Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013228.1 Kokia drynarioides strain JFW-HI SEQ_128247, 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: 14543
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Found at i:74 original size:12 final size:12
Alignment explanation
Indices: 53--110 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
43 ATGTTTCGAA
*
53 AATATCATTAAT
1 AATATTATTAAT
65 AATATTATTAAT
1 AATATTATTAAT
* **
77 TATATTGGTAAT
1 AATATTATTAAT
89 AATA--A-TAAT
1 AATATTATTAAT
*
98 AATATTACTAAT
1 AATATTATTAAT
110 A
1 A
111 TCATTAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 8 0.22
11 1 0.03
12 28 0.76
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (12 bp):
AATATTATTAAT
Found at i:122 original size:21 final size:21
Alignment explanation
Indices: 98--159 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
88 TAATAATAAT
*
98 AATATTACTAATATCATTAAC
1 AATATTAATAATATCATTAAC
* * * * *
119 AATAATAATGACATCAATAAT
1 AATATTAATAATATCATTAAC
*
140 AATATTAATAATAGCATTAA
1 AATATTAATAATATCATTAA
160 TTTAAAAAAG
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (21 bp):
AATATTAATAATATCATTAAC
Found at i:1307 original size:59 final size:59
Alignment explanation
Indices: 1240--1569 Score: 324
Period size: 59 Copynumber: 5.6 Consensus size: 59
1230 AAAATTATCA
* * * *
1240 TTTT-ACCCCCGAACTTCCAAAAATTACCATTTTACCCCCAAACTCCCAAAAATTCCTT
1 TTTTGACCCCCAAACTTCCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCAT
* * * **
1298 TTTTGA-CCCCAAACCTTCCAAAAATTACAATTTTACCCTTGAACTTACAAAAATCCCAT
1 TTTTGACCCCCAAA-CTTCCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCAT
* * * * * *
1357 TTTTGACCTCGAACCCTCTAAAAATTACCATTTCACCCCTAAACTCCCAAAAATCCCAT
1 TTTTGACCCCCAAACTTCCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCAT
* ** * * *
1416 TTTTGACCCCAAAACTTTTAAAAATTACCATTTTGCCCTTAAACTCACAAAAATCCCAT
1 TTTTGACCCCCAAACTTCCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCAT
*** * ** *
1475 TTTTGACCATAAAACTTCTAAAAATTACCATTTTACCCCCCGAACTTCC-AAAATCCCAT
1 TTTTGACCCCCAAACTTCCAAAAATTACCATTTTA-CCCCTAAACTCCCAAAAATCCCAT
* * * * *
1534 TTTTAACCTCGAAACATCCAAAAATTACTATTTTAC
1 TTTTGACCCCCAAACTTCCAAAAATTACCATTTTAC
1570 TCCCGGATGT
Statistics
Matches: 223, Mismatches: 45, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
58 11 0.05
59 200 0.90
60 12 0.05
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (59 bp):
TTTTGACCCCCAAACTTCCAAAAATTACCATTTTACCCCTAAACTCCCAAAAATCCCAT
Found at i:1319 original size:30 final size:29
Alignment explanation
Indices: 1220--1569 Score: 194
Period size: 29 Copynumber: 11.9 Consensus size: 29
1210 GGAGGTCCCT
*
1220 AAACTATCCAAAAATTATCATTTTACCCCC
1 AAACT-TCCAAAAATTACCATTTTACCCCC
*
1250 GAACTTCCAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
1279 AAACTCCCAAAAATT-CCTTTTTTGA-CCCC
1 AAACTTCCAAAAATTACC-ATTTT-ACCCCC
* **
1308 AAACCTTCCAAAAATTACAATTTTACCCTT
1 AAA-CTTCCAAAAATTACCATTTTACCCCC
* * * * *
1338 GAACTTACAAAAA-TCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* * * * *
1368 AACCCTCTAAAAATTACCATTTCACCCCT
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * *
1397 AAACTCCCAAAAA-TCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
** * **
1427 AAACTTTTAAAAATTACCATTTTGCCCTT
1 AAACTTCCAAAAATTACCATTTTACCCCC
* ***
1456 AAAC-TCACAAAAA-TCCCATTTTTGACCATA
1 AAACTTC-CAAAAATTACCA-TTTT-ACCCCC
*
1486 AAACTTCTAAAAATTACCATTTTACCCCCC
1 AAACTTCCAAAAATTACCATTTTA-CCCCC
* * * *
1516 GAACTTCC-AAAA-TCCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
1545 AAACATCCAAAAATTACTATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
1570 TCCCGGATGT
Statistics
Matches: 239, Mismatches: 60, Indels: 43
0.70 0.18 0.13
Matches are distributed among these distances:
28 18 0.08
29 113 0.47
30 90 0.38
31 18 0.08
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:1466 original size:118 final size:118
Alignment explanation
Indices: 1258--1569 Score: 403
Period size: 118 Copynumber: 2.6 Consensus size: 118
1248 CCGAACTTCC
* * *
1258 AAAAATTACCATTTTACCCCCAAACTCCCAAAAATTCCTTTTTTGACCCCAAACCTTCCAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
* * * *
1323 TACAATTTTACCCTTGAACTTACAAAAATCCCATTTTTGACC-TCGAACCCTCT
66 TACAATTTTACCCTTAAACTCACAAAAATCCCATTTTTGACCAT-AAAACCTCT
* * **
1376 AAAAATTACCATTTCACCCCTAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTTTAAAAAT
1 AAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
* * *
1441 TACCATTTTGCCCTTAAACTCACAAAAATCCCATTTTTGACCATAAAACTTCT
66 TACAATTTTACCCTTAAACTCACAAAAATCCCATTTTTGACCATAAAACCTCT
* * * * * *
1494 AAAAATTACCATTTTACCCCCCGAACTTCC-AAAATCCCATTTTTAACCTCGAAACATCCAAAAA
1 AAAAATTACCATTTTA-CCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAA
*
1558 TTACTATTTTAC
65 TTACAATTTTAC
1570 TCCCGGATGT
Statistics
Matches: 166, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
118 155 0.93
119 11 0.07
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (118 bp):
AAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAT
TACAATTTTACCCTTAAACTCACAAAAATCCCATTTTTGACCATAAAACCTCT
Found at i:1596 original size:12 final size:12
Alignment explanation
Indices: 1579--1603 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1569 CTCCCGGATG
1579 TCTGAAGACTGT
1 TCTGAAGACTGT
1591 TCTGAAGACTGT
1 TCTGAAGACTGT
1603 T
1 T
1604 TTCGAACTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TCTGAAGACTGT
Found at i:13367 original size:206 final size:207
Alignment explanation
Indices: 13027--13461 Score: 687
Period size: 206 Copynumber: 2.1 Consensus size: 207
13017 CTACCTAATG
* * *
13027 AGATACTGAGAAAAAGACCAAATCAAACTCACGCTCGATGTGAGCAAATCTTCGAACCACAGCTT
1 AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCACAACTT
13092 CCTAATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACTAAG
66 CCTAATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACTAAG
*
13157 AAGTGGACCAAATTCGTCTTCCTGATGAGATACATAGAAGCGGACTGAAACAGACGACGCAGTCA
131 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAGTCA
*
13222 TCTT-CTCGAT-A
196 GCTTCCT-GATGA
*
13233 AGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGAACCACAACTT
1 AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCACAACTT
* * * *
13298 CCTGATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAATGTTAGCTTCTTGATGAAATACTGAG
66 CCTAATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACTAAG
* * * * *
13363 AAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAGTGGATTGAAACAGACGACTCAGTTA
131 AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAGTCA
*
13428 GCTTCCTTATGA
196 GCTTCCTGATGA
*
13440 A-ATACTGAGAAGTAGACCAAAT
1 AGATACTGAGAAGAAGACCAAAT
13462 TCGTCTTCCT
Statistics
Matches: 210, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
206 206 0.98
207 4 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (207 bp):
AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCACAACTT
CCTAATGAGATACTGAGAAGCAAGTCGAAGTGATAAAAAGGTTAGCTTCCTGATGAAATACTAAG
AAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGACTGAAACAGACGACGCAGTCA
GCTTCCTGATGA
Found at i:13444 original size:86 final size:86
Alignment explanation
Indices: 13338--13633 Score: 450
Period size: 86 Copynumber: 3.4 Consensus size: 86
13328 TGATAAAAAT
* * *
13338 GTTAGCTTCTTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCTTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
**
13403 TGGATTGAAACAGACGACTCA
66 CAGATTGAAACAGACGACTCA
*
13424 GTTAGCTTCCTTATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
* *
13489 CAGATTGAAGCAGACGACGCA
66 CAGATTGAAACAGACGACTCA
*
13510 GTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
1 GTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
13575 CAGATTGAAACAGACGACGT-A
66 CAGATTGAAACAGACGAC-TCA
* * * * *
13596 GTCATCTTCCCGATGAGATACTGAGAAGAAGACCAAAT
1 GTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAAT
13634 CAAACTCACG
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
86 191 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (86 bp):
GTTAGCTTCCTGATGAAATACTGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CAGATTGAAACAGACGACTCA
Found at i:13487 original size:37 final size:37
Alignment explanation
Indices: 13429--13574 Score: 94
Period size: 37 Copynumber: 3.6 Consensus size: 37
13419 ACTCAGTTAG
* *
13429 CTTCCTTATGAAATACTGAGAAGTAGACCAAATTCGT
1 CTTCCTGATGAAATACAGAGAAGTAGACCAAATTCGT
* * * **
13466 CTTCCTGATGAGATACAGAGAAGCAGATTGAAGCAGACGACGCAGTT
1 CTTCCTGATGAAATACAGAG-A--AG-TAG-ACCA-A--ATTC-G-T
* *
13513 AGCTTCCTGATGAAATACTGAGAAGTGGACCAAATTCGT
1 --CTTCCTGATGAAATACAGAGAAGTAGACCAAATTCGT
*
13552 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAAATACAGAGAAG
13575 CAGATTGAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
37 38 0.46
38 1 0.01
39 1 0.01
40 3 0.04
41 4 0.05
42 3 0.04
43 2 0.02
44 3 0.04
45 4 0.05
46 3 0.04
47 1 0.01
48 1 0.01
49 18 0.22
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (37 bp):
CTTCCTGATGAAATACAGAGAAGTAGACCAAATTCGT
Found at i:14210 original size:6 final size:6
Alignment explanation
Indices: 14189--14265 Score: 56
Period size: 6 Copynumber: 13.5 Consensus size: 6
14179 TTTAAATTGG
** *
14189 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TGTCAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
** *
14236 TTT-GC CTTAAA TTTAAA TTT-AA -TTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
14266 GAATGGATTT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
4 4 0.08
5 7 0.13
6 40 0.75
7 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:14226 original size:17 final size:18
Alignment explanation
Indices: 14189--14233 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
14179 TTTAAATTGG
* *
14189 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTGTCAAA
14207 TTTAAATTTA-TGTCAAA
1 TTTAAATTTATTGTCAAA
14224 TTTAAATTTA
1 TTTAAATTTA
14234 AATTTGCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTGTCAAA
Found at i:14230 original size:23 final size:23
Alignment explanation
Indices: 14201--14257 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
14191 TAAATTTATT
**
14201 TTTAAATTTAAATTTATGTCAAA
1 TTTAAATTTAAATTTACCTCAAA
* *
14224 TTTAAATTTAAATTTGCCTTAAA
1 TTTAAATTTAAATTTACCTCAAA
14247 TTTAAATTTAA
1 TTTAAATTTAA
14258 TTAAATTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAAATTTAAATTTACCTCAAA
Found at i:14307 original size:13 final size:14
Alignment explanation
Indices: 14291--14322 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
14281 CTTAAAATTT
14291 AAAATTAAAAG-CC
1 AAAATTAAAAGTCC
14304 AAAATTAAAAGTCC
1 AAAATTAAAAGTCC
14318 AAAAT
1 AAAAT
14323 AATTACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATTAAAAGTCC
Done.