Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006477.1 Kokia drynarioides strain JFW-HI SEQ_121060, 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: 17676
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:44 original size:29 final size:30
Alignment explanation
Indices: 3--223 Score: 166
Period size: 30 Copynumber: 7.4 Consensus size: 30
1 CG
* * * *
3 AAAATTCCATTTTT-ACCTTCAAACTTCTA
1 AAAATCCCATTTTTGACCCTAAAACTTCCA
32 AAAATCCCATTTTTGACCCTAAAACTTCCA
1 AAAATCCCATTTTTGACCCTAAAACTTCCA
* * *
62 AAAATCCTATTTTTGACCGTAAAACTTCAA
1 AAAATCCCATTTTTGACCCTAAAACTTCCA
* ***
92 AAAATTCCATTTTT-ACCCCCGAACTTCCA
1 AAAATCCCATTTTTGACCCTAAAACTTCCA
* **
121 AAATTCCCATTTTTTGACCCCGAAACTTCC-
1 AAAATCCCA-TTTTTGACCCTAAAACTTCCA
* **
151 AAAATTCCATTTTT-ACCCTCGAA-TCTCCA
1 AAAATCCCATTTTTGACCCTAAAACT-TCCA
* * * *
180 AAATTTCCATTTTTGACACC-GAAACTTTCA
1 AAAATCCCATTTTTGAC-CCTAAAACTTCCA
*
210 AAAATTACCATTTT
1 AAAA-TCCCATTTT
224 GCCTCCTGGG
Statistics
Matches: 154, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.01
28 9 0.06
29 48 0.31
30 73 0.47
31 23 0.15
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATCCCATTTTTGACCCTAAAACTTCCA
Found at i:117 original size:59 final size:57
Alignment explanation
Indices: 3--223 Score: 214
Period size: 59 Copynumber: 3.7 Consensus size: 57
1 CG
* * **
3 AAAATTCCATTTTT-ACCTTC-AAACTTCTAAAAATCCCATTTTTGACCCTAAAACTTCC
1 AAAATTCCATTTTTGACC-CCAAAACTTC-AAAAATTCCATTTTT-ACCCTCGAACTTCC
* ** *
61 AAAAATCCTATTTTTGACCGTAAAACTTCAAAAAATTCCATTTTTACCCCCGAACTTCC
1 AAAATTCC-ATTTTTGACCCCAAAACTTC-AAAAATTCCATTTTTACCCTCGAACTTCC
* *
120 AAAATTCCCATTTTTTGACCCCGAAACTTCCAAAATTCCATTTTTACCCTCGAA-TCTCC
1 AAAATT-CCA-TTTTTGACCCCAAAACTTCAAAAATTCCATTTTTACCCTCGAACT-TCC
* *
179 AAAATTTCCATTTTTGACACCGAAACTTTCAAAAATTACCATTTT
1 AAAA-TTCCATTTTTGACCCCAAAAC-TTCAAAAATT-CCATTTT
224 GCCTCCTGGG
Statistics
Matches: 138, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
58 23 0.17
59 64 0.46
60 51 0.37
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
AAAATTCCATTTTTGACCCCAAAACTTCAAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:133 original size:28 final size:28
Alignment explanation
Indices: 3--193 Score: 134
Period size: 29 Copynumber: 6.5 Consensus size: 28
1 CG
** * *
3 AAAATTCCATTTTTACCTTCAAACTTCTA
1 AAAATTCCATTTTTACCCCCGAACTTC-C
* ***
32 AAAATCCCATTTTTGACCCTAAAACTTCC
1 AAAATTCCATTTTT-ACCCCCGAACTTCC
* **** *
61 AAAAATCCTATTTTTGACCGTAAAACTTCAA
1 AAAATTCC-ATTTTT-ACCCCCGAACTTC-C
92 AAAATTCCATTTTTACCCCCGAACTTCC
1 AAAATTCCATTTTTACCCCCGAACTTCC
120 AAAATTCCCATTTTTTGA-CCCCGAAACTTCC
1 AAAATT-CCA-TTTTT-ACCCCCG-AACTTCC
*
151 AAAATTCCATTTTTACCCTCGAA-TCTCC
1 AAAATTCCATTTTTACCCCCGAACT-TCC
179 AAAATTTCCATTTTT
1 AAAA-TTCCATTTTT
194 GACACCGAAA
Statistics
Matches: 137, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
27 1 0.01
28 16 0.12
29 50 0.36
30 49 0.36
31 21 0.15
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCCGAACTTCC
Found at i:2330 original size:31 final size:31
Alignment explanation
Indices: 2273--2331 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2263 ATAGTTATTG
*
2273 AACTATTCAAAAATTTTCATTGAAGTCACTA
1 AACTATTCAAAAATTTCCATTGAAGTCACTA
2304 AACTATT-AGAAAATTTCCACTT-AAGTCA
1 AACTATTCA-AAAATTTCCA-TTGAAGTCA
2332 TTGGACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 1 0.04
31 22 0.88
32 2 0.08
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (31 bp):
AACTATTCAAAAATTTCCATTGAAGTCACTA
Found at i:2754 original size:31 final size:29
Alignment explanation
Indices: 2683--2754 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
2673 GTGATTATTT
*
2683 TGTAATTTTTTAAAATTTAATAATTAAAA
1 TGTAATTTATTAAAATTTAATAATTAAAA
* *
2712 TGTAAACTTATTAATAATTTAATGAACTT-AGA
1 TGT-AATTTATTAA-AATTTAAT-AA-TTAAAA
2744 TGTAATTTATT
1 TGTAATTTATT
2755 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 3 0.09
30 8 0.23
31 15 0.43
32 7 0.20
33 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (29 bp):
TGTAATTTATTAAAATTTAATAATTAAAA
Found at i:15163 original size:16 final size:15
Alignment explanation
Indices: 15138--15173 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
15128 ATATATATAA
*
15138 TTTTTCTTTTCCTTT
1 TTTTTCTTTTCATTT
15153 TTTTTCATTTTCATTT
1 TTTTTC-TTTTCATTT
15169 TTTTT
1 TTTTT
15174 AGTGTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTCATTT
Done.