Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010409.1 Kokia drynarioides strain JFW-HI SEQ_125294, 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: 5810
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:3151 original size:59 final size:59
Alignment explanation
Indices: 2965--3400 Score: 585
Period size: 59 Copynumber: 7.4 Consensus size: 59
2955 CATGGGGGGG
* * * *
2965 AAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTA
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * * *
3023 AAATAGTGATTTTTAGAAAGGTTCGGAGTCAAAAAATGAGATTTTTGGAAGTTCGTGGGTA
1 AAATGGTAATTTTTAG-AAGGTTCGGGGTC-AAAAATGGGATTTTTGGAAGTTCGAGGGTA
* *
3084 AAAT-GTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * **
3142 AAATGGTAATTTTTAAAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGCATA
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * *
3201 AAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAAATGGGTTTTTTGGAAGTTCG-GGTGTA
1 AAATGGTAATTTTTAGAAGGTTCGGGGT-CAAAAATGGGATTTTTGGAAGTTCGAGG-GTA
** *
3261 AAATGGTAATTTTTAGAAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT-AAGGGTA
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
3319 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC-AGGGATA
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG-TA
* *
3378 AAATAGTAATTTTTGGAAGGTTC
1 AAATGGTAATTTTTAGAAGGTTC
3401 AGGGACCTCC
Statistics
Matches: 335, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
58 94 0.28
59 137 0.41
60 73 0.22
61 31 0.09
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
Found at i:3154 original size:119 final size:118
Alignment explanation
Indices: 2965--3400 Score: 578
Period size: 119 Copynumber: 3.7 Consensus size: 118
2955 CATGGGGGGG
* * * * *
2965 AAATGGT-AGTTTTGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATAG
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAG
* * *
3029 TGATTTTTAGAAAGGTTCGGAGTCAAAAAATGAGATTTTTGGAAGTTCGTGGGTA
66 TAATTTTTAGAAAGGTTCGG-GTC-AAAAATGGGATTTTTGGAAGTTCGAGGGTA
* *
3084 AAAT-GTAATTTTTAGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGG
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAG
* **
3148 TAATTTTTA-AAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGCATA
66 TAATTTTTAGAAAGG-TTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* * * * *
3201 AAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAAATGGGTTTTTTGGAAGTTCGGGTGTAAAATG
1 AAATGGTAATTTTTAGAAGGTTCGGGGT-CAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATA
* *
3266 GTAATTTTTAG-AAGGTTTAGGGTCAAAAATGGGATTTTTGGAAGTT-AAGGGTA
65 GTAATTTTTAGAAAGG-TTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
* *
3319 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCAGGGATAAAATAG
1 AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAG
*
3384 TAATTTTT-GGAAGGTTC
66 TAATTTTTAGAAAGGTTC
3401 AGGGACCTCC
Statistics
Matches: 281, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
116 3 0.01
117 73 0.26
118 62 0.22
119 143 0.51
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (118 bp):
AAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATAG
TAATTTTTAGAAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTA
Found at i:4238 original size:21 final size:23
Alignment explanation
Indices: 4205--4246 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4195 TAAAAAAACG
*
4205 GATCTAGGTCTAGAT-CAAACCA
1 GATCTAGGCCTAGATCCAAACCA
4227 GATCTA-GCCTAGATCCAAAC
1 GATCTAGGCCTAGATCCAAAC
4247 GGTTTTCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (23 bp):
GATCTAGGCCTAGATCCAAACCA
Found at i:4550 original size:24 final size:23
Alignment explanation
Indices: 4517--4563 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4507 AAACCGCCCA
4517 CTTGTCATTAATGCC-ATTATTATT
1 CTTGTCATTAA--CCAATTATTATT
*
4541 CTTGTTATTAACCAATTATTATT
1 CTTGTCATTAACCAATTATTATT
4564 AATGATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 9 0.43
24 10 0.48
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (23 bp):
CTTGTCATTAACCAATTATTATT
Found at i:5175 original size:17 final size:17
Alignment explanation
Indices: 5153--5220 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
5143 TGGACTTTTC
* *
5153 TAAATTTAATTTTATAA
1 TAAACTTAAATTTATAA
*
5170 TAAATTTAAATTTCA-AA
1 TAAACTTAAATTT-ATAA
*
5187 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTATAA
5204 TAAACTTAAATTTATAA
1 TAAACTTAAATTTATAA
5221 GGTTGAAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
16 1 0.02
17 44 0.96
18 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAACTTAAATTTATAA
Done.