355890 original size:42 final size:43
Alignment explanation
Indices: 355811--355925 Score: 119
Period size: 42 Copynumber: 2.7 Consensus size: 43
355801 CGTTTATGCA
* * * **
355811 AAAAATGCCACAAAAGGTAAAGACCAATAGCGGCGTTTA-TGG
1 AAAAACGCCGCAAAAGGTTAAGACCAATAGCAACGTTTATTGG
* * *
355853 GAAAACGCCGCAAAAGGTTAAGAGCACTAGCAACGTTTATTGG
1 AAAAACGCCGCAAAAGGTTAAGACCAATAGCAACGTTTATTGG
* *
355896 AAAAACACCGCTAAAGGTTAAGA--AATAGCA
1 AAAAACGCCGCAAAAGGTTAAGACCAATAGCA
355926 GTGTTTTCTC
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 6 0.10
42 31 0.52
43 23 0.38
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (43 bp):
AAAAACGCCGCAAAAGGTTAAGACCAATAGCAACGTTTATTGG
Found at i:356686 original size:15 final size:15
Alignment explanation
Indices: 356662--356694 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
356652 AACACTTGAG
356662 TTTGTGTTAAAATTT
1 TTTGTGTTAAAATTT
*
356677 TTTGTTTTAAAATTT
1 TTTGTGTTAAAATTT
356692 TTT
1 TTT
356695 TCCCTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTGTGTTAAAATTT
Found at i:359646 original size:13 final size:13
Alignment explanation
Indices: 359628--359672 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
359618 AATAATTTAT
359628 TATAAATTAATAA
1 TATAAATTAATAA
* *
359641 TATAAAATAATTTAT
1 TATAAATTAA--TAA
359656 TATAAATTAATAA
1 TATAAATTAATAA
359669 TATA
1 TATA
359673 TACAAATTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 15 0.58
15 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAAATTAATAA
Found at i:359674 original size:15 final size:15
Alignment explanation
Indices: 359628--359674 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
359618 AATAATTTAT
359628 TATAAATTAATAATA
1 TATAAATTAATAATA
*
359643 TA-AAA-TAAT-TTA
1 TATAAATTAATAATA
359655 TTATAAATTAATAATA
1 -TATAAATTAATAATA
359671 TATA
1 TATA
359675 CAAATTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.08
13 6 0.23
14 6 0.23
15 10 0.38
16 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAATTAATAATA
Found at i:359680 original size:28 final size:28
Alignment explanation
Indices: 359618--359672 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
359608 ATACCGAAAG
359618 AATAATTTATTATAAATTAATAATATAA
1 AATAATTTATTATAAATTAATAATATAA
359646 AATAATTTATTATAAATTAATAATATA
1 AATAATTTATTATAAATTAATAATATA
359673 TACAAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAATTTATTATAAATTAATAATATAA
Done.