Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012841.1 Kokia drynarioides strain JFW-HI SEQ_127854, 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: 9908
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.33
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:4880 original size:58 final size:60
Alignment explanation
Indices: 4843--5191 Score: 493
Period size: 58 Copynumber: 6.0 Consensus size: 60
4833 TTTGTAGACA
4843 TTTTGGGG-T-AAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
** * *
4901 TTTTAAGGTTAAAAATGAGATTTTTTTGAAGTTTCGA--GGTAAAAATGGAATTTTTGGGAG
1 TTTTGGGGTTAAAAATGGGA-TTTTTGGAAG-TTCGAGGGGTAAAAATGGAATTTTTGGGAG
*
4961 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGA-GGGT-TAAATGGAATTTTTGGGAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
** *
5019 TTTTGGGGTTAAAAATGGGATTTTTGGAA-TTTTAAGGGTAAAAATGGAATTTTTGGGAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
* * *
5078 TTTTGGGGTTAAAAATTGGATTTTTGGAAGTTTG-GGGGTAAAAATGAAATTTTTGGGAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
* *
5137 TTTT-GGGTTAAAAATGGGATTTTTGGAAGTTCG-GGGGTAAAAACGAAATTTTTGG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGG
5192 ACAGTTTAGG
Statistics
Matches: 264, Mismatches: 19, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
57 3 0.01
58 110 0.42
59 86 0.33
60 51 0.19
61 9 0.03
62 5 0.02
ACGTcount: A:0.29, C:0.01, G:0.32, T:0.38
Consensus pattern (60 bp):
TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGGTAAAAATGGAATTTTTGGGAG
Found at i:4888 original size:30 final size:29
Alignment explanation
Indices: 4847--5198 Score: 323
Period size: 29 Copynumber: 12.0 Consensus size: 29
4837 TAGACATTTT
* *
4847 GGGGT-AAAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* *
4875 AGGGGTAAAAATGGAATTTTTGGGAGTTTTA
1 -GGGGTAAAAATGGAATTTTTGGAAG-TTTG
* * * * *
4906 AGGTTAAAAATGAGATTTTTTTGAAGTTTC
1 GGGGTAAAAATG-GAATTTTTGGAAGTTTG
* *
4936 GAGGTAAAAATGGAATTTTTGGGAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
* * *
4966 GGGTTAAAAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* * *
4995 AGGGT-TAAATGGAATTTTTGGGAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
* * * *
5024 GGGTTAAAAATGGGATTTTTGGAATTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* *
5053 AGGGTAAAAATGGAATTTTTGGGAGTTTTG
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTG
*
5083 GGGTTAAAAATTGG-ATTTTTGGAAGTTTG
1 GGGGTAAAAA-TGGAATTTTTGGAAGTTTG
* * *
5112 GGGGTAAAAATGAAATTTTTGGGAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* * *
5141 GGGTTAAAAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTG
* *
5170 GGGGTAAAAACGAAATTTTTGGACAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
5199 AGGGACCTCC
Statistics
Matches: 254, Mismatches: 59, Indels: 19
0.77 0.18 0.06
Matches are distributed among these distances:
28 18 0.07
29 118 0.46
30 103 0.41
31 15 0.06
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTG
Found at i:6692 original size:30 final size:29
Alignment explanation
Indices: 6598--6973 Score: 339
Period size: 29 Copynumber: 12.7 Consensus size: 29
6588 TAAATTGTCC
* *
6598 AAAATTCCATTTTTATCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
6627 AAAA-TCCTATTTATTTTTACCCCCAAAACTT-CA
1 AAAATTCC-----ATTTTTACCCCC-AAACTTCCA
*
6660 AAAATTCCATTTTTACCCCCCGAACTTCC-
1 AAAATTCCATTTTTA-CCCCCAAACTTCCA
*
6689 AAAATTCTCATTTTTGACCCCCGAAACTTCTA
1 AAAATTC-CATTTTT-ACCCCC-AAACTTCCA
6721 AAAATTCCATTTTTACCCCCAAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* * ***
6750 AAAATCCCATTTTGACCTTGAAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* *
6779 AAAATTCCATTTTTA-CCCTAAACTTTCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* * *
6807 AAAATCCCATTTTTGACCCCAAAACTCCCA
1 AAAATTCCATTTTT-ACCCCCAAACTTCCA
* *
6837 AAAATTCCAATTTTACCCTCAAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
** *
6866 AAAA-TCTCATTTTTGACCCTAAAACTCCCA
1 AAAATTC-CATTTTT-ACCCCCAAACTTCCA
**
6896 AAAATTCCATTTTTTACCCCTGAACTTCCA
1 AAAATTCCA-TTTTTACCCCCAAACTTCCA
* * * * *
6926 AAAAATCCATTTTTACCCTCGAACCTGCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* *
6955 AAAATGCCATTTTTGCCCC
1 AAAATTCCATTTTTACCCC
6974 TGGATGTCCA
Statistics
Matches: 286, Mismatches: 42, Indels: 38
0.78 0.11 0.10
Matches are distributed among these distances:
28 27 0.09
29 122 0.43
30 84 0.29
31 21 0.07
32 7 0.02
33 17 0.06
34 8 0.03
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCAAACTTCCA
Found at i:6944 original size:59 final size:58
Alignment explanation
Indices: 6598--7016 Score: 368
Period size: 58 Copynumber: 7.1 Consensus size: 58
6588 TAAATTGTCC
* *
6598 AAAATTCCATTTTTATCCCC-GAACTTCCAAAAATCCTATTTATTTTTACCCCCAAAACT-TCA
1 AAAATTCCATTTTTA-CCCCTGAACTTCCAAAAATCC-A--T-TTTTGA-CCCCAAAACTCCCA
* * * * *
6660 AAAATTCCATTTTTACCCCCCGAACTTCCAAAATTCTCATTTTTGACCCCCGAAACTTCTA
1 AAAATTCCATTTTTA-CCCCTGAACTTCCAAAAATC-CATTTTTGA-CCCCAAAACTCCCA
** *** *
6721 AAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCTTGAAACTTCCA
1 AAAATTCCATTTTTACCCCTGAACTTCCAAAAAT-CCATTTTTGACCCCAAAACTCCCA
* *
6779 AAAATTCCATTTTTA-CCCTAAACTTTCAAAAATCCCATTTTTGACCCCAAAACTCCCA
1 AAAATTCCATTTTTACCCCTGAACTTCCAAAAAT-CCATTTTTGACCCCAAAACTCCCA
* * *
6837 AAAATTCCAATTTTA-CCCTCAAACTTCCAAAAATCTCATTTTTGACCCTAAAACTCCCA
1 AAAATTCCATTTTTACCCCT-GAACTTCCAAAAATC-CATTTTTGACCCCAAAACTCCCA
* * *
6896 AAAATTCCATTTTTTACCCCTGAACTTCCAAAAAATCCATTTTT-ACCCTCGAACCT-GCA
1 AAAATTCCA-TTTTTACCCCTGAACTTCC-AAAAATCCATTTTTGACCC-CAAAACTCCCA
* * * * * * *
6955 AAAATGCCATTTTTGCCCCTGGA-TGTCCAAAAACTCCATTTTCGACCTCGAAACTCTCA
1 AAAATTCCATTTTTACCCCTGAACT-TCCAAAAA-TCCATTTTTGACCCCAAAACTCCCA
7014 AAA
1 AAA
7017 TTACTCTTTT
Statistics
Matches: 309, Mismatches: 33, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
57 26 0.08
58 90 0.29
59 72 0.23
60 57 0.18
61 29 0.09
62 19 0.06
63 15 0.05
64 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCCTGAACTTCCAAAAATCCATTTTTGACCCCAAAACTCCCA
Found at i:7073 original size:27 final size:28
Alignment explanation
Indices: 7041--7102 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
7031 TCGAATTTTC
7041 CCAAAATCACCATTTTG-TCCCGAGAAT
1 CCAAAATCACCATTTTGCTCCCGAGAAT
* * *
7068 CCAAAATTACCATTTTGCTCTCGAGCAT
1 CCAAAATCACCATTTTGCTCCCGAGAAT
7096 CCGAAAA
1 CC-AAAA
7103 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 16 0.53
28 10 0.33
29 4 0.13
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (28 bp):
CCAAAATCACCATTTTGCTCCCGAGAAT
Found at i:9505 original size:46 final size:46
Alignment explanation
Indices: 9434--9529 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
9424 ACACTAGCGC
*
9434 GCTCTCTGTTTAGCACGTCTCGTGCTCTCTAATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACGTCTCGTGCTCTCTAATTAGCACTGTGTGT
* * *
9480 GCTCTCTGATTAGCACTTCGT-GTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACGTC-TCGTGCTCTCTAATTAGCACTGTGTGT
9526 GCTC
1 GCTC
9530 AGTACTTTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACGTCTCGTGCTCTCTAATTAGCACTGTGTGT
Found at i:9519 original size:23 final size:23
Alignment explanation
Indices: 9434--9529 Score: 124
Period size: 23 Copynumber: 4.2 Consensus size: 23
9424 ACACTAGCGC
* *
9434 GCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTTCGT-GT
*
9457 GCTCTCTAATTAGCACTGT-GTGT
1 GCTCTCTGATTAGCACT-TCGTGT
9480 GCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTTCGTGT
*
9503 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGT
9526 GCTC
1 GCTC
9530 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
22 1 0.02
23 62 0.95
24 2 0.03
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTCGTGT
Found at i:9556 original size:14 final size:16
Alignment explanation
Indices: 9517--9557 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
9507 TCTGATTAGC
9517 ACTTTGTGTGCTCAGT
1 ACTTTGTGTGCTCAGT
9533 ACTTTGTGTGCTCAGT
1 ACTTTGTGTGCTCAGT
9549 ACTTTGTGT
1 ACTTTGTGT
9558 ACTCTCTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.24, T:0.46
Consensus pattern (16 bp):
ACTTTGTGTGCTCAGT
Done.