Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011833.1 Kokia drynarioides strain JFW-HI SEQ_126829, 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: 61619
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:13329 original size:15 final size:14
Alignment explanation
Indices: 13311--13367 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
13301 CCGCAAAATG
13311 AGTGTTCGCAACTC
1 AGTGTTCGCAACTC
*
13325 TAGTGTTAGCAACATC
1 -AGTGTTCGCAAC-TC
13341 AGTGTTCGCAACTCC
1 AGTGTTCGCAACT-C
*
13356 AGTGTTCACAAC
1 AGTGTTCGCAAC
13368 ATGAGTGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 1 0.03
15 34 0.92
16 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (14 bp):
AGTGTTCGCAACTC
Found at i:13347 original size:30 final size:30
Alignment explanation
Indices: 13311--13383 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
13301 CCGCAAAATG
*
13311 AGTGTTCGCAACTCTAGTGTT-AGCAACATC
1 AGTGTTCGCAACTCCAGTGTTCA-CAACATC
*
13341 AGTGTTCGCAACTCCAGTGTTCACAACATG
1 AGTGTTCGCAACTCCAGTGTTCACAACATC
* *
13371 AGTGCTAGCAACT
1 AGTGTTCGCAACT
13384 TCCAAGCTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (30 bp):
AGTGTTCGCAACTCCAGTGTTCACAACATC
Found at i:13374 original size:15 final size:15
Alignment explanation
Indices: 13311--13374 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
13301 CCGCAAAATG
*
13311 AGTGTTCGCAAC-TC
1 AGTGTTCACAACATC
13325 TAGTGTT-AGCAACATC
1 -AGTGTTCA-CAACATC
*
13341 AGTGTTCGCAAC-TCC
1 AGTGTTCACAACAT-C
*
13356 AGTGTTCACAACATG
1 AGTGTTCACAACATC
13371 AGTG
1 AGTG
13375 CTAGCAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 36 0.90
16 3 0.08
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (15 bp):
AGTGTTCACAACATC
Found at i:14519 original size:87 final size:87
Alignment explanation
Indices: 14373--14548 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
14363 TCTCAAAGAG
14373 AAACAAACAAGCAAACAAAGAAACAATCCTTACAAGATTAGGATGTTTGTCAATTAAACACAAAT
1 AAACAAACAAGCAAACAAAGAAACAATCCTTACAAGATTAGGATGTTTGTCAATTAAACACAAAT
14438 ACAAAGCAGAACACTTGAGCTA
66 ACAAAGCAGAACACTTGAGCTA
14460 AAACAAACAAGCAAACAAAGAAACAATCCTTACAAGATTAGGATGTTTGTCAATTAAACACAAAT
1 AAACAAACAAGCAAACAAAGAAACAATCCTTACAAGATTAGGATGTTTGTCAATTAAACACAAAT
14525 ACAAAGCAGAACACTTGAGCTA
66 ACAAAGCAGAACACTTGAGCTA
14547 AA
1 AA
14549 TGAATAAAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (87 bp):
AAACAAACAAGCAAACAAAGAAACAATCCTTACAAGATTAGGATGTTTGTCAATTAAACACAAAT
ACAAAGCAGAACACTTGAGCTA
Found at i:18325 original size:18 final size:18
Alignment explanation
Indices: 18277--18318 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
18267 TATAGCGAAA
18277 TATATTAACCAATAAGGC
1 TATATTAACCAATAAGGC
18295 TATATTAACCAATAAGGC
1 TATATTAACCAATAAGGC
*
18313 TTTATT
1 TATATT
18319 TAACAATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (18 bp):
TATATTAACCAATAAGGC
Found at i:23483 original size:17 final size:16
Alignment explanation
Indices: 23448--23483 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
23438 GAGAGGAAAG
23448 AAAATTGAAGGGATGA
1 AAAATTGAAGGGATGA
23464 AAAATTAGAA-GGATGA
1 AAAATT-GAAGGGATGA
23480 AAAA
1 AAAA
23484 CATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (16 bp):
AAAATTGAAGGGATGA
Found at i:32453 original size:28 final size:28
Alignment explanation
Indices: 32416--32606 Score: 240
Period size: 28 Copynumber: 6.8 Consensus size: 28
32406 GTAAGGAAAA
* * *
32416 CCTTTATGGCTATCTCTATTAAAGGAAG
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
* *
32444 CCTTTGTGGCTATCTCTGTTAAAAGAAG
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
* *
32472 CTTTTATGGTTATCTCTGTTAAAGGAAG
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
* *
32500 ACTTTATGGTTATCTCTGTTAAAGGAAG
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
* *
32528 CCTTTGTGGTTATCTCTTTTAAAGGAAA
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
* *
32556 ACTTTGTGGTTATCTCTTTTAAAGGAAG
1 CCTTTGTGGTTATCTCTGTTAAAGGAAG
*
32584 CCTTTGTGGGTATC-CTTGTTAAA
1 CCTTTGTGGTTATCTC-TGTTAAA
32607 AGAATACCTT
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
27 1 0.01
28 143 0.99
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (28 bp):
CCTTTGTGGTTATCTCTGTTAAAGGAAG
Found at i:49963 original size:3 final size:3
Alignment explanation
Indices: 49940--49994 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
49930 ATTGAGGCAA
*
49940 AAG AAG GAG AAAG AA- AAG AAG AAG AAG AAG AAG -AG AAGG AAG AA-
1 AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG
49984 AATG AAG AAG A
1 AA-G AAG AAG A
49995 TGTTGCCCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 6 0.14
3 31 0.70
4 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:49981 original size:21 final size:22
Alignment explanation
Indices: 49940--49994 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
49930 ATTGAGGCAA
*
49940 AAGAAGGAGAA-AGAAAAGAAG
1 AAGAAGAAGAAGAGAAAAGAAG
*
49961 AAGAAGAAGAAGAG-AAGGAAG
1 AAGAAGAAGAAGAGAAAAGAAG
49982 AA-AATGAAGAAGA
1 AAGAA-GAAGAAGA
49995 TGTTGCCCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (22 bp):
AAGAAGAAGAAGAGAAAAGAAG
Found at i:50413 original size:18 final size:18
Alignment explanation
Indices: 50387--50425 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50377 CATGCAATTC
50387 TTTTAATTGTCAT-TGCAT
1 TTTTAATTGTC-TCTGCAT
*
50405 TTTTTATTGTCTCTGCAT
1 TTTTAATTGTCTCTGCAT
50423 TTT
1 TTT
50426 ATTTGTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (18 bp):
TTTTAATTGTCTCTGCAT
Found at i:50427 original size:16 final size:16
Alignment explanation
Indices: 50406--50448 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
50396 TCATTGCATT
50406 TTTTATTGTCTCT-GCA
1 TTTTATTGT-TCTAGCA
50422 TTTTATTTGTTCTAGCA
1 TTTTA-TTGTTCTAGCA
50439 TTTGTATTGT
1 TTT-TATTGT
50449 AGTTGCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.33
17 14 0.58
18 2 0.08
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (16 bp):
TTTTATTGTTCTAGCA
Found at i:51123 original size:24 final size:24
Alignment explanation
Indices: 51096--51171 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
51086 TATATATATA
51096 TGTATATTATTATACAATAAATGC
1 TGTATATTATTATACAATAAATGC
** * * *
51120 TGTAT-TGGTTA-AGAAGATATAT-A
1 TGTATATTATTATA-CA-ATAAATGC
51143 TGTATATTATTATACAATAAATGC
1 TGTATATTATTATACAATAAATGC
51167 TGTAT
1 TGTAT
51172 TGGTTAAGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
22 1 0.03
23 15 0.41
24 20 0.54
25 1 0.03
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (24 bp):
TGTATATTATTATACAATAAATGC
Found at i:51158 original size:47 final size:47
Alignment explanation
Indices: 51089--51184 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
51079 ATATATATAT
51089 ATATATATGTATATTATTATACAATAAATGCTGTATTGGTTAAGAAG
1 ATATATATGTATATTATTATACAATAAATGCTGTATTGGTTAAGAAG
51136 ATATATATGTATATTATTATACAATAAATGCTGTATTGGTTAAGAAG
1 ATATATATGTATATTATTATACAATAAATGCTGTATTGGTTAAGAAG
51183 AT
1 AT
51185 TTAAGATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.41
Consensus pattern (47 bp):
ATATATATGTATATTATTATACAATAAATGCTGTATTGGTTAAGAAG
Found at i:56753 original size:28 final size:28
Alignment explanation
Indices: 56722--56807 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 28
56712 ACAACTAGGA
* *
56722 AAGCATTTATAGCTATCTTTGTTAAAGG
1 AAGCCTTTATGGCTATCTTTGTTAAAGG
*
56750 AAGCCTTTATGGCTATCTTTATTAAAGG
1 AAGCCTTTATGGCTATCTTTGTTAAAGG
* * *
56778 AAGCCTTTGTGGGTATCTCTGTTAAAGG
1 AAGCCTTTATGGCTATCTTTGTTAAAGG
56806 AA
1 AA
56808 CACCTTCGTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (28 bp):
AAGCCTTTATGGCTATCTTTGTTAAAGG
Found at i:60287 original size:28 final size:29
Alignment explanation
Indices: 60255--60315 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
60245 AAAAGGGTCG
*
60255 AAAATG-AAGTTTCG-AAGAGTTTAGGGTT
1 AAAATGTAAGTTTCGAAAGA-TTTAGGGGT
* *
60283 AAAATGTAATTTTGGAAAGATTTAGGGGT
1 AAAATGTAAGTTTCGAAAGATTTAGGGGT
60312 AAAA
1 AAAA
60316 ATGTCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 18 0.64
30 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.26, T:0.31
Consensus pattern (29 bp):
AAAATGTAAGTTTCGAAAGATTTAGGGGT
Found at i:60319 original size:30 final size:30
Alignment explanation
Indices: 60272--60747 Score: 405
Period size: 29 Copynumber: 16.3 Consensus size: 30
60262 AGTTTCGAAG
* *
60272 AGTTTA-GGGTTAAAATGTAATTTTGGA-A
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* **
60300 AGATTTAGGGGTAAAAATGTCATTTAGGA-A
1 AG-TTTAGGGGTAAAAATGTAATTTTTGAGA
* * *** *
60330 AG-TTCGAGGTAAAAACAAAATTTTGGA-A
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* ** *
60358 AGTTTTGAGGGTAAAAATGTAATGCTTGAAA
1 AGTTTAG-GGGTAAAAATGTAATTTTTGAGA
* * *
60389 AG-TTCGAGGGTAAAAATCTGATTTTTGA-A
1 AGTTTAG-GGGTAAAAATGTAATTTTTGAGA
* *
60418 AGTTCAGGGG-CAAAATGTAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* *
60447 AGTTTGGGGGTAAAAATGTGATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
60477 AGTTTAGGGGTAAAAATGTAATTTTT-AGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* *
60506 AGTTTGGGGGTAAAAATATAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* *
60536 AG-TTCGAGGGT-AAAATGTGATTTTTGA-A
1 AGTTTAG-GGGTAAAAATGTAATTTTTGAGA
* *
60564 AGTTTAAGGGCAAAAATGTAATTTTT-AGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
*
60593 AGTTTGGGGGTAAAAATGTAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
*
60623 AGTTT-GAGGGTAAAAA-GTGATTTTT-AGA
1 AGTTTAG-GGGTAAAAATGTAATTTTTGAGA
*
60651 AGTTTAGGGGTAAAAATGT-ATTTTTTAGA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* *** * *
60680 AGTTCAATTGCAAAAATGTAATTTTGGA-A
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
* * *
60709 AGTTTAGGGGTTAAAATATGATTTTTG-GA
1 AGTTTAGGGGTAAAAATGTAATTTTTGAGA
60738 TAGTTTAGGG
1 -AGTTTAGGG
60748 ACCTTTTAGG
Statistics
Matches: 364, Mismatches: 63, Indels: 40
0.78 0.13 0.09
Matches are distributed among these distances:
28 67 0.18
29 154 0.42
30 140 0.38
31 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AGTTTAGGGGTAAAAATGTAATTTTTGAGA
Found at i:60589 original size:29 final size:30
Alignment explanation
Indices: 60272--60747 Score: 391
Period size: 30 Copynumber: 16.3 Consensus size: 30
60262 AGTTTCGAAG
* *
60272 AGTTT-AGGGTTAAAATGTAATTTTGGA-A
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* **
60300 AGATTT-AGGGGTAAAAATGTCATTTAGGA-A
1 AG-TTTGA-GGGTAAAAATGTAATTTTTGAGA
* *** *
60330 AGTTCGA-GGTAAAAACAAAATTTTGGA-A
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
** *
60358 AGTTTTGAGGGTAAAAATGTAATGCTTGAAA
1 AG-TTTGAGGGTAAAAATGTAATTTTTGAGA
* * *
60389 AGTTCGAGGGTAAAAATCTGATTTTTGA-A
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* **
60418 AG-TTCAGGGGCAAAATGTAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* *
60447 AGTTTGGGGGTAAAAATGTGATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
60477 AGTTT-AGGGGTAAAAATGTAATTTTT-AGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGAGA
* *
60506 AGTTTGGGGGTAAAAATATAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* *
60536 AGTTCGAGGGT-AAAATGTGATTTTTGA-A
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* *
60564 AGTTTAAGGGCAAAAATGTAATTTTT-AGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
*
60593 AGTTTGGGGGTAAAAATGTAATTTTTGAGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
*
60623 AGTTTGAGGGTAAAAA-GTGATTTTT-AGA
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
*
60651 AGTTT-AGGGGTAAAAATGT-ATTTTTTAGA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGAGA
** ** * *
60680 AGTTCAATTGCAAAAATGTAATTTTGGA-A
1 AGTTTGAGGGTAAAAATGTAATTTTTGAGA
* * *
60709 AGTTT-AGGGGTTAAAATATGATTTTTG-GA
1 AGTTTGA-GGGTAAAAATGTAATTTTTGAGA
60738 TAGTTT-AGGG
1 -AGTTTGAGGG
60748 ACCTTTTAGG
Statistics
Matches: 363, Mismatches: 63, Indels: 43
0.77 0.13 0.09
Matches are distributed among these distances:
27 1 0.00
28 73 0.20
29 141 0.39
30 145 0.40
31 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AGTTTGAGGGTAAAAATGTAATTTTTGAGA
Done.