Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002114.1 Kokia drynarioides strain JFW-HI SEQ_114039, 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: 11653
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1005 original size:14 final size:14
Alignment explanation
Indices: 968--1007 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
958 ATTTATTTTA
* *
968 TTTTATTTTTTGAT
1 TTTTATTTTTGGGT
982 TTTT-TTTTTGGGT
1 TTTTATTTTTGGGT
995 TTTTATTTTTGGG
1 TTTTATTTTTGGG
1008 CCCGATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTGGGT
Found at i:1598 original size:78 final size:77
Alignment explanation
Indices: 1470--1840 Score: 296
Period size: 78 Copynumber: 4.8 Consensus size: 77
1460 GTAAGATATT
* * * * * * * *
1470 GAATGGTTGCAATTTGCCCCTGTCGCGGGGTAAGAGATTGGTTGACGGTGATTTGCCCCATAATT
1 GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA-AATC
1535 AGGGTAAAAGATC
65 AGGGTAAAAGATC
* * * *
1548 GAATGGTTGCAATTTGCCCCAGGCTCGAGGTAAGAGATTAGCTGATGGTGATTTGCCCC-AATCT
1 GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAATC-
*
1612 CGAGGTAAAAGATC
65 AG-GGTAAAAGATC
* ** * * ** * * * * **
1626 GGATGACTGCTATCTACCTTAGGCTCGGGGTAGGAGATTGGTTGATAGTGATCTGCCCTAGGCTC
1 GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA-AATC
*
1691 GGGGTAAAAGATC
65 AGGGTAAAAGATC
* * * * * * *
1704 GGATGGTTGCTATCTACCCCAGGCTCGGGGTAACAGATTGGCTAATGGTGATCT-ACCCAAGCTC
1 GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA-ATC
*
1768 ATGGTAAAAGATC
65 AGGGTAAAAGATC
* * * * * ** *
1781 AAATAGCTACAATCTGCCCCAGGGTTAGGGTAAGAGATTGACTGATGGTGATCTGCCCCA
1 GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
1841 TGATCGCGGT
Statistics
Matches: 232, Mismatches: 55, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
76 3 0.01
77 59 0.25
78 167 0.72
79 1 0.00
80 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (77 bp):
GAATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAATCA
GGGTAAAAGATC
Found at i:1728 original size:39 final size:39
Alignment explanation
Indices: 1536--1741 Score: 132
Period size: 39 Copynumber: 5.3 Consensus size: 39
1526 CCCATAATTA
* * *
1536 GGGTAAAAGATCGAATGGTTGCAATTTGCCCCAGGCTCG
1 GGGTAAAAGATCGGATGGTTGCTATCTGCCCCAGGCTCG
* * * * **
1575 AGGTAAGAGATTAGCTGATGG-TG--ATTTGCCCCAATCTCG
1 GGGTAAAAGA-T--CGGATGGTTGCTATCTGCCCCAGGCTCG
* ** * **
1614 AGGTAAAAGATCGGATGACTGCTATCTACCTTAGGCTCG
1 GGGTAAAAGATCGGATGGTTGCTATCTGCCCCAGGCTCG
** * * * * *
1653 GGGTAGGAGATTGGTTGATAG-TGATCTGCCCTAGGCTCG
1 GGGTAAAAGATCGGATGGTTGCT-ATCTGCCCCAGGCTCG
*
1692 GGGTAAAAGATCGGATGGTTGCTATCTACCCCAGGCTCG
1 GGGTAAAAGATCGGATGGTTGCTATCTGCCCCAGGCTCG
*
1731 GGGTAACAGAT
1 GGGTAAAAGAT
1742 TGGCTAATGG
Statistics
Matches: 126, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
36 5 0.04
37 2 0.02
38 2 0.02
39 108 0.86
40 2 0.02
41 2 0.02
42 5 0.04
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
GGGTAAAAGATCGGATGGTTGCTATCTGCCCCAGGCTCG
Found at i:1758 original size:39 final size:39
Alignment explanation
Indices: 1564--1779 Score: 118
Period size: 39 Copynumber: 5.6 Consensus size: 39
1554 TTGCAATTTG
* * * * * *
1564 CCCCAGGCTCGAGGTAAGAGATTAGCTGATGGTGATTTG
1 CCCCAGGCTCGGGGTAAAAGATTGGCTAATGGTGATCTA
** * * * * *
1603 CCCCAATCTCGAGGTAAAAGATCGGATGACTGCT-ATCTA
1 CCCCAGGCTCGGGGTAAAAGATTGGCT-AATGGTGATCTA
** ** * * * *
1642 CCTTAGGCTCGGGGTAGGAGATTGGTTGATAGTGATCTG
1 CCCCAGGCTCGGGGTAAAAGATTGGCTAATGGTGATCTA
* *
1681 CCCTAGGCTCGGGGTAAAAGATCGG---ATGGTTGCTATCTA
1 CCCCAGGCTCGGGGTAAAAGATTGGCTAATGG-TG--ATCTA
*
1720 CCCCAGGCTCGGGGTAACAGATTGGCTAATGGTGATCTA
1 CCCCAGGCTCGGGGTAAAAGATTGGCTAATGGTGATCTA
* **
1759 -CCCAAGCTCATGGTAAAAGAT
1 CCCCAGGCTCGGGGTAAAAGAT
1780 CAAATAGCTA
Statistics
Matches: 131, Mismatches: 38, Indels: 17
0.70 0.20 0.09
Matches are distributed among these distances:
36 3 0.02
37 2 0.02
38 19 0.15
39 98 0.75
40 3 0.02
41 2 0.02
42 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
CCCCAGGCTCGGGGTAAAAGATTGGCTAATGGTGATCTA
Found at i:3154 original size:112 final size:112
Alignment explanation
Indices: 2851--3168 Score: 401
Period size: 112 Copynumber: 2.8 Consensus size: 112
2841 ACTAACCGTC
* ** * *
2851 ATTTCAATACAAAAAATGCTTAAACAGGGTT-GTAAGGTAAATAAAATTGAATTTTATTGGAGGC
1 ATTTCAATGC-AAAAATGCTTAAACA-GGTTCACAAGGCAGATAAAATTGAATTTTATTGGAGGC
*
2915 AAAGCT--CACGCAGATGAAAAGAATAAAAATCATTGGTCCACTTACCATT
64 AAAGCTGACACG-A-ATGAAAAGATTAAAAATCATTGGTCCACTTACCATT
* * * *
2964 ATTTCAATGCAAAAATGCTTAAACAGGTTCGCAAGGCGGATAAAATTGAATTGTATTGGACGCAA
1 ATTTCAATGCAAAAATGCTTAAACAGGTTCACAAGGCAGATAAAATTGAATTTTATTGGAGGCAA
* *
3029 AGGTCGA-ATGAATGAAAAGATTAAAAATCATTGGTCCACTTACCATT
66 AGCT-GACACGAATGAAAAGATTAAAAATCATTGGTCCACTTACCATT
* * * *
3076 ATTTCAATGCAAAAATGCTTGAATAGGTTCACAAGGCAGATAAAATTAAATTTTATTGGAGGTAA
1 ATTTCAATGCAAAAATGCTTAAACAGGTTCACAAGGCAGATAAAATTGAATTTTATTGGAGGCAA
* *
3141 AACTGACACGAATGAAAAAATTAAAAAT
66 AGCTGACACGAATGAAAAGATTAAAAAT
3169 AACCTACATA
Statistics
Matches: 178, Mismatches: 22, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
111 6 0.03
112 160 0.90
113 10 0.06
114 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.27
Consensus pattern (112 bp):
ATTTCAATGCAAAAATGCTTAAACAGGTTCACAAGGCAGATAAAATTGAATTTTATTGGAGGCAA
AGCTGACACGAATGAAAAGATTAAAAATCATTGGTCCACTTACCATT
Found at i:3443 original size:21 final size:21
Alignment explanation
Indices: 3417--3464 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3407 AATCTCCTTA
3417 GGTTTTGAGATGCCCTTTATG
1 GGTTTTGAGATGCCCTTTATG
3438 GGTTTTGAGATGCCCTTTATG
1 GGTTTTGAGATGCCCTTTATG
3459 GGTTTT
1 GGTTTT
3465 CACCTCGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.46
Consensus pattern (21 bp):
GGTTTTGAGATGCCCTTTATG
Done.