Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008003.1 Kokia drynarioides strain JFW-HI SEQ_122655, 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: 68966
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 187 characters in sequence are not A, C, G, or T
Found at i:431 original size:27 final size:27
Alignment explanation
Indices: 371--435 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
361 GGTGCTTTTG
* *
371 GGGTAGGCGACACCAATGATGCCTTTC
1 GGGTAGGCGGCACCAATGATGCCTCTC
* *
398 GGATAGGCGGCACCAATGGTGCCTACT-
1 GGGTAGGCGGCACCAATGATGCCT-CTC
425 GGGTAGGCGGC
1 GGGTAGGCGGC
436 GCTAGTGCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.37, T:0.18
Consensus pattern (27 bp):
GGGTAGGCGGCACCAATGATGCCTCTC
Found at i:3809 original size:13 final size:13
Alignment explanation
Indices: 3753--3818 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
3743 TGAGGTTTAT
*
3753 GGTTTAAGGTTAAA
1 GGTTTAGGGTT-AA
*
3767 GGATTTAGGATTAA
1 GG-TTTAGGGTTAA
* *
3781 AGTTTAGAGTTTAA
1 GGTTTAG-GGTTAA
3795 GGTTTAGGGTTAA
1 GGTTTAGGGTTAA
*
3808 GGTTAAGGGTT
1 GGTTTAGGGTT
3819 TTGGGTTAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
13 20 0.47
14 16 0.37
15 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.38
Consensus pattern (13 bp):
GGTTTAGGGTTAA
Found at i:3836 original size:20 final size:20
Alignment explanation
Indices: 3791--3829 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3781 AGTTTAGAGT
3791 TTAA-GGTTTAGGGTTAAGG
1 TTAAGGGTTTAGGGTTAAGG
*
3810 TTAAGGGTTTTGGGTTAAGG
1 TTAAGGGTTTAGGGTTAAGG
3830 ATTAGGGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (20 bp):
TTAAGGGTTTAGGGTTAAGG
Found at i:4400 original size:27 final size:27
Alignment explanation
Indices: 4353--4425 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
4343 AATGATACTT
* *
4353 ATCACCTGACCACGATGGAACATATCC
1 ATCACCTGACCACCATAGAACATATCC
* * * *
4380 ATTACCTGACCACCCTAGAACGTATCT
1 ATCACCTGACCACCATAGAACATATCC
*
4407 ATCACCTGACCACCTTAGA
1 ATCACCTGACCACCATAGA
4426 TGATACGACT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (27 bp):
ATCACCTGACCACCATAGAACATATCC
Found at i:6937 original size:12 final size:11
Alignment explanation
Indices: 6920--6965 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
6910 TTTCTTTTTT
6920 TTATTATTAATA
1 TTATT-TTAATA
6932 TTATTATTAATA
1 TTATT-TTAATA
6944 TT-TTTTAA-A
1 TTATTTTAATA
6953 -TATTTTAATA
1 TTATTTTAATA
6963 TTA
1 TTA
6966 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.03
9 7 0.23
10 5 0.16
11 4 0.13
12 14 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:25593 original size:34 final size:31
Alignment explanation
Indices: 25535--25613 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 31
25525 ATTAAATTAA
25535 ATTTTTTTTTATTTTAAAACAAATACAAATATG
1 ATTTTTTTTTATTTTAAAACAAATA-AAAT-TG
* * **
25568 TTTTATTTTTTATTTTGAAGTAAATAAAATTG
1 ATTT-TTTTTTATTTTAAAACAAATAAAATTG
*
25600 ATTTTTTTTAATTT
1 ATTTTTTTTTATTT
25614 AGACTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 9 0.23
32 5 0.13
33 7 0.18
34 18 0.46
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTTTTTTTATTTTAAAACAAATAAAATTG
Found at i:33506 original size:23 final size:23
Alignment explanation
Indices: 33452--33508 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
33442 CATCCATCCT
*
33452 TACTGACTAGACATTCTAGAAGC
1 TACTGACTGGACATTCTAGAAGC
*
33475 TACTGACTGGACCTTCTAGAAGC
1 TACTGACTGGACATTCTAGAAGC
*
33498 TGCTGACTGGA
1 TACTGACTGGA
33509 TGCCACGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (23 bp):
TACTGACTGGACATTCTAGAAGC
Found at i:36231 original size:37 final size:37
Alignment explanation
Indices: 36188--36270 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
36178 TATTCAAATT
*
36188 ATTCGAGTCAACTCGAATAAGAAATTTCTGATTTCGG
1 ATTCGAGTCAACTCGAATAAGAAATTTCTGACTTCGG
36225 ATTCGAGTCAACTCGAATAAGAAATTTCTGACTTCGG
1 ATTCGAGTCAACTCGAATAAGAAATTTCTGACTTCGG
36262 ATTCGAGTC
1 ATTCGAGTC
36271 GGGTTGAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (37 bp):
ATTCGAGTCAACTCGAATAAGAAATTTCTGACTTCGG
Found at i:36428 original size:19 final size:19
Alignment explanation
Indices: 36406--36447 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
36396 AAAAAAATCA
36406 AAATAATTT-TTAAAATTTT
1 AAAT-ATTTATTAAAATTTT
36425 AAATATTTATTAAAATTTT
1 AAATATTTATTAAAATTTT
36444 AAAT
1 AAAT
36448 TTTGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATTTATTAAAATTTT
Found at i:63737 original size:24 final size:24
Alignment explanation
Indices: 63691--63736 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
63681 TTCTTTTTCT
* *
63691 TTTCTTTATTTTTTGGTATTTTTA
1 TTTCTTCATTTTTTGGGATTTTTA
63715 TTTCTTCA-TTTTTGGGATTTTT
1 TTTCTTCATTTTTTGGGATTTTT
63737 TTACATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.11, C:0.07, G:0.11, T:0.72
Consensus pattern (24 bp):
TTTCTTCATTTTTTGGGATTTTTA
Found at i:65335 original size:25 final size:25
Alignment explanation
Indices: 65294--65345 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
65284 CTTTTTTATC
*
65294 ATAATTTTTTATAAATAAATATATT
1 ATAATTTTTTATAAATAAATAAATT
*
65319 ATAATATTTTTAT-AATATATAAATT
1 ATAAT-TTTTTATAAATAAATAAATT
65344 AT
1 AT
65346 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTTTTTATAAATAAATAAATT
Found at i:68168 original size:18 final size:18
Alignment explanation
Indices: 68122--68170 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
68112 ATTTTAATTT
68122 TCAATTTCATTTTCTT-C
1 TCAATTTCATTTTCTTCC
68139 TC-A-TT-A-TTTCTTCC
1 TCAATTTCATTTTCTTCC
68153 TCAATTTCATTTTCTTCC
1 TCAATTTCATTTTCTTCC
68171 CCATTTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 3 0.11
16 3 0.11
17 3 0.11
18 8 0.30
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCATTTTCTTCC
Done.