Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005503.1 Kokia drynarioides strain JFW-HI SEQ_119567, 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: 294659
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 34 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:257908 original size:18 final size:18
Alignment explanation
Indices: 257874--257908 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
257864 ACCCCATTGT
*
257874 TAAAAATAATAGAGAATG
1 TAAAAATAAAAGAGAATG
*
257892 TAAAAATAAAAGTGAAT
1 TAAAAATAAAAGAGAAT
257909 AAATACTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATG
Found at i:272517 original size:16 final size:16
Alignment explanation
Indices: 272496--272535 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
272486 AAATATTAGC
*
272496 CCAATATAAACTCAAT
1 CCAATATAAACTAAAT
272512 CCAATATAAACTAAAT
1 CCAATATAAACTAAAT
272528 CCAATATA
1 CCAATATA
272536 TATAAACCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (16 bp):
CCAATATAAACTAAAT
Found at i:277218 original size:23 final size:23
Alignment explanation
Indices: 277186--277249 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
277176 CTCAATTATT
*
277186 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
277209 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
* *
277232 -GTTAAACGAACATGTTCG
1 TGTT-CATGAACATGTTCG
277250 TGAACATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:277259 original size:23 final size:23
Alignment explanation
Indices: 277216--277261 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
277206 TAATGTTCGT
* *
277216 GAACATGTTCGATTAAGTTAAAC
1 GAACATGTTCGATGAAATTAAAC
277239 GAACATGTTCG-TGAACATTAAAC
1 GAACATGTTCGATGAA-ATTAAAC
277262 AAACGAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (23 bp):
GAACATGTTCGATGAAATTAAAC
Found at i:280874 original size:22 final size:22
Alignment explanation
Indices: 280849--280894 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
280839 TATCATTTTA
*
280849 CATATCAAAGCAT-ATCATAAAT
1 CATAACAAAGC-TCATCATAAAT
*
280871 CATAACAAAGCTCATCATATAT
1 CATAACAAAGCTCATCATAAAT
280893 CA
1 CA
280895 AAACGTTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.48, C:0.22, G:0.04, T:0.26
Consensus pattern (22 bp):
CATAACAAAGCTCATCATAAAT
Found at i:280996 original size:5 final size:5
Alignment explanation
Indices: 280988--281031 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
280978 GTATTAGATT
* * * *
280988 ATATC ATATC ACATC ATACC ATATC ATATC ATGTC GTATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
281032 AATGTCCTAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (5 bp):
ATATC
Found at i:283458 original size:32 final size:32
Alignment explanation
Indices: 283414--283475 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
283404 AAGGTAAATT
283414 TATTTTTTATACTTATAATTTATTT-ATTTAA
1 TATTTTTTATACTTATAATTTATTTGATTTAA
* *
283445 TATTTTTTAATACTTATTATTTGTTTGATTT
1 TATTTTTT-ATACTTATAATTTATTTGATTT
283476 TTAATTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 8 0.30
32 15 0.56
33 4 0.15
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (32 bp):
TATTTTTTATACTTATAATTTATTTGATTTAA
Found at i:284390 original size:7 final size:7
Alignment explanation
Indices: 284374--284407 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
284364 TTTCTATTTT
284374 TTCTTCC
1 TTCTTCC
*
284381 TTCTTTC
1 TTCTTCC
284388 TTCTTCC
1 TTCTTCC
284395 TTCTT-C
1 TTCTTCC
284401 TTCTTCC
1 TTCTTCC
284408 CCCAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (7 bp):
TTCTTCC
Found at i:287537 original size:85 final size:86
Alignment explanation
Indices: 287412--287786 Score: 301
Period size: 81 Copynumber: 4.5 Consensus size: 86
287402 TGGTGTTGTA
* * * * * * *
287412 ACTTCAATCTACCCCTTTAGATTAGGGGTAAGAGATTGGATGATGACTTTAATTTTCCCTTCAGG
1 ACTTCAATCT-GCCCTCTGGATTA-GGGTAAAAGATTGGATGATGACTTCAATCTGCCCTTCAGG
287477 TTAGGCTAAAAGA-TGGATGGTTG
64 TTAGGCTAAAAGATTGGAT-GTTG
* * * * **
287500 -CTTCAATTTGTCCTCTGGATTAGGGTAAAAGATTGGATGGTGACTTCAATCTGCTCTTTGGGTT
1 ACTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATGATGACTTCAATCTGCCCTTCAGGTT
*
287564 AGGGTAAAAGATTGGATGTTG
66 AGGCTAAAAGATTGGATGTTG
* * * * *
287585 ACTTTAATCTGCCCTTTGGATTAGGGTAAAAGATTGGATG--G-CTTCGATCT--ACTCCATGGT
1 ACTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATGATGACTTCAATCTGCCCTTCA-GGT
* * * *
287645 TAGGTTAAGAGATTGAATGGTG
65 TAGGCTAAAAGATTGGATGTTG
* *
287667 TCTTCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGGATG--G-CTTCAATCTGCCC--CATGGT
1 ACTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATGATGACTTCAATCTGCCCTTCA-GGT
** * *
287726 CGGGGTAAAAGATTGGATGATG
65 TAGGCTAAAAGATTGGATGTTG
* ** * *
287748 TCTTCAATCCACCCTCTGG-TTAGGGTAGAAGATTAGATG
1 ACTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
287787 GCTTCAATCA
Statistics
Matches: 238, Mismatches: 44, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
81 87 0.37
82 36 0.15
83 9 0.04
84 1 0.00
85 48 0.20
86 49 0.21
87 8 0.03
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.33
Consensus pattern (86 bp):
ACTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATGATGACTTCAATCTGCCCTTCAGGTT
AGGCTAAAAGATTGGATGTTG
Found at i:287566 original size:43 final size:41
Alignment explanation
Indices: 287437--287800 Score: 296
Period size: 42 Copynumber: 8.8 Consensus size: 41
287427 TTTAGATTAG
* * * * * *
287437 GGGTAAGAGATTGGATGATGACTTTAATTTTCCCTTCAGGTTA
1 GGGTAAAAGATTGGATGGTG-CTTCAATCTGCCC-TCTGGTTA
* * *
287480 GGCTAAAAGA-TGGATGGTTGCTTCAATTTGTCCTCTGGATTA
1 GGGTAAAAGATTGGATGG-TGCTTCAATCTGCCCTCTGG-TTA
* *
287522 GGGTAAAAGATTGGATGGTGACTTCAATCTGCTCTTTGGGTTA
1 GGGTAAAAGATTGGATGGTG-CTTCAATCTGCCCTCT-GGTTA
* * *
287565 GGGTAAAAGATTGGATGTTGACTTTAATCTGCCCTTTGGATTA
1 GGGTAAAAGATTGGATGGTG-CTTCAATCTGCCCTCTGG-TTA
* * *
287608 GGGTAAAAGATTGGAT-G-GCTTCGATCTACTCC-ATGGTTA
1 GGGTAAAAGATTGGATGGTGCTTCAATCTGC-CCTCTGGTTA
* * * *
287647 GGTTAAGAGATTGAATGGTGTCTTCAATCTGCCCTCTAGTTA
1 GGGTAAAAGATTGGATGGTG-CTTCAATCTGCCCTCTGGTTA
**
287689 GGGTAAAAGATTGGAT-G-GCTTCAATCTGCCC-CATGGTCG
1 GGGTAAAAGATTGGATGGTGCTTCAATCTGCCCTC-TGGTTA
* **
287728 GGGTAAAAGATTGGATGATGTCTTCAATCCACCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTG-CTTCAATCTGCCCTCTGGTTA
* * *
287770 GGGTAGAAGATTAGAT-G-GCTTCAATCAGCCC
1 GGGTAAAAGATTGGATGGTGCTTCAATCTGCCC
287801 CATGGTCAAG
Statistics
Matches: 262, Mismatches: 43, Indels: 36
0.77 0.13 0.11
Matches are distributed among these distances:
38 1 0.00
39 59 0.23
40 14 0.05
41 12 0.05
42 88 0.34
43 86 0.33
44 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (41 bp):
GGGTAAAAGATTGGATGGTGCTTCAATCTGCCCTCTGGTTA
Found at i:287690 original size:42 final size:39
Alignment explanation
Indices: 287499--287800 Score: 169
Period size: 43 Copynumber: 7.4 Consensus size: 39
287489 ATGGATGGTT
* * * *
287499 GCTTCAATTTGTCCTCTGGATTAGGGTAAAAGATTGGATGG
1 GCTTCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGAAT-G
* * * *
287540 TGACTTCAATCTGCTCTTTGGGTTAGGGTAAAAGATTGGATG
1 -G-CTTCAATCTGCCCTCT-AGTTAGGGTAAAAGATTGAATG
* * * *
287582 TTGACTTTAATCTGCCCTTTGGATTAGGGTAAAAGATTGGATG
1 --G-CTTCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGAATG
* * * * * *
287625 GCTTCGATCTACTCC-ATGGTTAGGTTAAGAGATTGAATGG
1 GCTTCAATCTGC-CCTCTAGTTAGGGTAAAAGATTGAAT-G
*
287665 TGTCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGGATG
1 -G-CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAATG
* **
287706 GCTTCAATCTGCCC-CATGGTCGGGGTAAAAGATTGGATGATG
1 GCTTCAATCTGCCCTC-TAGTTAGGGTAAAAGATT-GA--ATG
* ** * *
287748 TCTTCAATCCACCCTCTGGTTAGGGTAGAAGATT-AGATG
1 GCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGA-ATG
*
287787 GCTTCAATCAGCCC
1 GCTTCAATCTGCCC
287801 CATGGTCAAG
Statistics
Matches: 213, Mismatches: 33, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.00
39 59 0.28
40 15 0.07
41 7 0.03
42 60 0.28
43 69 0.32
44 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
GCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAATG
Found at i:287710 original size:81 final size:82
Alignment explanation
Indices: 287475--287806 Score: 366
Period size: 81 Copynumber: 4.0 Consensus size: 82
287465 TTTCCCTTCA
* * *
287475 GGTTAGGCTAAAAGA-TGGATGGT-TGCTTCAATTTGTCCTCTGGATTAGGGTAAAAGATTGGAT
1 GGTTAGGGTAAAAGATTGGATGGTGT-CTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGAT
**
287538 GGTGACTTCAATCTGCTCTTT
65 -G-G-CTTCAATCTGCTCCAT
* * * *
287559 GGGTTAGGGTAAAAGATTGGATGTTGACTTTAATCTGCCCTTTGGATTAGGGTAAAAGATTGGAT
1 -GGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGAT
* *
287624 GGCTTCGATCTACTCCAT
65 GGCTTCAATCTGCTCCAT
* * * *
287642 GGTTAGGTTAAGAGATTGAATGGTGTCTTCAATCTGCCCTCTAG-TTAGGGTAAAAGATTGGATG
1 GGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
*
287706 GCTTCAATCTGCCCCAT
66 GCTTCAATCTGCTCCAT
** * ** * *
287723 GGTCGGGGTAAAAGATTGGATGATGTCTTCAATCCACCCTCTGG-TTAGGGTAGAAGATTAGATG
1 GGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
* *
287787 GCTTCAATCAGCCCCAT
66 GCTTCAATCTGCTCCAT
287804 GGT
1 GGT
287807 CAAGGGAGGA
Statistics
Matches: 211, Mismatches: 34, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
81 106 0.50
82 36 0.17
83 12 0.06
84 1 0.00
85 15 0.07
86 41 0.19
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (82 bp):
GGTTAGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCTCTGGATTAGGGTAAAAGATTGGATG
GCTTCAATCTGCTCCAT
Found at i:294605 original size:26 final size:25
Alignment explanation
Indices: 294576--294656 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 25
294566 TAATAAAAAA
* *
294576 AATAATAAATAATTTAATCATATTTT
1 AATAATAAATAATTAAAT-ATAATTT
*
294602 AAT-ATAATTATTATTAAATATAATTT
1 AATAATAA--ATAATTAAATATAATTT
*
294628 AATAA-AAATAA-AAATATATAATTT
1 AATAATAAATAATTAA-ATATAATTT
294652 AATAA
1 AATAA
294657 CAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
23 2 0.04
24 17 0.37
25 4 0.09
26 14 0.30
27 9 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AATAATAAATAATTAAATATAATTT
Done.