Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010526.1 Kokia drynarioides strain JFW-HI SEQ_125440, 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: 9808
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Found at i:776 original size:9 final size:9
Alignment explanation
Indices: 740--812 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
730 TTATTTCAAA
740 AATATTAAAT
1 AATATT-AAT
*
750 AA-ATCAAT
1 AATATTAAT
758 AATA--AAT
1 AATATTAAT
765 AATATTAAT
1 AATATTAAT
*
774 AATAATAACT
1 AATATTAA-T
784 -AT-TTAAT
1 AATATTAAT
791 AA-ATATAAT
1 AATAT-TAAT
*
800 AATATTTAT
1 AATATTAAT
809 AATA
1 AATA
813 AAGGATGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
7 8 0.16
8 10 0.20
9 28 0.55
10 5 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
AATATTAAT
Found at i:1445 original size:18 final size:18
Alignment explanation
Indices: 1422--1456 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1412 GGTCGATCGT
1422 GGTTTGA-AGGAAAAGGGG
1 GGTTTGAGA-GAAAAGGGG
1440 GGTTTGAGAGAAAAGGG
1 GGTTTGAGAGAAAAGGG
1457 AAAGAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTTTGAGAGAAAAGGGG
Found at i:2009 original size:30 final size:31
Alignment explanation
Indices: 1971--2074 Score: 103
Period size: 30 Copynumber: 3.5 Consensus size: 31
1961 CTAAACTATA
* *
1971 CAAAAATTATATTTTTACCCCCCGAAC-TTT
1 CAAAAATTACATTTTTACCCCCCAAACTTTT
* *
2001 CTAAAATTACATTATTTA--CCCTAAACTTTT
1 CAAAAATTACATT-TTTACCCCCCAAACTTTT
2031 CAAAAATTACATTTTTA-CCCCCAAA-TTTT
1 CAAAAATTACATTTTTACCCCCCAAACTTTT
* *
2060 C-CAAATTCCATTTTT
1 CAAAAATTACATTTTT
2075 GACCTTGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.19
29 15 0.24
30 32 0.51
31 4 0.06
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.40
Consensus pattern (31 bp):
CAAAAATTACATTTTTACCCCCCAAACTTTT
Found at i:2153 original size:58 final size:58
Alignment explanation
Indices: 1971--2220 Score: 226
Period size: 59 Copynumber: 4.3 Consensus size: 58
1961 CTAAACTATA
* * * * *
1971 CAAAAATTATATTTTTACCCCCCGAACTTTCTAAAATTACATTATTTACCCTAAACTTTT
1 CAAAAATTACATTTTTA-CCCCCGAACTTTCCAAAATTCCATT-TTTACCCCAAACTTTC
* * *** *
2031 CAAAAATTACATTTTTACCCCCAAATTTTCC-AAATTCCATTTTTGA-CCTTGATTTATC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTT-ACCCCAAACTT-TC
* * * *
2089 AAAAAAATACATTTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCCAATCTTTC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTT-ACCCCAAACTTTC
*
2148 CAAAAATTATC-GTTTTACCCCCGAAC-TTCCAAAAATTCCA-TTTTACCCCCAAAC-TTC
1 CAAAAATTA-CATTTTTACCCCCGAACTTTCC-AAAATTCCATTTTTA-CCCCAAACTTTC
2205 CAAAAATT-CTATTTTT
1 CAAAAATTAC-ATTTTT
2221 GACCTCGATT
Statistics
Matches: 156, Mismatches: 25, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
55 1 0.01
57 25 0.16
58 52 0.33
59 57 0.37
60 21 0.13
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTACCCCAAACTTTC
Found at i:2182 original size:87 final size:88
Alignment explanation
Indices: 2090--2279 Score: 231
Period size: 87 Copynumber: 2.2 Consensus size: 88
2080 TGATTTATCA
* * *
2090 AAAAAATACATTTTTACCCTCGAACTTTCC-AAAATTCCATTTTTGACCCCAATCTTTCCAAAAA
1 AAAAAATCCATTTTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCAATCTTTCCAAAAA
* * *
2154 TTATCGTTTTACCCCCGAACTTCC
65 TTACCATTTTACCCCCGAACTTCT
* * * * * *
2178 AAAAATTCCA-TTTTACCCCCAAACTTCCAAAAATTCTATTTTTGACCTCGATTTTTTCAAAAAT
1 AAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATCTTTCCAAAAAT
**
2242 TACCATTTTACCCTTGAACTTCT
66 TACCATTTTACCCCCGAACTTCT
2265 AAAAAATCCATTTTT
1 AAAAAATCCATTTTT
2280 TGACCCCTAT
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 4 0.05
87 69 0.81
88 12 0.14
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (88 bp):
AAAAAATCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAATCTTTCCAAAAAT
TACCATTTTACCCCCGAACTTCT
Found at i:2240 original size:146 final size:148
Alignment explanation
Indices: 2031--2328 Score: 367
Period size: 146 Copynumber: 2.0 Consensus size: 148
2021 CTAAACTTTT
* *
2031 CAAAAATTACATTTTTACCCCCAAATTTTCCAAATTCCATTTTTGACCTTGATTTATCAAAAAAA
1 CAAAAATTACATTTTTACCCCCAAATCTTCCAAATTCCATTTTTGACCTCGATTTATCAAAAAAA
* * *
2096 TA-CATTTTTACCCTCGAACTT-TCCAAAATTCCA-TTTTTGACCCCAATCTTTCCAAAAATTAT
66 TACCA-TTTTACCCTCGAACTTCT-AAAAAATCCATTTTTTGACCCCAATCTTTCCAAAAATTAC
*
2158 CGTTTTACCCC-CGAACTTC
129 CATTTTACCCCTCGAACTTC
* * *
2177 CAAAAATTCCA-TTTTACCCCCAAA-CTTCCAAAAATTCTATTTTTGACCTCGATTTTTTC-AAA
1 CAAAAATTACATTTTTACCCCCAAATCTTCC--AAATTCCATTTTTGACCTCGA-TTTATCAAAA
* * * * *
2239 AATTACCATTTTACCCTTGAACTTCTAAAAAATCCATTTTTTGACCCCTATTTTTCTAAAAATTA
63 AAATACCATTTTACCCTCGAACTTCTAAAAAATCCATTTTTTGACCCCAATCTTTCCAAAAATTA
*
2304 CCATTTTACCCCTTGAACTTC
128 CCATTTTACCCCTCGAACTTC
2325 CAAA
1 CAAA
2329 TACTCCACTT
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
144 4 0.03
145 13 0.10
146 59 0.45
147 43 0.33
148 11 0.08
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (148 bp):
CAAAAATTACATTTTTACCCCCAAATCTTCCAAATTCCATTTTTGACCTCGATTTATCAAAAAAA
TACCATTTTACCCTCGAACTTCTAAAAAATCCATTTTTTGACCCCAATCTTTCCAAAAATTACCA
TTTTACCCCTCGAACTTC
Found at i:2248 original size:59 final size:59
Alignment explanation
Indices: 2177--2399 Score: 222
Period size: 59 Copynumber: 3.8 Consensus size: 59
2167 CCCGAACTTC
* *
2177 CAAAAATT-CCATTTTACCCCCAAACTTCCAAAAATTCTA-TTTTTGACCTCGATTTTTT
1 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCACTTTTTGACCTCGA-TTTTT
** * * * * *
2235 CAAAAATTACCATTTTACCCTTGAACTTCTAAAAAATCCATTTTTTGACCCCTATTTTT
1 CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCACTTTTTGACCTCGATTTTT
* * * *
2294 CTAAAAATTACCATTTTACCCCTTGAACTTCCAAATACTCCACTTTTT-ACCTTGATTTTT
1 C-AAAAATTACCATTTTACCCC-CGAACTTCCAAAAATTCCACTTTTTGACCTCGATTTTT
** * *
2354 CCCAAATTACCATTTTACCCTCGAA-TGTCTAAAAATTCCA-TTTTTG
1 CAAAAATTACCATTTTACCCCCGAACT-TCCAAAAATTCCACTTTTTG
2400 CCCCAAGTTA
Statistics
Matches: 136, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
57 6 0.04
58 21 0.15
59 48 0.35
60 40 0.29
61 21 0.15
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCACTTTTTGACCTCGATTTTT
Found at i:2270 original size:30 final size:29
Alignment explanation
Indices: 2149--2397 Score: 86
Period size: 30 Copynumber: 8.5 Consensus size: 29
2139 CAATCTTTCC
* * ** *
2149 AAAAATTATCGTTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCTTGAACTTCT
*** *
2178 AAAAATT-CCATTTTACCCCCAAACTTCC
1 AAAAATTACCATTTTACCCTTGAACTTCT
* * ** *
2206 AAAAATT-CTATTTTTGA-CCTCGATTTTTT
1 AAAAATTACCA-TTTT-ACCCTTGAACTTCT
2235 CAAAAATTACCATTTTACCCTTGAACTTCT
1 -AAAAATTACCATTTTACCCTTGAACTTCT
* * **
2265 AAAAAAT-CCATTTTTTGACCCCT-ATTTTTCT
1 AAAAATTACCA--TTTT-ACCCTTGA-ACTTCT
*
2296 AAAAATTACCATTTTACCCCTTGAACTTCC
1 AAAAATTACCATTTTA-CCCTTGAACTTCT
* * * *
2326 AAATACT-CCACTTTTTA-CCTTG-ATTTTT
1 AAAAATTACCA--TTTTACCCTTGAACTTCT
** *
2354 CCCAAATTACCATTTTACCCTCGAA-TGTCT
1 -AAAAATTACCATTTTACCCTTGAACT-TCT
2384 AAAAATT-CCATTTT
1 AAAAATTACCATTTT
2398 TGCCCCAAGT
Statistics
Matches: 164, Mismatches: 37, Indels: 39
0.68 0.15 0.16
Matches are distributed among these distances:
28 45 0.27
29 46 0.28
30 47 0.29
31 23 0.14
32 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTTGAACTTCT
Found at i:2361 original size:119 final size:118
Alignment explanation
Indices: 2178--2398 Score: 295
Period size: 119 Copynumber: 1.9 Consensus size: 118
2168 CCGAACTTCC
* *
2178 AAAAATTCCATTTTACCCCCAAACTTCCAAAAATTCTATTTTTGACCTCGATTTTTTCAAAAATT
1 AAAAATTCCATTTTACCCCCAAACTTCCAAAAACTCCATTTTTGACCTCGATTTTTTCAAAAATT
*
2243 ACCATTTTACCCTTGAACT-TCTAAAAAATCCATTTTTTGACCCCTATTTTTCT
66 ACCATTTTACCCTCGAA-TGTCTAAAAAATCCATTTTTTGACCCCTATTTTTCT
** * * **
2296 AAAAATTACCATTTTACCCCTTGAACTTCCAAATACTCCACTTTTT-ACCTTGA-TTTTTCCCAA
1 AAAAATT-CCATTTTACCCC-CAAACTTCCAAAAACTCCA-TTTTTGACCTCGATTTTTTCAAAA
*
2359 ATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTT
63 ATTACCATTTTACCCTCGAATGTCTAAAAAATCCATTTTT
2399 GCCCCAAGTT
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 8 0.09
119 56 0.63
120 20 0.22
121 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (118 bp):
AAAAATTCCATTTTACCCCCAAACTTCCAAAAACTCCATTTTTGACCTCGATTTTTTCAAAAATT
ACCATTTTACCCTCGAATGTCTAAAAAATCCATTTTTTGACCCCTATTTTTCT
Found at i:2441 original size:28 final size:27
Alignment explanation
Indices: 2385--2453 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
2375 CGAATGTCTA
*
2385 AAAATTCCATTTTTGCCCCAAGTTACC
1 AAAATTCCATTTTTGCCCCAAGGTACC
**
2412 AAAATTACCA-TTTTGCCCCCGGGTATCC
1 AAAATT-CCATTTTTGCCCCAAGGTA-CC
*
2440 AAAAATCACATTTT
1 AAAATTC-CATTTT
2454 CAACTCCGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
27 19 0.56
28 12 0.35
29 3 0.09
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTCCATTTTTGCCCCAAGGTACC
Done.