Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009983.1 Kokia drynarioides strain JFW-HI SEQ_124735, 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: 11317
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:72 original size:15 final size:15
Alignment explanation
Indices: 54--135 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
44 TATTAATAGC
54 AATAATAACTATT-TT
1 AATAATAA-TATTATT
69 AATAATAATATTATT
1 AATAATAATATTATT
* *
84 AGTAATAATAATGA-T
1 AATAATAAT-ATTATT
*
99 AATAACT-ATAATATT
1 AATAA-TAATATTATT
*
114 --TAATAA-ATAATT
1 AATAATAATATTATT
126 AATAATAATA
1 AATAATAATA
136 ATAAAGGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
12 5 0.10
13 4 0.08
14 12 0.23
15 27 0.52
16 4 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
AATAATAATATTATT
Found at i:74 original size:3 final size:3
Alignment explanation
Indices: 68--139 Score: 56
Period size: 3 Copynumber: 23.0 Consensus size: 3
58 ATAACTATTT
* * * * *
68 TAA TAA TAA TAT TAT TAG TAA TAA TAA TGA TAA TAA CT-A TAA TATT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA-A
114 TAA TAAA TAA TTAA TAA TAA TAA TAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA
140 AGGAAAGTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 1 0.02
3 47 0.82
4 9 0.16
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:384 original size:116 final size:115
Alignment explanation
Indices: 180--410 Score: 444
Period size: 116 Copynumber: 2.0 Consensus size: 115
170 TGATTTGCGT
180 TGCCGTCGCCGGAGTTTACGTCGGAGCCTCCGTTGAAACCCGCCCAACGTTGTCCGTACCGTGTC
1 TGCCGTCGCCGGAGTTTACGTCGGAGCCTCCGTTGAAACCCGCCCAACGTTGTCCGTACCGTGTC
245 AAACGTGGATCTGCGAAGAAACAAAGAACTGGGTTTCTAAAATCTTAAAG
66 AAACGTGGATCTGCGAAGAAACAAAGAACTGGGTTTCTAAAATCTTAAAG
*
295 NTGCCGTCGCCGGAGTTTACGTCGGAGCCTCCGTTGAAACCCGCCCAACGTTGTCCGTACCTTGT
1 -TGCCGTCGCCGGAGTTTACGTCGGAGCCTCCGTTGAAACCCGCCCAACGTTGTCCGTACCGTGT
360 CAAACGTGGATCTGCGAAGAAACAAAGAACTGGGTTTCTAAAATCTTAAAG
65 CAAACGTGGATCTGCGAAGAAACAAAGAACTGGGTTTCTAAAATCTTAAAG
411 CAGGAATTAA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (115 bp):
TGCCGTCGCCGGAGTTTACGTCGGAGCCTCCGTTGAAACCCGCCCAACGTTGTCCGTACCGTGTC
AAACGTGGATCTGCGAAGAAACAAAGAACTGGGTTTCTAAAATCTTAAAG
Found at i:821 original size:74 final size:73
Alignment explanation
Indices: 738--887 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 73
728 TGAAAAATGG
738 AAAAAAAAAAACAATTTGAGCTTTATATAAGCTTCCAAAACGGCATCGTTTTGGGGGCTGACTCT
1 AAAAAAAAAAACAATTTGAGCTTTATATAAGCTTCCAAAACGGCATCGTTTTGGGGGCTGACTCT
803 CAGCCTCNA
66 CAGCCTC-A
812 AAAAAAAAAAACAATTTGAGCTTTATATAAGCTTCCAAAACGGCATCGTTTTGGGGGCTGACTCT
1 AAAAAAAAAAACAATTTGAGCTTTATATAAGCTTCCAAAACGGCATCGTTTTGGGGGCTGACTCT
877 CAGCCTCA
66 CAGCCTCA
885 AAA
1 AAA
888 CGGTGTCGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 4 0.05
74 72 0.95
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (73 bp):
AAAAAAAAAAACAATTTGAGCTTTATATAAGCTTCCAAAACGGCATCGTTTTGGGGGCTGACTCT
CAGCCTCA
Found at i:1361 original size:30 final size:29
Alignment explanation
Indices: 1318--1466 Score: 106
Period size: 29 Copynumber: 5.0 Consensus size: 29
1308 GAGGTCTCTA
*
1318 AACTATCCAAAAATTCCATTTTTGACCTTG
1 AACT-TCCAAAAATTCCATTTTTGACCTCG
*** **
1348 AAACTTTTGAAAATTATATTTTT-ACACTCG
1 -AACTTCCAAAAATTCCATTTTTGAC-CTCG
* *
1378 AACTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTGACCTC-G
** *
1408 AACTTCCAAAAATTATATTTTT-ACCCCCG
1 AACTTCCAAAAATTCCATTTTTGA-CCTCG
* *
1437 AA-TATCCAAAAATTTCATTTTTGATCTCG
1 AACT-TCCAAAAATTCCATTTTTGACCTCG
1466 A
1 A
1467 TTTTTTAAAA
Statistics
Matches: 92, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
28 1 0.01
29 44 0.48
30 43 0.47
31 4 0.04
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:1395 original size:59 final size:60
Alignment explanation
Indices: 1318--1460 Score: 191
Period size: 59 Copynumber: 2.4 Consensus size: 60
1308 GAGGTCTCTA
*** *** *
1318 AACTATCCAAAAATTCCATTTTTGACCTTGAAACTTTTGAAAATTATATTTTTACACTCG
1 AACTATCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTACACCCG
*
1378 AACT-TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTACCCCCG
1 AACTATCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTACACCCG
*
1437 AA-TATCCAAAAATTTCATTTTTGA
1 AACTATCCAAAAATTCCATTTTTGA
1461 TCTCGATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
58 1 0.01
59 68 0.93
60 4 0.05
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.37
Consensus pattern (60 bp):
AACTATCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTATATTTTTACACCCG
Found at i:2393 original size:23 final size:23
Alignment explanation
Indices: 2363--2408 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2353 GGTGATCCAA
2363 TTACACCGAATAAAGGATTGGTG
1 TTACACCGAATAAAGGATTGGTG
2386 TTACACCGAATAAAGGATTGGTG
1 TTACACCGAATAAAGGATTGGTG
2409 GCGATTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (23 bp):
TTACACCGAATAAAGGATTGGTG
Found at i:10948 original size:46 final size:45
Alignment explanation
Indices: 10882--10972 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 45
10872 TCAACTTTAG
*
10882 TCAACATCCAGTTTTCTCATTCTTCTAGAGCCCTTGGCCAAATCT
1 TCAACATCCAGTTTTCTCATTCTTCTACAGCCCTTGGCCAAATCT
10927 TCAACATCCAAGTTTTCTCATTCTTCTACAGCCCTTGGCCAAATCT
1 TCAACATCC-AGTTTTCTCATTCTTCTACAGCCCTTGGCCAAATCT
10973 ACAATATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 9 0.20
46 35 0.80
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.35
Consensus pattern (45 bp):
TCAACATCCAGTTTTCTCATTCTTCTACAGCCCTTGGCCAAATCT
Done.