Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014599.1 Kokia drynarioides strain JFW-HI SEQ_129638, 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: 35715
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:6534 original size:18 final size:18
Alignment explanation
Indices: 6511--6547 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6501 ATTTCTTTTC
6511 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
*
6529 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
6547 T
1 T
6548 AGATTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:6540 original size:23 final size:23
Alignment explanation
Indices: 6506--6549 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
6496 AAGACATTTC
6506 TTTTCTTTCTATTA-TATTAGTA
1 TTTTCTTTCTATTAGTATTAGTA
6528 TTTTCTATTCTATTAGTATTAG
1 TTTTCT-TTCTATTAGTATTAG
6550 ATTAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 8 0.40
24 6 0.30
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTTCTTTCTATTAGTATTAGTA
Found at i:10429 original size:19 final size:18
Alignment explanation
Indices: 10394--10430 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
10384 ATTAAACCTT
10394 TAATTAATCAAAATTAAC
1 TAATTAATCAAAATTAAC
*
10412 TAATTAATACATAATTAAC
1 TAATTAAT-CAAAATTAAC
10431 ATTATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTAATCAAAATTAAC
Found at i:12003 original size:21 final size:21
Alignment explanation
Indices: 11979--12018 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11969 AGTGATATCT
11979 AATTCATTTTGATC-TAATTAA
1 AATTCA-TTTGATCTTAATTAA
*
12000 AATTTATTTGATCTTAATT
1 AATTCATTTGATCTTAATT
12019 TCACAAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTCATTTGATCTTAATTAA
Found at i:13046 original size:19 final size:18
Alignment explanation
Indices: 13011--13047 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
13001 ATTAAACCTT
13011 TAATTAATCAAAATTAAC
1 TAATTAATCAAAATTAAC
*
13029 TAATTAATACATAATTAAC
1 TAATTAAT-CAAAATTAAC
13048 ACTATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTAATCAAAATTAAC
Found at i:13705 original size:45 final size:45
Alignment explanation
Indices: 13637--13736 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
13627 TTCCGATTTT
* *
13637 GGAGATGCTGCCTCCCCTGAACTCAAAAGTACCCATTCGGCTTCC
1 GGAGATGGTGCCTCCACTGAACTCAAAAGTACCCATTCGGCTTCC
* * ** *
13682 GGAGATGGTGCCTCCAGTTAACTCAAAAGTACCTTTTCGGCTTTC
1 GGAGATGGTGCCTCCACTGAACTCAAAAGTACCCATTCGGCTTCC
*
13727 GAAGATGGTG
1 GGAGATGGTG
13737 AGTCATCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (45 bp):
GGAGATGGTGCCTCCACTGAACTCAAAAGTACCCATTCGGCTTCC
Found at i:18995 original size:16 final size:17
Alignment explanation
Indices: 18965--19007 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
18955 AAATTAAAAT
18965 AAAC-ATAAAACCATAA
1 AAACAATAAAACCATAA
18981 AAACAATAAAA-CATAA
1 AAACAATAAAACCATAA
*
18997 ACACACATAAA
1 AAACA-ATAAA
19008 GTTTATGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.70, C:0.19, G:0.00, T:0.12
Consensus pattern (17 bp):
AAACAATAAAACCATAA
Found at i:23979 original size:196 final size:196
Alignment explanation
Indices: 23638--24077 Score: 673
Period size: 196 Copynumber: 2.2 Consensus size: 196
23628 AATTGAAGCA
* *
23638 ATGGCTGAGGTACCGCATATGTTGCGAGACCTTGACAACTCGTGTGAGTAGCATCGTGAGTCAAG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGTAGCATCGTGAGTCAAG
* *
23703 AAAATGAGAAATGAATCCAAGAATGGATTATAGGCCCTACAATGTCTGAGATTTATGCATAAGTG
66 AAAATGAGAAATGAATCCAAGAATGAATTATAGGCCCTACAATGGCTGAGATTTATGCATAAGTG
* * * *
23768 CATATTCTTGACAGCTTGTGCAAGCAGCATCATTAGGGAATAGTTATATGCACAGATACCGTATC
131 CATATTCTCGACAGCTCGTGCAAGCAACATCATTAGGGAACAGTTATATGCACAGATACCGTATC
23833 G
196 G
* * * **
23834 ATGGCTGAGGTACCGCATATGTTACGATTCCTCGACAGCTCGTGTGAGTAGCATCGTGAGTGGAG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGTAGCATCGTGAGTCAAG
* *
23899 GAAATGAGAAATGAATCCAAGAATGAATTATAGGCCCTACGATGGCTGAGATTTATGCATAAGTG
66 AAAATGAGAAATGAATCCAAGAATGAATTATAGGCCCTACAATGGCTGAGATTTATGCATAAGTG
** * *
23964 CATATTCTCGACAGCTCGTGTGAGCAACATCATTAGGGAACAGTTATATGCATAGATATCGTATC
131 CATATTCTCGACAGCTCGTGCAAGCAACATCATTAGGGAACAGTTATATGCACAGATACCGTATC
24029 G
196 G
* * * *
24030 ATGGTTGGGGTACCGCATATGTTGCAAGTCCTTGATAGCTCGTGTGAG
1 ATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAG
24078 CAGTATCATG
Statistics
Matches: 218, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
196 218 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (196 bp):
ATGGCTGAGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTGTGAGTAGCATCGTGAGTCAAG
AAAATGAGAAATGAATCCAAGAATGAATTATAGGCCCTACAATGGCTGAGATTTATGCATAAGTG
CATATTCTCGACAGCTCGTGCAAGCAACATCATTAGGGAACAGTTATATGCACAGATACCGTATC
G
Found at i:26423 original size:160 final size:160
Alignment explanation
Indices: 26069--26681 Score: 852
Period size: 160 Copynumber: 3.9 Consensus size: 160
26059 ACTAGCTATA
* *
26069 AAAAAAGGG-TCTGCTCACACGAGTTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACA
1 AAAAAAGGGCT-TGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACG
* * *
26133 AG-TCGTGGAGAATCCGCAATAAATGTCGAATCGT-AGCCATTAGTAGG-CATCTAAGACCAACA
65 AGCT-GTGGAGAATCCGCAATAAATGTCGGATC-TCAACCATCAGTAGGACATCTAAGACCAACA
* *
26195 CCCATATAACTTGTAATGCTCACACGAGTTGTG
128 CCCATATAACCTGTAATGCTCACACGAGCTGTG
* *
26228 AAAAAAGGGCCTGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACATGA
1 AAAAAAGGGCTTGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACGA
* * * *
26293 GCTGTGGAGAATTCGCAATGAATGTTGGATCTCAACCATCAGTAGGACATCTAAGACCAACACCT
66 GCTGTGGAGAATCCGCAATAAATGTCGGATCTCAACCATCAGTAGGACATCTAAGACCAACACCC
26358 ATATAACCTGTAATGCTCACACGAGCTGTG
131 ATATAACCTGTAATGCTCACACGAGCTGTG
* * *
26388 AAAAAAGGGCTTGCTTACACGAGATGTGGGTCAAGATGTTGGGCTACACGATGCTGCTCACACGA
1 AAAAAAGGGCTTGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACGA
* * * *
26453 GCTGTGGAGAATTCGCAATGAATGTTGGATCTCAA-C--CA-T--GACATCTAAGACCAACACCT
66 GCTGTGGAGAATCCGCAATAAATGTCGGATCTCAACCATCAGTAGGACATCTAAGACCAACACCC
* *
26512 ATATAACTTGTAATGCTCACACGAGCTNTG
131 ATATAACCTGTAATGCTCACACGAGCTGTG
* * *
26542 AAAAAAGGGCTTGCTCACACGAGCTGTGGGTCAAGATGTTAGGCTACACAATGCTGCTCACACGA
1 AAAAAAGGGCTTGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACGA
* * *
26607 GCTGTGGAGAATCCGCAATAAATGTCGGATCTCAGCCATTC-GTAGGACATCTAAGATCAGCACC
66 GCTGTGGAGAATCCGCAATAAATGTCGGATCTCAACCA-TCAGTAGGACATCTAAGACCAACACC
*
26671 CATAAAACCTG
130 CATATAACCTG
26682 AATCCCGATG
Statistics
Matches: 410, Mismatches: 33, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
154 140 0.34
155 1 0.00
156 1 0.00
157 2 0.00
158 3 0.01
159 97 0.24
160 166 0.40
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (160 bp):
AAAAAAGGGCTTGCTCACACGAGCTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACGA
GCTGTGGAGAATCCGCAATAAATGTCGGATCTCAACCATCAGTAGGACATCTAAGACCAACACCC
ATATAACCTGTAATGCTCACACGAGCTGTG
Found at i:26654 original size:314 final size:318
Alignment explanation
Indices: 26069--26681 Score: 900
Period size: 314 Copynumber: 1.9 Consensus size: 318
26059 ACTAGCTATA
*
26069 AAAAAAGGGTCTGCTCACACGAGTTGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACAA
1 AAAAAAGGGTCTGCTCACACGAGATGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACAA
*
26134 GTCGTGGAGAATCCGCAATAAATGTCGAATCGTAGCCATTAGTAGGCATCTAAGACCAACACCCA
66 GTCGTGGAGAATCCGCAATAAATGTCGAATCGTAACCATTAGTA-GCATCTAAGACCAACACCCA
*
26199 TATAACTTGTAATGCTCACACGAGTTGTGAAAAAAGGGCCTGCTCACACGAGCTGTGAGTCAAGA
130 TATAACTTGTAATGCTCACACGAGCTGTGAAAAAAGGGCCTGCTCACACGAGCTGTGAGTCAAGA
* * * * * *
26264 TGTTGGGCTACACGATGCTGCTCACATGAGCTGTGGAGAATTCGCAATGAATGTTGGATCTCAAC
195 TGTTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAAATGTCGGATCTCAAC
* *
26329 CATCAGTAGGACATCTAAGACCAACACCTATATAACCTGTAATGCTCACACGAGCTGTG
260 CATCAGTAGGACATCTAAGACCAACACCCATAAAACCTGTAATGCTCACACGAGCTGTG
* * *
26388 AAAAAAGGG-CTTGCTTACACGAGATGTGGGTCAAGATGTTGGGCTACACGATGCTGCTCACACG
1 AAAAAAGGGTC-TGCTCACACGAGATGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACA
* * * *
26452 AG-CTGTGGAGAATTCGCAATGAATGTTGGATC-TCAACCA-T-G-A-CATCTAAGACCAACACC
65 AGTC-GTGGAGAATCCGCAATAAATGTCGAATCGT-AACCATTAGTAGCATCTAAGACCAACACC
* * * *
26511 TATATAACTTGTAATGCTCACACGAGCTNTGAAAAAAGGGCTTGCTCACACGAGCTGTGGGTCAA
128 CATATAACTTGTAATGCTCACACGAGCTGTGAAAAAAGGGCCTGCTCACACGAGCTGTGAGTCAA
26576 GATGTTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAAATGTCGGATCTCA
193 GATGTTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAAATGTCGGATCTCA
* * *
26641 GCCATTC-GTAGGACATCTAAGATCAGCACCCATAAAACCTG
258 ACCA-TCAGTAGGACATCTAAGACCAACACCCATAAAACCTG
26682 AATCCCGATG
Statistics
Matches: 265, Mismatches: 25, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
314 169 0.64
315 2 0.01
316 1 0.00
317 1 0.00
318 4 0.02
319 88 0.33
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (318 bp):
AAAAAAGGGTCTGCTCACACGAGATGTGAGTCAAGATGTTGGGCTACACGATGCTGCTCACACAA
GTCGTGGAGAATCCGCAATAAATGTCGAATCGTAACCATTAGTAGCATCTAAGACCAACACCCAT
ATAACTTGTAATGCTCACACGAGCTGTGAAAAAAGGGCCTGCTCACACGAGCTGTGAGTCAAGAT
GTTAGGCTACACAATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAAATGTCGGATCTCAACC
ATCAGTAGGACATCTAAGACCAACACCCATAAAACCTGTAATGCTCACACGAGCTGTG
Found at i:27783 original size:105 final size:105
Alignment explanation
Indices: 27601--27813 Score: 410
Period size: 105 Copynumber: 2.0 Consensus size: 105
27591 TGTTTACTAA
27601 AATTTTAACCACAAAATCTTGATAGTGGTTCACCCACCACCACTAATCCTAGACTAGGGTATAAT
1 AATTTTAACCACAAAATCTTGATAGTGGTTCACCCACCACCACTAATCCTAGACTAGGGTATAAT
27666 TATCCCTTTGAGTCCTCTCTCTTTCATTTCATGTTTGTTT
66 TATCCCTTTGAGTCCTCTCTCTTTCATTTCATGTTTGTTT
27706 AATTTTAACCACAAAATCTAT-ATAGTGGTTCACCCACCACCACTAATCCTAGACTAGGGTATAA
1 AATTTTAACCACAAAATCT-TGATAGTGGTTCACCCACCACCACTAATCCTAGACTAGGGTATAA
27770 TTATCCCTTTGAGTCCTCTCTCTTTCATTTCATGTTTGTTT
65 TTATCCCTTTGAGTCCTCTCTCTTTCATTTCATGTTTGTTT
27811 AAT
1 AAT
27814 CCTTTTTCTT
Statistics
Matches: 107, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 106 0.99
106 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (105 bp):
AATTTTAACCACAAAATCTTGATAGTGGTTCACCCACCACCACTAATCCTAGACTAGGGTATAAT
TATCCCTTTGAGTCCTCTCTCTTTCATTTCATGTTTGTTT
Found at i:28813 original size:75 final size:75
Alignment explanation
Indices: 28690--28838 Score: 289
Period size: 75 Copynumber: 2.0 Consensus size: 75
28680 AGAATTATTG
28690 AAAATGTTTAAGGAACATTTTTATATGTTTTATGGTGATTTCAGGCTTATTTTAGGCTCTCTTAC
1 AAAATGTTTAAGGAACATTTTTATATGTTTTATGGTGATTTCAGGCTTATTTTAGGCTCTCTTAC
28755 ACCTAGGTAA
66 ACCTAGGTAA
*
28765 AAAATGTTTAAGGAACATTTTTATATGTTTTATGGTGATTTCAGGCTTATTTTAGGCTCTCTTGC
1 AAAATGTTTAAGGAACATTTTTATATGTTTTATGGTGATTTCAGGCTTATTTTAGGCTCTCTTAC
28830 ACCTAGGTA
66 ACCTAGGTA
28839 CCAATATTAG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (75 bp):
AAAATGTTTAAGGAACATTTTTATATGTTTTATGGTGATTTCAGGCTTATTTTAGGCTCTCTTAC
ACCTAGGTAA
Found at i:32455 original size:24 final size:24
Alignment explanation
Indices: 32410--32455 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
32400 GGGTCCCCAT
* *
32410 AAAAAATTTTCTGACAATATGTTC
1 AAAAAATTTACTGACAAGATGTTC
32434 AAAAAATTTCACTGA-AAGATGT
1 AAAAAATTT-ACTGACAAGATGT
32456 CTCATATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (24 bp):
AAAAAATTTACTGACAAGATGTTC
Found at i:34623 original size:20 final size:20
Alignment explanation
Indices: 34598--34640 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
34588 AATATTTTAA
34598 AAAAATTATAAA-ATAAATAT
1 AAAAATTATAAAGA-AAATAT
*
34618 AAAAATTCTAAAGAAAATAT
1 AAAAATTATAAAGAAAATAT
34638 AAA
1 AAA
34641 GAGTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATAAAGAAAATAT
Found at i:35285 original size:26 final size:26
Alignment explanation
Indices: 35249--35302 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
35239 AGAGCAAAAC
35249 TAAGTACTTAAAATTAAACTTTTATT
1 TAAGTACTTAAAATTAAACTTTTATT
35275 TAAGTACTTAAAATTAAACTTTTATT
1 TAAGTACTTAAAATTAAACTTTTATT
35301 TA
1 TA
35303 CCTTTACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAGTACTTAAAATTAAACTTTTATT
Done.