Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006760.1 Kokia drynarioides strain JFW-HI SEQ_121358, 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: 37820
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:2823 original size:34 final size:35
Alignment explanation
Indices: 2768--2849 Score: 112
Period size: 34 Copynumber: 2.3 Consensus size: 35
2758 TACAGGCTGT
* * *
2768 TGAAAAGACAAAAGCAGATAAAATATTT-AACTAA
1 TGAAAAGACAAAAACAAATAAAATATTTAAACCAA
*
2802 TGAAAAGATAAAAACAAATAAAATATTTACAACCAA
1 TGAAAAGACAAAAACAAATAAAATATTTA-AACCAA
2838 TGAAAAGACAAA
1 TGAAAAGACAAA
2850 CCAAGCAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 25 0.61
36 16 0.39
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (35 bp):
TGAAAAGACAAAAACAAATAAAATATTTAAACCAA
Found at i:2979 original size:7 final size:7
Alignment explanation
Indices: 2967--3000 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2957 TTAGCCTTCT
2967 CAAATCC
1 CAAATCC
2974 CAAATCC
1 CAAATCC
2981 CAAATCC
1 CAAATCC
2988 CAAATCC
1 CAAATCC
2995 CAAATC
1 CAAATC
3001 AATTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
CAAATCC
Found at i:3288 original size:40 final size:41
Alignment explanation
Indices: 3238--3317 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
3228 AGGTTATTGT
*
3238 ATTTTCAATTTATTTATTGTTTT-ATAATTGTTTTAATATC
1 ATTTTCAATTTATTTATTGTTTTAATAATTATTTTAATATC
* * * *
3278 ATTTTTAATTTGTTTGTTGTTTTAATATTTATTTTAATAT
1 ATTTTCAATTTATTTATTGTTTTAATAATTATTTTAATAT
3318 TTTTAAGTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 20 0.59
41 14 0.41
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (41 bp):
ATTTTCAATTTATTTATTGTTTTAATAATTATTTTAATATC
Found at i:3869 original size:9 final size:9
Alignment explanation
Indices: 3826--3870 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
3816 AAATTTCTCT
*
3826 TCAAAACTC
1 TCAAAATTC
3835 TCAAAATTC
1 TCAAAATTC
**
3844 TCTAAAGCTC
1 TC-AAAATTC
3854 TCAAAATTC
1 TCAAAATTC
3863 TCAAAATT
1 TCAAAATT
3871 TGTTTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 23 0.77
10 7 0.23
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.31
Consensus pattern (9 bp):
TCAAAATTC
Found at i:5477 original size:23 final size:23
Alignment explanation
Indices: 5380--5527 Score: 117
Period size: 23 Copynumber: 6.5 Consensus size: 23
5370 AGTGCTGGGG
5380 AAACAGTAAGCACAC-ACAGTGCA
1 AAACAGTAAGCACACGA-AGTGCA
** *
5403 ATCCAGTAGGCACAC-ACAGTGC-
1 AAACAGTAAGCACACGA-AGTGCA
* * * *
5425 AATCAGTAGGCGCAC-ATAGCGCA
1 AAACAGTAAGCACACGA-AGTGCA
* * *
5448 AATCAGTAGGCACACGAGGTGCA
1 AAACAGTAAGCACACGAAGTGCA
5471 AAACAGTAAGCACACGAAGTG-A
1 AAACAGTAAGCACACGAAGTGCA
* *
5493 GAAACAGTAAGCACACAAAGTGCG
1 -AAACAGTAAGCACACGAAGTGCA
5517 AAACAGTAAGC
1 AAACAGTAAGC
5528 GCGCTAGCGT
Statistics
Matches: 105, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
22 18 0.17
23 86 0.82
24 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGTAAGCACACGAAGTGCA
Found at i:6171 original size:32 final size:32
Alignment explanation
Indices: 6135--6200 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6125 TTATATACAA
6135 TTTTTGGTGAATTTTTGAAGTTAGTCCTCTGC
1 TTTTTGGTGAATTTTTGAAGTTAGTCCTCTGC
*
6167 TTTTTGGTTAATTTTTGAAGTTAGTCCTCTGC
1 TTTTTGGTGAATTTTTGAAGTTAGTCCTCTGC
6199 TT
1 TT
6201 CTGTCCAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (32 bp):
TTTTTGGTGAATTTTTGAAGTTAGTCCTCTGC
Found at i:8287 original size:21 final size:22
Alignment explanation
Indices: 8245--8305 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 22
8235 CCATAACTCT
*
8245 TAATTTAAAATACCCTACATCC
1 TAATTTAAAATACCCTAAATCC
*
8267 TTATTTAAAATA-CCTAAATCC
1 TAATTTAAAATACCCTAAATCC
8288 TAATTTAAAA-ACCCTAAA
1 TAATTTAAAATACCCTAAA
8306 CATAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.03
21 23 0.66
22 11 0.31
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATTTAAAATACCCTAAATCC
Found at i:10067 original size:21 final size:22
Alignment explanation
Indices: 10026--10075 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
10016 TTCATGATAT
*
10026 TTATTTTATTTATATTGTTAAA
1 TTATTTTATTTATAATGTTAAA
*
10048 TTATTTTGTTT-TAATGTTAAA
1 TTATTTTATTTATAATGTTAAA
10069 TT-TTTTA
1 TTATTTTA
10076 AAATATTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.16
21 11 0.44
22 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TTATTTTATTTATAATGTTAAA
Found at i:10104 original size:17 final size:17
Alignment explanation
Indices: 10049--10119 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
10039 ATTGTTAAAT
* *
10049 TATTTTGTTTTAATGTTA
1 TATTTT-TTATAATTTTA
* * * *
10067 AATTTTTTAAAATATTC
1 TATTTTTTATAATTTTA
10084 TATTTTTTATAATTTTA
1 TATTTTTTATAATTTTA
10101 TATTTATTT-TAATTCTTA
1 TATTT-TTTATAATT-TTA
10119 T
1 T
10120 TATATGCGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTTTTTATAATTTTA
Found at i:12532 original size:30 final size:31
Alignment explanation
Indices: 12471--12538 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
12461 GTAAGTAGAA
*
12471 GATTATTTTGTCACTTTTCGATAACTTTAGT
1 GATTGTTTTGTCACTTTTCGATAACTTTAGT
*
12502 GATTGTTTTGTCACATTTTC-A-AAGTTTAGT
1 GATTGTTTTGTCAC-TTTTCGATAACTTTAGT
*
12532 GACTGTT
1 GATTGTT
12539 GTGTTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.42
31 14 0.42
32 5 0.15
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (31 bp):
GATTGTTTTGTCACTTTTCGATAACTTTAGT
Found at i:35856 original size:32 final size:33
Alignment explanation
Indices: 35820--35901 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 33
35810 CCATTTCATT
35820 ATTTAAAAATAATAAAATTTATTTT-TATTAAA
1 ATTTAAAAATAATAAAATTTATTTTATATTAAA
** * * **
35852 ATTTAATCATAA-AATTATTTATTTTATTTTATT
1 ATTTAAAAATAATAA-AATTTATTTTATATTAAA
*
35885 ATTTATAAATAATAAAA
1 ATTTAAAAATAATAAAA
35902 CTGCCTTAGA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
31 2 0.05
32 19 0.51
33 14 0.38
34 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
ATTTAAAAATAATAAAATTTATTTTATATTAAA
Found at i:37759 original size:27 final size:27
Alignment explanation
Indices: 37723--37777 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
37713 TATCTAACAC
*
37723 CCAATGGAGGAA-CTCGAAGTGGCGGCA
1 CCAATGGAGGAATATC-AAGTGGCGGCA
37750 CCAATGGAGGAATATCAAGTGGCGGCA
1 CCAATGGAGGAATATCAAGTGGCGGCA
37777 C
1 C
37778 TAAGGGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.31, C:0.22, G:0.35, T:0.13
Consensus pattern (27 bp):
CCAATGGAGGAATATCAAGTGGCGGCA
Done.