Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011060.1 Kokia drynarioides strain JFW-HI SEQ_126031, 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: 41781
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:273 original size:18 final size:17
Alignment explanation
Indices: 224--291 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
214 ATCACCTTTT
* *
224 TTTTCTCTCATTCTTCC
1 TTTTCTTTCTTTCTTCC
* *
241 CTTTCTTCTCCTTCTTCC
1 TTTTCTT-TCTTTCTTCC
*
259 TTCTTCTTTCTTTCTTTC
1 TT-TTCTTTCTTTCTTCC
277 TTTCTCTTT-TTTCTT
1 TTT-TCTTTCTTTCTT
292 TTTTTTTTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 12 0.29
18 25 0.60
19 5 0.12
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTCTTTCTTTCTTCC
Found at i:309 original size:21 final size:21
Alignment explanation
Indices: 242--309 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
232 CATTCTTCCC
*
242 TTTCTTCTCCTTC-TTCCTTCTT
1 TTTCTT-TCTTTCTTTCCTTC-T
264 CTTTCTTTCTTTCTTTCTCTT-T
1 -TTTCTTTCTTTCTTTC-CTTCT
*
286 TTTCTTT-TTTTTTTCCTTCAT
1 TTTCTTTCTTTCTTTCCTTC-T
307 TTT
1 TTT
310 TCGTTGGTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 3 0.08
20 7 0.18
21 11 0.28
22 6 0.15
23 9 0.23
24 3 0.08
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCTTTCTTTCTTTCCTTCT
Found at i:7013 original size:17 final size:17
Alignment explanation
Indices: 6986--7031 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
6976 TTCTCCTTCC
6986 TTTCATTTTTTT-TCGAAT
1 TTTC-TTTTTTTAT-GAAT
*
7004 TTTGTTTTTTTATGAAT
1 TTTCTTTTTTTATGAAT
7021 TTTCTTTTTTT
1 TTTCTTTTTTT
7032 GGGCCATAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTTTATGAAT
Found at i:10075 original size:39 final size:39
Alignment explanation
Indices: 10032--10154 Score: 92
Period size: 39 Copynumber: 3.1 Consensus size: 39
10022 CTGTATTATA
10032 AAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
1 AAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
* *** ** * * *
10071 AAACCGGAAT-TTGGTTGGTCAAATCTGT-TCCTGTATTATA--
1 AAACC-AAATAAAAG-TAAT-AACT-TGTATCCAG-CTTATAGG
10111 AAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
1 AAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
10150 AAACC
1 AAACC
10155 GGAATTTGGT
Statistics
Matches: 57, Mismatches: 18, Indels: 18
0.61 0.19 0.19
Matches are distributed among these distances:
37 8 0.14
38 7 0.12
39 16 0.28
40 11 0.19
41 7 0.12
42 8 0.14
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (39 bp):
AAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
Found at i:10137 original size:79 final size:79
Alignment explanation
Indices: 10006--10245 Score: 453
Period size: 79 Copynumber: 3.0 Consensus size: 79
9996 ATTTGCAGTA
10006 TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
1 TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
10071 AAACCGGAATTTGG
66 AAACCGGAATTTGG
10085 TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
1 TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
10150 AAACCGGAATTTGG
66 AAACCGGAATTTGG
* *
10164 TTGGTAAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCATATAGG
1 TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
*
10229 AGACCGGAATTTGG
66 AAACCGGAATTTGG
10243 TTG
1 TTG
10246 TCCCTGCCTT
Statistics
Matches: 158, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 158 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (79 bp):
TTGGTCAAATCTGTTCCTGTATTATAAAACCAAATAAAAGTAATAACTTGTATCCAGCTTATAGG
AAACCGGAATTTGG
Found at i:10424 original size:79 final size:79
Alignment explanation
Indices: 10293--10451 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
10283 CCTAAAACAA
*
10293 TTTGTATTTCTAGTTAAGGATAACAAATAGACAGTCCAAAATGCGTATGTTAACTTAGGATTCTG
1 TTTGTATTTCTAGTTAAGGATAACAAATAGACAGTCCAAAATGCGTATGTTAACTTAGGATTCGG
10358 TATTTCACTTGATT
66 TATTTCACTTGATT
10372 TTTGTATTTCTAGTTAAGGATAACAAATAGACAGTCCAAAATGCGTATGTTAACTTAGGATTCGG
1 TTTGTATTTCTAGTTAAGGATAACAAATAGACAGTCCAAAATGCGTATGTTAACTTAGGATTCGG
10437 TATTTCACTTGATT
66 TATTTCACTTGATT
10451 T
1 T
10452 AATAACTAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (79 bp):
TTTGTATTTCTAGTTAAGGATAACAAATAGACAGTCCAAAATGCGTATGTTAACTTAGGATTCGG
TATTTCACTTGATT
Found at i:14098 original size:28 final size:28
Alignment explanation
Indices: 14058--14118 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
14048 ATTGATCGTC
* * *
14058 TCTTATTTTCTTTCCTTTCATTTTTTTT
1 TCTTATTTGCTTTCCTTTCACTTTTCTT
14086 TCTTATTTGCTTTCCTTTCACTTTTCTT
1 TCTTATTTGCTTTCCTTTCACTTTTCTT
14114 TCTTA
1 TCTTA
14119 CCAAACACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (28 bp):
TCTTATTTGCTTTCCTTTCACTTTTCTT
Found at i:21613 original size:21 final size:20
Alignment explanation
Indices: 21589--21637 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
21579 TGTTGTGTTG
*
21589 TCATTGTTTACTTGAATTTTT
1 TCATTGTTTACTTCAA-TTTT
* *
21610 TCATTTATTTATTTCAATTTT
1 TCA-TTGTTTACTTCAATTTT
21631 TCATTGT
1 TCATTGT
21638 ATAGTCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.63
Consensus pattern (20 bp):
TCATTGTTTACTTCAATTTT
Found at i:21620 original size:22 final size:21
Alignment explanation
Indices: 21595--21635 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21585 GTTGTCATTG
*
21595 TTTACTTGAATTTTTTCATTTA
1 TTTACTTCAA-TTTTTCATTTA
*
21617 TTTATTTCAATTTTTCATT
1 TTTACTTCAATTTTTCATT
21636 GTATAGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTACTTCAATTTTTCATTTA
Found at i:22083 original size:36 final size:40
Alignment explanation
Indices: 22043--22121 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
22033 TAAAATATAG
22043 ATGTAT-GTTTGAAAATAA-T-A-TATAATAA-ATAATGAA
1 ATGTATGGTTTGAAAATAATTAATTATAATAACAT-ATGAA
*
22079 ATGTATGGTTTGAAACTAATTAATTATAATAACATATGAA
1 ATGTATGGTTTGAAAATAATTAATTATAATAACATATGAA
22119 ATG
1 ATG
22122 CATGCAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 6 0.16
37 11 0.30
38 1 0.03
39 1 0.03
40 16 0.43
41 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.37
Consensus pattern (40 bp):
ATGTATGGTTTGAAAATAATTAATTATAATAACATATGAA
Found at i:27346 original size:21 final size:21
Alignment explanation
Indices: 27322--27370 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
27312 TATTGTGTTG
*
27322 TCATTGTTTACTTGAATTTTT
1 TCATTGTTTACTTCAATTTTT
* *
27343 TCATTTATTTATTTCAATTTTT
1 TCA-TTGTTTACTTCAATTTTT
27365 T-ATTGT
1 TCATTGT
27371 ATAATCATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.13
21 4 0.17
22 16 0.70
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.65
Consensus pattern (21 bp):
TCATTGTTTACTTCAATTTTT
Found at i:41014 original size:17 final size:17
Alignment explanation
Indices: 40974--41023 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
40964 TCTGGGCCTA
* *
40974 TTGAAAATTGAATTTAT
1 TTGAAATTTAAATTTAT
40991 TTGAAATTTAAATTTAT
1 TTGAAATTTAAATTTAT
*
41008 TAT-AAATTTAATTTTA
1 T-TGAAATTTAAATTTA
41024 AAATGTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 28 0.97
18 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TTGAAATTTAAATTTAT
Found at i:41594 original size:3 final size:3
Alignment explanation
Indices: 41578--41635 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
41568 AAACGTTTAT
* * **
41578 TAA TAA TCAT TAA TAA TAA TAA TAA CT-G TTT TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
41624 TAA TAA TAA TAA
1 TAA TAA TAA TAA
41636 CATTAATGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
2 1 0.02
3 42 0.91
4 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:41698 original size:25 final size:25
Alignment explanation
Indices: 41663--41715 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
41653 ACAAACGAAC
*
41663 AATTTTCTT-AATAATTATTAATAAT
1 AATTTTCTTAAATAA-TAATAATAAT
*
41688 AATTTTTTTAAATAATAATAATAAT
1 AATTTTCTTAAATAATAATAATAAT
41713 AAT
1 AAT
41716 AATGAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTTTCTTAAATAATAATAATAAT
Done.