Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000055.1 Kokia drynarioides strain JFW-HI SEQ_110588, 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: 2904
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Found at i:38 original size:5 final size:5
Alignment explanation
Indices: 10--101 Score: 61
Period size: 5 Copynumber: 19.2 Consensus size: 5
1 GGTTGATAG
* * * **
10 GAAAA TGAATA GAAAA -ATAA GAAAA GAAAA G-AAA -AAAA GAAAA GGAGG
1 GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
* *
58 GAAAA TGAATA GAAAA -ATAA GAAAA GAAAA G-AAA -AAAA GAAAA G
1 GAAAA -GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G
102 GAGGGGAAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
4 18 0.28
5 39 0.60
6 8 0.12
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.07
Consensus pattern (5 bp):
GAAAA
Found at i:62 original size:18 final size:19
Alignment explanation
Indices: 10--53 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1 GGTTGATAG
*
10 GAAAATGAATAGAAAAATAA
1 GAAAA-GAAAAGAAAAATAA
30 GAAAAGAAAAGAAAAA-AA
1 GAAAAGAAAAGAAAAATAA
48 GAAAAG
1 GAAAAG
54 GAGGGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 10 0.43
20 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (19 bp):
GAAAAGAAAAGAAAAATAA
Found at i:80 original size:48 final size:48
Alignment explanation
Indices: 9--111 Score: 197
Period size: 48 Copynumber: 2.1 Consensus size: 48
1 GGTTGATA
9 GGAAAATGAATAGAAAAATAAGAAAAGAAAAGAAAAAAAGAAAAGGAG
1 GGAAAATGAATAGAAAAATAAGAAAAGAAAAGAAAAAAAGAAAAGGAG
57 GGAAAATGAATAGAAAAATAAGAAAAGAAAAGAAAAAAAGAAAAGGAG
1 GGAAAATGAATAGAAAAATAAGAAAAGAAAAGAAAAAAAGAAAAGGAG
*
105 GGGAAAT
1 GGAAAAT
112 AAAAAAGAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (48 bp):
GGAAAATGAATAGAAAAATAAGAAAAGAAAAGAAAAAAAGAAAAGGAG
Found at i:2747 original size:529 final size:528
Alignment explanation
Indices: 1476--2804 Score: 1878
Period size: 529 Copynumber: 2.5 Consensus size: 528
1466 TTCGGGATGG
*
1476 CAAAATAATACGAATCCGTCGGGTTTTGACCTTGCCTGACCATATCGGGAGGTTTTTTCTTCTTT
1 CAAAATAATACGAATCCGTCGGGTTTTGACCTTGCCTGACCATATTGGGAGGTTTTTTCTTCTTT
* ** **
1541 TGAGATTGAGTTTGGGGATGAGAT--GAGA-TGACTCAGTGGGTCGGTGGGTTTTTGTTTAAATT
66 TGAAATTGAGTTTGGGGATGAGATGAGAGAGTGACTGGGTGGGTCGGTGGGTTTTTG-TTAAAAA
* *
1603 TTTTTGTTCAGGTCGAATCGGGTTTAGATCAAGCATGTATCTCTTCTTTAATCCTGAAATAGGTA
130 TTTTTGTTCAGGTCGAATCGGGTTTAGATCAAGCATGTATCTCTTCTTTGATCCTGAATTAGGTA
* * * *
1668 GAAATTTGACGAGCTAATTTAAAAGGGAAAATCTAGAAATGCTTCTTAGGGGTGGCTAAAATTTA
195 GAAGTTTGACGAGCTAGTTTAAGAGGGAAAATCTAGAAATGCTT-TTA-GGGTGGCTGAAATTTA
*
1733 ATTATAAATTTTTTAGAGGTCAAAACATAATTTTATCATTTAAGAGACCATTTTAAGGGACCAAA
258 ATTATAAATTTTTTAGAGGTCAAAACATAATTTTATCATTTAAGAGACAATTTTAAGGGACCAAA
* * * *
1798 AATATTTTTTTTTTTTCATTTTTTAGGTCAAAGTGCAATTTTACCATATACTATTTTGTGATTTC
323 AAGA-TTTTTATTTTTCATTTTTGAGGTCAAAGTGCAATTTTAACATATACTATTTTGTGATTTC
*
1863 ATTATTTATGAGAAGACTGAATTTACAATTCTTCTTTTTGAGGGCCAAGGCAGCTACCTACCCCT
387 ATTATTTATGAGAAGACTGAATTTACAATTCTTCTTTTTGAGGGCCAAGGCAGCTACCTACCCCA
* * *
1928 TAAATTCACCCCTAAGGATGGTAAATTAATCCGAATACATTTAGTTTCGTCTCAACCTTATATGA
452 TAAATTCACCCCTAAGGATGGTAAATTAATCCGAATACATTGAGTTTCATCCCAACCTTATATGA
* *
1993 ACTTAGGAATGG
517 ACTTAGAAATGA
*
2005 CAAAATAATACGAATCCGTCTGGTTTTGACCTTGCCTGACCATATTGGGAGGTTTTTTTCTTCTT
1 CAAAATAATACGAATCCGTCGGGTTTTGACCTTGCCTGACCATATTGGGAGG-TTTTTTCTTCTT
* * * * *
2070 TTGAAATTGAGTTTGGGGATGAGATGAGATGAGATGATTGGGTGGGTAGGTGGG---TCGGT--G
65 TTGAAATTGAGTTTGGGGATGAGATGAGA-GAG-TGACTGGGTGGGTCGGTGGGTTTTTGTTAAA
* * *
2130 AGTTTTTGTTCAGGTCGAATCGAGTTTAGATCAAGCATGTATCTTTTCTTTGATCCTGAATTAGG
128 AATTTTTGTTCAGGTCGAATCGGGTTTAGATCAAGCATGTATCTCTTCTTTGATCCTGAATTAGG
* *
2195 TAGAAGTTTGACAAGCTAGTTTAAGAGGGCAAATCTAGAAATGCATTTTAGGGTGGCTGAAATTT
193 TAGAAGTTTGACGAGCTAGTTTAAGAGGGAAAATCTAGAAATGC-TTTTAGGGTGGCTGAAATTT
* *
2260 AATTATAAATTTTTTAGAGGTCAAAATATAATTTTATCATTTAAG-GACAATTTTAAGGGATCAA
257 AATTATAAATTTTTTAGAGGTCAAAACATAATTTTATCATTTAAGAGACAATTTTAAGGGACCAA
2324 AAAGA-TTTTATTTTT-ATTTTTGAGGTCAAAGTGCAATTTTAACATATACTATTTTGTGATTTC
322 AAAGATTTTTATTTTTCATTTTTGAGGTCAAAGTGCAATTTTAACATATACTATTTTGTGATTTC
* * * * *
2387 ATTATTTATGAGGAGACTGAATTTACAATT-TTCCTTTTTTG-TGGTCAAGGCGGCTACCTATCC
387 ATTATTTATGAGAAGACTGAATTTACAATTCTT-C-TTTTTGAGGGCCAAGGCAGCTACCTACCC
* * * *
2450 CAT-AATTCGCCCTTAAGGATGGTAAATTAGTCCGAATACATTGAGTTTCATCCCAACCTTGTAT
450 CATAAATTCACCCCTAAGGATGGTAAATTAATCCGAATACATTGAGTTTCATCCCAACCTTATAT
2514 GAACTTAGAAATGA
515 GAACTTAGAAATGA
* * * * *
2528 CAACATAATAAGAATTCATCGGGTTTTGACCTTGCCTGACCATTTTGGGAGGTTTTTTCTTCTTT
1 CAAAATAATACGAATCCGTCGGGTTTTGACCTTGCCTGACCATATTGGGAGGTTTTTTCTTCTTT
2593 TGAAATTGAGTTTGGGGATGAGATGAGACGAGGTGACTGGGTGGGTCGGTGGGTTTTTGTTAAAA
66 TGAAATTGAGTTTGGGGATGAGATGAGA-GA-GTGACTGGGTGGGTCGGTGGGTTTTTGTT--AA
* * * * * *
2658 AAAATTTAGTTTAAGTCGAATCGGGTTTAGATCAAGCATGTATCCCTTCTTTGATTCTGAATTAG
127 AAATTTTTGTTCAGGTCGAATCGGGTTTAGATCAAGCATGTATCTCTTCTTTGATCCTGAATTAG
* *
2723 GTAGAAGTTTGTA-GTGCTAGTTTAAGAGGGAAAATCTAGAAATGTTTTTTAGGAGTGGCTGAAA
192 GTAGAAGTTTG-ACGAGCTAGTTTAAGAGGGAAAATCTAGAAATG-CTTTTAGG-GTGGCTGAAA
2787 TTTAATTATAAATTTTTT
254 TTTAATTATAAATTTTTT
2805 GGAGAATTTT
Statistics
Matches: 711, Mismatches: 69, Indels: 39
0.87 0.08 0.05
Matches are distributed among these distances:
522 61 0.09
523 115 0.16
524 96 0.14
525 18 0.03
527 21 0.03
528 58 0.08
529 252 0.35
530 67 0.09
531 1 0.00
532 4 0.01
533 2 0.00
535 16 0.02
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (528 bp):
CAAAATAATACGAATCCGTCGGGTTTTGACCTTGCCTGACCATATTGGGAGGTTTTTTCTTCTTT
TGAAATTGAGTTTGGGGATGAGATGAGAGAGTGACTGGGTGGGTCGGTGGGTTTTTGTTAAAAAT
TTTTGTTCAGGTCGAATCGGGTTTAGATCAAGCATGTATCTCTTCTTTGATCCTGAATTAGGTAG
AAGTTTGACGAGCTAGTTTAAGAGGGAAAATCTAGAAATGCTTTTAGGGTGGCTGAAATTTAATT
ATAAATTTTTTAGAGGTCAAAACATAATTTTATCATTTAAGAGACAATTTTAAGGGACCAAAAAG
ATTTTTATTTTTCATTTTTGAGGTCAAAGTGCAATTTTAACATATACTATTTTGTGATTTCATTA
TTTATGAGAAGACTGAATTTACAATTCTTCTTTTTGAGGGCCAAGGCAGCTACCTACCCCATAAA
TTCACCCCTAAGGATGGTAAATTAATCCGAATACATTGAGTTTCATCCCAACCTTATATGAACTT
AGAAATGA
Done.