Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012734.1 Kokia drynarioides strain JFW-HI SEQ_127745, 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: 18335
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:12000 original size:29 final size:29
Alignment explanation
Indices: 11944--12181 Score: 239
Period size: 29 Copynumber: 8.1 Consensus size: 29
11934 TTTGAGGTCG
* * *
11944 AAAATGGAGTTTTTGGACA-TCCGAGGGTA
1 AAAATGGAATTTTTGGA-AGTTCGGGGGTA
*
11973 AAAATGGAATTTTTGGGAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
** *
12002 AAAATGGAATTTTTAGG-AGTTTTGAGGTAA
1 AAAATGGAATTTTT-GGAAGTTCGGGGGT-A
* * *
12032 AAAATGGGATTTTTTGAAGTTCGGAGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
* *
12061 AAAATGGAATTTTTGGAAGTTTTGGGGATA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
*
12091 AAAATGGAATTTTTTGAAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
* * * *
12119 AAAATAGAATTTTTAGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGTA
* *
12149 AAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
12178 AAAA
1 AAAA
12182 CAAAATTTTT
Statistics
Matches: 173, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
28 18 0.10
29 89 0.51
30 66 0.38
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTA
Found at i:12037 original size:30 final size:29
Alignment explanation
Indices: 11924--12181 Score: 175
Period size: 30 Copynumber: 8.8 Consensus size: 29
11914 AAAAGAGTAA
* * * *
11924 TTTTAAGAGTTTTGAGGTCGAAAATGGAGT
1 TTTTAGGAGTTCTGAGGT-AAAAATGGAAT
** *
11954 TTTT-GGACATCCGAGGGTAAAAATGGAAT
1 TTTTAGGAGTTCTGA-GGTAAAAATGGAAT
* * *
11983 TTTTGGGAGTTCGGGGGTAAAAATGGAAT
1 TTTTAGGAGTTCTGAGGTAAAAATGGAAT
* *
12012 TTTTAGGAGTTTTGAGGTAAAAAATGGGAT
1 TTTTAGGAGTTCTGAGGT-AAAAATGGAAT
* * *
12042 TTTTTGAAGTTCGGAGGTAAAAATGGAAT
1 TTTTAGGAGTTCTGAGGTAAAAATGGAAT
* *
12071 TTTT-GGAAGTTTTGGGGATAAAAATGGAAT
1 TTTTAGG-AGTTCTGAGG-TAAAAATGGAAT
* * * * *
12101 TTTTTGAAGTTCGGGGGT-AAAATAGAAT
1 TTTTAGGAGTTCTGAGGTAAAAATGGAAT
* * * *
12129 TTTTAGAAGTTTTGGGGTTAAAAATGGGAT
1 TTTTAGGAGTTCTGAGG-TAAAAATGGAAT
12159 TTTT-GGAAGTTC-GAGGGTAAAAA
1 TTTTAGG-AGTTCTGA-GGTAAAAA
12182 CAAAATTTTT
Statistics
Matches: 181, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
28 24 0.13
29 77 0.43
30 79 0.44
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
TTTTAGGAGTTCTGAGGTAAAAATGGAAT
Found at i:12045 original size:59 final size:58
Alignment explanation
Indices: 11968--12181 Score: 272
Period size: 59 Copynumber: 3.7 Consensus size: 58
11958 GGACATCCGA
*
11968 GGGT-AAAAATGGAATTTTTGGGAGTTCGGGGGTAAAAATGGAATTTTTAGGAGTTTT
1 GGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAGGAGTTTT
* * *
12025 GAGGTAAAAAATGGGATTTTTTGAAGTTCGGAGGTAAAAATGGAATTTTT-GGAAGTTTT
1 G-GGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAGG-AGTTTT
* * * *
12084 GGGGATAAAAATGGAATTTTTTGAAGTTCGGGGGT-AAAATAGAATTTTTAGAAGTTTT
1 GGGTA-AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAGGAGTTTT
* * *
12142 GGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAA
1 -GGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAA
12182 CAAAATTTTT
Statistics
Matches: 136, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
57 1 0.01
58 53 0.39
59 82 0.60
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (58 bp):
GGGTAAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTAGGAGTTTT
Found at i:13303 original size:3 final size:3
Alignment explanation
Indices: 13286--13409 Score: 52
Period size: 3 Copynumber: 39.0 Consensus size: 3
13276 TTTCCCTTTT
* * * * * *
13286 TTA TTCA TT- TTA TTA TTA ATA TTT TTA TTA ATA TTTA TTA ATG CTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * *
13332 TTTA TTA CTA CTA TTTA TTA TTA ATA ATA TTA TTA TTTA TTAA ATA GTTA
1 -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA -TTA
* *
13382 TTA TTA TTA TTAA CTA TTA TTA CTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA
13410 ATGTTACTTA
Statistics
Matches: 91, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
2 2 0.02
3 71 0.78
4 18 0.20
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:13366 original size:15 final size:17
Alignment explanation
Indices: 13346--13387 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
13336 TTACTACTAT
13346 TTATTATTAAT-AATA-
1 TTATTATTAATAAATAG
*
13361 TTATTATTTATTAAATAG
1 TTATTA-TTAATAAATAG
13379 TTATTATTA
1 TTATTATTA
13388 TTATTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 6 0.26
16 4 0.17
17 7 0.30
18 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTATTATTAATAAATAG
Found at i:13401 original size:13 final size:12
Alignment explanation
Indices: 13295--13403 Score: 65
Period size: 13 Copynumber: 8.5 Consensus size: 12
13285 TTTATTCATT
13295 TTATTATTAATA
1 TTATTATTAATA
*
13307 TTTTTATTAATA
1 TTATTATTAATA
* **
13319 TTTATTAATGCTA
1 -TTATTATTAATA
* *
13332 TTTATTACTACTA
1 -TTATTATTAATA
13345 TTTATTATTAATA
1 -TTATTATTAATA
* *
13358 ATATTATTATTTA
1 TTATTATTA-ATA
* *
13371 TTAAATAGTTATTA
1 TT-ATTA-TTAATA
13385 TTATTATTAACTA
1 TTATTATTAA-TA
13398 TTATTA
1 TTATTA
13404 CTATTAATGT
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
12 22 0.29
13 44 0.57
14 8 0.10
15 3 0.04
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:13401 original size:16 final size:16
Alignment explanation
Indices: 13380--13410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13370 ATTAAATAGT
*
13380 TATTATTATTATTAAC
1 TATTATTACTATTAAC
13396 TATTATTACTATTAA
1 TATTATTACTATTAA
13411 TGTTACTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTACTATTAAC
Found at i:14173 original size:17 final size:17
Alignment explanation
Indices: 14148--14237 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
14138 GACTTTTTAA
* **
14148 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
14165 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
14182 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
14199 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
14218 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
14236 TT
1 TT
14238 GAATCAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.08
17 27 0.44
18 10 0.16
19 18 0.30
20 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:14177 original size:6 final size:6
Alignment explanation
Indices: 14163--14228 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
14153 TTTTAAATCC
* **
14163 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
**
14210 AGATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
14229 AATAAATTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:16725 original size:17 final size:19
Alignment explanation
Indices: 16691--16727 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
16681 TATTACACAC
16691 CTAACTACAATAAACTTAA
1 CTAACTACAATAAACTTAA
16710 CTAACTA-AAT-AACTTAA
1 CTAACTACAATAAACTTAA
16727 C
1 C
16728 ATAAAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (19 bp):
CTAACTACAATAAACTTAA
Found at i:17077 original size:69 final size:69
Alignment explanation
Indices: 16964--17108 Score: 218
Period size: 69 Copynumber: 2.1 Consensus size: 69
16954 GAATCAACAT
* * *
16964 TCCAATCCTTGAATAAAGAGTAATGTCAAACTGCTAATTATCATCCCAGTATGTGGGATCCCACC
1 TCCAATCCTTGAATAAAGAGCAACGTCAAACTGCTAACTATCATCCCAGTATGTGGGATCCCACC
17029 ACAA
66 ACAA
* * * *
17033 TTCAATCCTTGAATGAAGAGCAACGTCGAACTGCTAACTATCATCCCAGTATTTGGGATCCCACC
1 TCCAATCCTTGAATAAAGAGCAACGTCAAACTGCTAACTATCATCCCAGTATGTGGGATCCCACC
*
17098 ACCA
66 ACAA
17102 TCCAATC
1 TCCAATC
17109 TTTTACCACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (69 bp):
TCCAATCCTTGAATAAAGAGCAACGTCAAACTGCTAACTATCATCCCAGTATGTGGGATCCCACC
ACAA
Done.