Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005040.1 Kokia drynarioides strain JFW-HI SEQ_118814, 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: 7390
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1337 original size:25 final size:23
Alignment explanation
Indices: 1309--1354 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1299 GTTTGATCCA
1309 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
1334 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
1355 CTCTATTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:2423 original size:16 final size:16
Alignment explanation
Indices: 2402--2440 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
2392 TTTCTCCTTC
2402 TTTTTTCCAATCTTTT
1 TTTTTTCCAATCTTTT
*
2418 TTTTTT-CAATTTTTT
1 TTTTTTCCAATCTTTT
2433 TTATTTTC
1 TT-TTTTC
2441 TTTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCCAATCTTTT
Found at i:2461 original size:15 final size:15
Alignment explanation
Indices: 2416--2462 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2406 TTCCAATCTT
2416 TTTTTTTTCAATTTTT-
1 TTTTTTTTC--TTTTTC
*
2432 TTTATTTTCTTTTTC
1 TTTTTTTTCTTTTTC
2447 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
2462 T
1 T
2463 AAATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 5 0.18
15 15 0.54
16 8 0.29
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:3407 original size:6 final size:6
Alignment explanation
Indices: 3400--3431 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3390 AATAAAATTA
3400 AAAAT- AAAATG AAAATG AAAATG AAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAA
3432 TATATAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:3420 original size:18 final size:17
Alignment explanation
Indices: 3387--3431 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3377 CGTGCATAAT
*
3387 TAAAAT-AAAATTAAAAA
1 TAAAATGAAAA-TGAAAA
3404 TAAAATGAAAATGAAAA
1 TAAAATGAAAATGAAAA
3421 TGAAAATGAAA
1 T-AAAATGAAA
3432 TATATAGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (17 bp):
TAAAATGAAAATGAAAA
Found at i:4369 original size:42 final size:42
Alignment explanation
Indices: 4316--4626 Score: 435
Period size: 42 Copynumber: 7.6 Consensus size: 42
4306 CTTAATTTAA
*
4316 GGGTAAAAGATTGGATGATGTCTTCAA-CTTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATC-TGCCCCATGATCG
*
4358 GGGTAAGAGATTGGATG--G-CTTCAATCTGCCTCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
4397 GGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATCA
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* *
4439 AGGTAAGAGATTGG-T-TTGTCTTCAATCTGCCCCATGATC-
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
* * * * *
4478 AGGTAAAAGATTGGATGATGTCTTCAATTTACCCCATAATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
4520 GGGTAAGAGATTGGATG--G-CTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
4559 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
*
4601 GGCTAAGAGATTGGATGATGTCTTCA
1 GGGTAAGAGATTGGATGATGTCTTCA
4627 CTGTTACGGC
Statistics
Matches: 241, Mismatches: 18, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
39 83 0.34
40 26 0.11
41 23 0.10
42 109 0.45
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (42 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCG
Found at i:4431 original size:81 final size:81
Alignment explanation
Indices: 4316--4617 Score: 455
Period size: 81 Copynumber: 3.7 Consensus size: 81
4306 CTTAATTTAA
4316 GGGTAAAAGATTGGATGATGTCTTCAA-CTTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTC
1 GGGTAAAAGATTGGATGATGTCTTCAATC-TGCCCCATGATCGGGGTAAGAGATTGGATGGCTTC
*
4380 AATCTGCCTCATGATCG
65 AATCTGCCCCATGATCG
* * ** * *
4397 GGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATCAAGGTAAGAGATTGGTTTGTCTTC
1 GGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGG-ATGGCTTC
4462 AATCTGCCCCATGATC-
65 AATCTGCCCCATGATCG
* * * *
4478 AGGTAAAAGATTGGATGATGTCTTCAATTTACCCCATAATCGGGGTAAGAGATTGGATGGCTTCA
1 GGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
4543 ATCTGCCCCATGATCG
66 ATCTGCCCCATGATCG
* *
4559 GGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGCTAAGAGATTGGATG
1 GGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATG
4618 ATGTCTTCAC
Statistics
Matches: 195, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
80 22 0.11
81 151 0.77
82 22 0.11
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (81 bp):
GGGTAAAAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCA
ATCTGCCCCATGATCG
Found at i:4586 original size:162 final size:162
Alignment explanation
Indices: 4317--4614 Score: 526
Period size: 162 Copynumber: 1.8 Consensus size: 162
4307 TTAATTTAAG
* *
4317 GGTAAAAGATTGGATGATGTCTTCAACTTGCCCCATGATCGGGGTAAGAGATTGGATGGCTTCAA
1 GGTAAAAGATTGGATGATGTCTTCAACTTACCCCATAATCGGGGTAAGAGATTGGATGGCTTCAA
*
4382 TCTGCCTCATGATCGGGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATCAAGG-TAAG
66 TCTGCCCCATGATCGGGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATC-AGGCTAAG
4446 AGATTGGTTTGTCTTCAATCTGCCCCATGATCA
130 AGATTGGTTTGTCTTCAATCTGCCCCATGATCA
*
4479 GGTAAAAGATTGGATGATGTCTTCAATTTACCCCATAATCGGGGTAAGAGATTGGATGGCTTCAA
1 GGTAAAAGATTGGATGATGTCTTCAACTTACCCCATAATCGGGGTAAGAGATTGGATGGCTTCAA
* *
4544 TCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATCGGGCTAAGA
66 TCTGCCCCATGATCGGGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATCAGGCTAAGA
4609 GATTGG
131 GATTGG
4615 ATGATGTCTT
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
161 2 0.02
162 127 0.98
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (162 bp):
GGTAAAAGATTGGATGATGTCTTCAACTTACCCCATAATCGGGGTAAGAGATTGGATGGCTTCAA
TCTGCCCCATGATCGGGGTAAGAGATTGGATGATGACTTCAATCTGCCCCATGATCAGGCTAAGA
GATTGGTTTGTCTTCAATCTGCCCCATGATCA
Found at i:6832 original size:52 final size:52
Alignment explanation
Indices: 6770--6875 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
6760 ACCATGCAAA
6770 GACCTTTACGAATTATCAAAGCAACTCTACGAAATCCCATTTTATTTTTGAG
1 GACCTTTACGAATTATCAAAGCAACTCTACGAAATCCCATTTTATTTTTGAG
6822 GACCTTTACGAATTATCAAAGCAACTCTACGAAATCCCATTTTATTTTTGAG
1 GACCTTTACGAATTATCAAAGCAACTCTACGAAATCCCATTTTATTTTTGAG
6874 GA
1 GA
6876 GATACATGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (52 bp):
GACCTTTACGAATTATCAAAGCAACTCTACGAAATCCCATTTTATTTTTGAG
Done.