Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009318.1 Kokia drynarioides strain JFW-HI SEQ_124025, 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: 99873
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:22101 original size:150 final size:151
Alignment explanation
Indices: 21830--22421 Score: 888
Period size: 150 Copynumber: 3.9 Consensus size: 151
21820 AGAAGAGAAA
*
21830 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGACA-GACTCCTAGAAGC
1 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGA-AGGACTCCTAGAAGT
**
21894 GAGACACACGA-TGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTTGG
65 GAGACACACGAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAG
21958 TGGAAGGTGCCTCCTCCAAATT
130 TGGAAGGTGCCTCCTCCAAATT
** * * * *
21980 GCACAGTGAAGAAAATCTTGAAAGGAAAACCGATAAAAGGAGTGGAGGAAGGAGTCCTAGAAGTG
1 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGAAGGACTCCTAGAAGTG
** *
22045 AGATGCA-GAGTGGAATTCCTCACTCTTCTCCGTCCAATGTGATGGGTAGTAGTAGATCCTCAGT
66 AGACACACGAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGT
*
22109 GAAAGGTGCCTCCTCCAAATT
131 GGAAGGTGCCTCCTCCAAATT
22130 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGAAGGACTCCTAGAAGTG
1 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGAAGGACTCCTAGAAGTG
* * * * *
22195 AGACACATG-GTGGAATTCCCCGCTCTTCTCCGTCCAATGTGATGGGGAGTAGTAGATCCTCAGT
66 AGACACACGAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGT
*
22259 GGAAGGTACCTCCTCCAAATT
131 GGAAGGTGCCTCCTCCAAATT
* ** * *
22280 GCATAGTGAAGAAAATCTTGGAAGGAAAACTAATAAGAAGAGTGGAGGAAGGACTCCTAGAAGTG
1 GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGAAGGACTCCTAGAAGTG
* * *
22345 AGACATAC-AGTGGAATTCCGCACTCTTCTCCATCCAATGTGGTGGGTAGTAGTAGATCCTCAGT
66 AGACACACGAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGT
*
22409 GGAATGTGCCTCC
131 GGAAGGTGCCTCC
22422 AGATCGCCTA
Statistics
Matches: 398, Mismatches: 40, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
149 3 0.01
150 394 0.99
151 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (151 bp):
GCACAGTGAAGAAAATAATGGAAGGAAAACTGATAAAAAGAGTGGAGGAAGGACTCCTAGAAGTG
AGACACACGAGTGGAATTCCTCACTCTTCTCCATCCAATGTGATGGGTAGTAGTAGATCCTCAGT
GGAAGGTGCCTCCTCCAAATT
Found at i:24374 original size:24 final size:25
Alignment explanation
Indices: 24315--24374 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
24305 CTTATTAAAT
* * *
24315 AATATTTTATATTTGAGATTTATTT
1 AATATTTTTTATTTGAGATTTAGTA
* *
24340 AATA-TTATTATTTGATATTT-GTA
1 AATATTTTTTATTTGAGATTTAGTA
24363 AATATTTTTTAT
1 AATATTTTTTAT
24375 ATACATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 5 0.18
24 19 0.68
25 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (25 bp):
AATATTTTTTATTTGAGATTTAGTA
Found at i:29680 original size:6 final size:7
Alignment explanation
Indices: 29653--29677 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29643 AATATGAGTG
29653 TTTTTAT
1 TTTTTAT
29660 TTTTTAT
1 TTTTTAT
29667 TTTTTAT
1 TTTTTAT
29674 TTTT
1 TTTT
29678 ATTGTCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:38564 original size:21 final size:22
Alignment explanation
Indices: 38509--38571 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
38499 AATCCTGAAT
*
38509 TCGCACTTCGGTGCCCCTGT-A
1 TCGCACTTCGATGCCCCTGTAA
*
38530 TCGTAC-TCGAATGCCCCTGTAA
1 TCGCACTTCG-ATGCCCCTGTAA
*
38552 T-GCACTTCGATGCCCGTGTA
1 TCGCACTTCGATGCCCCTGTA
38572 TTTTAATCGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.09
21 27 0.77
22 5 0.14
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (22 bp):
TCGCACTTCGATGCCCCTGTAA
Found at i:41543 original size:118 final size:114
Alignment explanation
Indices: 41339--41560 Score: 336
Period size: 118 Copynumber: 1.9 Consensus size: 114
41329 TTAAAATGAC
* *
41339 GAGGTTCGGCTTCGAAGTTCTTACCAACCCATTAATGGAATATGAGTATTTCAATTGTAACTCTC
1 GAGGTTCGGCTTCGAAGTTCTTACCAACCCATTAATAGAATATAAGTATTTCAATTGTAACTCTC
41404 AAATTATATAGATATAAAAGCAAGTGTGACCAACCCATTCATACAATAT
66 AAATTATATAGATATAAAAGCAAGTGTGACCAACCCATTCATACAATAT
* * * *
41453 GAGGTTCGGCTTCGAAGTTGTTATCAGCCCATTAATAGAATATAAGTACTTACTTCAATTGTAAG
1 GAGGTTCGGCTTCGAAGTTCTTACCAACCCATTAATAGAATATAAGTA--T--TTCAATTGTAAC
* *
41518 TCTCAAATTATATAGATATAAAAGCAAGTGTTATCAACCCATT
62 TCTCAAATTATATAGATATAAAAGCAAGTGTGACCAACCCATT
41561 AATGGAGTAC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
114 43 0.45
116 1 0.01
118 52 0.54
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (114 bp):
GAGGTTCGGCTTCGAAGTTCTTACCAACCCATTAATAGAATATAAGTATTTCAATTGTAACTCTC
AAATTATATAGATATAAAAGCAAGTGTGACCAACCCATTCATACAATAT
Found at i:56388 original size:13 final size:13
Alignment explanation
Indices: 56370--56394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56360 TGCATGAAAT
56370 ATTTACCTTATTG
1 ATTTACCTTATTG
56383 ATTTACCTTATT
1 ATTTACCTTATT
56395 TACACTATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTACCTTATTG
Found at i:58594 original size:2 final size:2
Alignment explanation
Indices: 58587--58631 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
58577 GCTAATCATT
* *
58587 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58629 AG A
1 AG A
58632 AAAGAACAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65265 original size:14 final size:14
Alignment explanation
Indices: 65246--65273 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
65236 TTTAGGATTC
65246 AAGATTTTAAATTT
1 AAGATTTTAAATTT
65260 AAGATTTTAAATTT
1 AAGATTTTAAATTT
65274 GATGTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AAGATTTTAAATTT
Found at i:65858 original size:3 final size:3
Alignment explanation
Indices: 65850--65891 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
65840 TCCATGCACT
65850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65892 AATTTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:68447 original size:21 final size:21
Alignment explanation
Indices: 68421--68496 Score: 91
Period size: 21 Copynumber: 3.4 Consensus size: 21
68411 CTTTTTGTGT
68421 TTATATTTTATATTTATTTAA
1 TTATATTTTATATTTATTTAA
*
68442 TTATATTTTATAATTATTTGAA
1 TTATATTTTATATTTATTT-AA
68464 TATATATTTGTA-ATTATATTATAA
1 T-TATATTT-TATATT-TATT-TAA
68488 TTATATTTT
1 TTATATTTT
68497 TTAAATTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
21 18 0.38
22 4 0.08
23 16 0.33
24 9 0.19
25 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTATATTTTATATTTATTTAA
Found at i:68451 original size:11 final size:11
Alignment explanation
Indices: 68421--68496 Score: 68
Period size: 11 Copynumber: 6.8 Consensus size: 11
68411 CTTTTTGTGT
68421 TTATATTTTATA
1 TTATATTTTA-A
68433 TT-TA-TTTAA
1 TTATATTTTAA
68442 TTATATTTT-A
1 TTATATTTTAA
* *
68452 TAATTATTTGAA
1 TTA-TATTTTAA
68464 TATATATTTGTAA
1 T-TATATTT-TAA
*
68477 TTATATTATAA
1 TTATATTTTAA
68488 TTATATTTT
1 TTATATTTT
68497 TTAAATTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
9 3 0.06
10 9 0.17
11 21 0.40
12 15 0.29
13 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:72686 original size:11 final size:11
Alignment explanation
Indices: 72670--72695 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
72660 TATCGTCTCA
72670 AAGGTGATCAT
1 AAGGTGATCAT
72681 AAGGTGATCAT
1 AAGGTGATCAT
72692 AAGG
1 AAGG
72696 CTATAGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (11 bp):
AAGGTGATCAT
Found at i:77905 original size:98 final size:98
Alignment explanation
Indices: 77736--77931 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
77726 GCCAATTCCT
77736 TTAACTGATATTTTTCATTAAACTTAGCAAATGAGAAAATCTATGACAACTTGGAAACCATAAAA
1 TTAACTGATATTTTTCATTAAACTTAGCAAATGAGAAAATCTATGACAACTTGGAAACCATAAAA
77801 CAAAATGGAACTCACGGTAAATTGAGCTTCAAC
66 CAAAATGGAACTCACGGTAAATTGAGCTTCAAC
77834 TTAACTGATATTTTTCATTAAACTTAGCAAATGAGAAAATCTATGACAACTTGGAAACCATAAAA
1 TTAACTGATATTTTTCATTAAACTTAGCAAATGAGAAAATCTATGACAACTTGGAAACCATAAAA
77899 CAAAATGGAACTCACGGTAAATTGAGCTTCAAC
66 CAAAATGGAACTCACGGTAAATTGAGCTTCAAC
77932 ACCCCAAAGA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (98 bp):
TTAACTGATATTTTTCATTAAACTTAGCAAATGAGAAAATCTATGACAACTTGGAAACCATAAAA
CAAAATGGAACTCACGGTAAATTGAGCTTCAAC
Found at i:81530 original size:30 final size:30
Alignment explanation
Indices: 81494--81554 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
81484 CAAATGGAAG
81494 TAAGAATTAAAAATGGTGGTTGACAATTCT
1 TAAGAATTAAAAATGGTGGTTGACAATTCT
81524 TAAGAATTAAAAATGGTGGTTGACAATTCT
1 TAAGAATTAAAAATGGTGGTTGACAATTCT
81554 T
1 T
81555 GCCTGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
TAAGAATTAAAAATGGTGGTTGACAATTCT
Found at i:95042 original size:23 final size:24
Alignment explanation
Indices: 95015--95073 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
95005 GTGCTGAGCA
*
95015 ACAGAGAGCACACACAATGCTAAT
1 ACAGAGAGCACAAACAATGCTAAT
* *
95039 -CAGAGAACACAAACAGTGCTAAT
1 ACAGAGAGCACAAACAATGCTAAT
95062 AACAGAGAGCAC
1 -ACAGAGAGCAC
95074 GAGACGTGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 20 0.69
25 9 0.31
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (24 bp):
ACAGAGAGCACAAACAATGCTAAT
Done.