Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014818.1 Kokia drynarioides strain JFW-HI SEQ_129860, 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: 35204
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:1266 original size:28 final size:28
Alignment explanation
Indices: 1222--1283 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
1212 CGTAAGAGGA
*
1222 GAAAGAAATTAGTAGACATGCCATGTCT
1 GAAAGAAATTAGCAGACATGCCATGTCT
1250 GAAAGAAATTAGCAGACATGCCATGTCT
1 GAAAGAAATTAGCAGACATGCCATGTCT
1278 GAAAGA
1 GAAAGA
1284 CAACACTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (28 bp):
GAAAGAAATTAGCAGACATGCCATGTCT
Found at i:17838 original size:16 final size:17
Alignment explanation
Indices: 17817--17849 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17807 GAAAATTTTA
17817 GCTTTTT-CTCAAAAGT
1 GCTTTTTGCTCAAAAGT
17833 GCTTTTTGGCTCAAAAG
1 GCTTTTT-GCTCAAAAG
17850 CACTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (17 bp):
GCTTTTTGCTCAAAAGT
Found at i:19053 original size:33 final size:33
Alignment explanation
Indices: 19015--19083 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
19005 TGAATAAATA
*
19015 AAAGTAATATAGTAATTAAATGAGAAGCTGCAT
1 AAAGTAATATAGTAATTAAATGAGAAGCAGCAT
19048 AAAGTAATATAGTAATTAAATGAGAAGCAGCAT
1 AAAGTAATATAGTAATTAAATGAGAAGCAGCAT
19081 AAA
1 AAA
19084 AAGTCTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (33 bp):
AAAGTAATATAGTAATTAAATGAGAAGCAGCAT
Found at i:22886 original size:20 final size:20
Alignment explanation
Indices: 22863--22908 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
22853 TTTTAATTAG
*
22863 AATATATAAAATAT-ATTTTA
1 AATAT-TAAAATATAATCTTA
*
22883 AATATTTAAATATAATCTTA
1 AATATTAAAATATAATCTTA
22903 AATATT
1 AATATT
22909 TTTAATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATTAAAATATAATCTTA
Found at i:22895 original size:19 final size:20
Alignment explanation
Indices: 22871--22909 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22861 AGAATATATA
*
22871 AAATAT-ATTTTAAATATTT
1 AAATATAATCTTAAATATTT
22890 AAATATAATCTTAAATATTT
1 AAATATAATCTTAAATATTT
22910 TTAATTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATAATCTTAAATATTT
Found at i:23477 original size:21 final size:21
Alignment explanation
Indices: 23378--23482 Score: 65
Period size: 21 Copynumber: 5.1 Consensus size: 21
23368 ATTTGTTGTT
*
23378 ATTACTATTAAATATAATA-A
1 ATTATTATTAAATATAATATA
*
23398 GATTATTATTAAATATAATTTA
1 -ATTATTATTAAATATAATATA
** * *
23420 A-TAAAAATAAAAATAA-ATA
1 ATTATTATTAAATATAATATA
* * * *
23439 ATT-TAATCATATTTTAATATA
1 ATTATTATTA-AATATAATATA
*
23460 ATTATTATTAAATATAATTTA
1 ATTATTATTAAATATAATATA
23481 AT
1 AT
23483 AAAAATAAAA
Statistics
Matches: 61, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
19 6 0.10
20 16 0.26
21 34 0.56
22 5 0.08
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (21 bp):
ATTATTATTAAATATAATATA
Found at i:23502 original size:8 final size:8
Alignment explanation
Indices: 23473--23516 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
23463 ATTATTAAAT
23473 ATAATTTA
1 ATAATTTA
**
23481 ATAAAAATA
1 AT-AATTTA
23490 A-AATTTA
1 ATAATTTA
23497 ATAATTTA
1 ATAATTTA
23505 ATAATTTA
1 ATAATTTA
23513 ATAA
1 ATAA
23517 CATTCTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 5 0.17
8 20 0.67
9 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATTTA
Found at i:23542 original size:14 final size:16
Alignment explanation
Indices: 23532--23617 Score: 54
Period size: 15 Copynumber: 5.4 Consensus size: 16
23522 TTAATATAAT
23532 TATTTTTATATTAAAA
1 TATTTTTATATTAAAA
**
23548 TATTTTTAT-TT-TTA
1 TATTTTTATATTAAAA
*
23562 TATTAAATTATATTAAAA
1 TATT--TTTATATTAAAA
*
23580 TA-TTTTATTTTAAATTA
1 TATTTTTATATTAAA--A
* *
23597 TATTTTGA-AATAAAA
1 TATTTTTATATTAAAA
23612 TATTTT
1 TATTTT
23618 ATTTTTATAT
Statistics
Matches: 53, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
14 5 0.09
15 18 0.34
16 13 0.25
17 10 0.19
18 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (16 bp):
TATTTTTATATTAAAA
Found at i:23549 original size:22 final size:22
Alignment explanation
Indices: 23524--23573 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
23514 TAACATTCTT
23524 AATATAATTATTTTTATATTAA
1 AATATAATTATTTTTATATTAA
**
23546 AATATTTTTATTTTTATATTAA
1 AATATAATTATTTTTATATTAA
*
23568 ATTATA
1 AATATA
23574 TTAAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATATAATTATTTTTATATTAA
Found at i:23573 original size:32 final size:31
Alignment explanation
Indices: 23537--23628 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 31
23527 ATAATTATTT
23537 TTATATTAAAATATTTTTATTTTTATATTAAA
1 TTATATTAAAATA-TTTTATTTTTATATTAAA
* *
23569 TTATATTAAAATATTTTA-TTTTAAATTATA
1 TTATATTAAAATATTTTATTTTTATATTAAA
* *
23599 TTTTGAAATAAAATATTTTATTTTTATATT
1 TTAT--ATTAAAATATTTTATTTTTATATT
23629 TTCAGAGTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.25
31 5 0.10
32 26 0.50
33 8 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTATATTAAAATATTTTATTTTTATATTAAA
Found at i:23958 original size:28 final size:29
Alignment explanation
Indices: 23901--23962 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
23891 TTATACTTAA
*
23901 AAAAAGGTAAATTATATATATACTAGATC
1 AAAAAGGTAAATTATATATATACTACATC
**
23930 AAAAA-GTAAATTA-ATATATTTGTACATC
1 AAAAAGGTAAATTATATATA-TACTACATC
23958 AAAAA
1 AAAAA
23963 TTTGATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 19 0.66
29 5 0.17
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAAGGTAAATTATATATATACTACATC
Found at i:29211 original size:91 final size:91
Alignment explanation
Indices: 29008--29192 Score: 361
Period size: 91 Copynumber: 2.0 Consensus size: 91
28998 AATATTTACG
29008 ATGTCATTAATATCATATTAAAATTTGGTTACGAAATTTTATTGTTTAGATAGTTAATTAAATAA
1 ATGTCATTAATATCATATTAAAATTTGGTTACGAAATTTTATTGTTTAGATAGTTAATTAAATAA
*
29073 AAAGGATTAAATTGAAAAATGTGAAA
66 AAAGGATTAAATTGAAAAAGGTGAAA
29099 ATGTCATTAATATCATATTAAAATTTGGTTACGAAATTTTATTGTTTAGATAGTTAATTAAATAA
1 ATGTCATTAATATCATATTAAAATTTGGTTACGAAATTTTATTGTTTAGATAGTTAATTAAATAA
29164 AAAGGATTAAATTGAAAAAGGTGAAA
66 AAAGGATTAAATTGAAAAAGGTGAAA
29190 ATG
1 ATG
29193 GTAGCATCTA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (91 bp):
ATGTCATTAATATCATATTAAAATTTGGTTACGAAATTTTATTGTTTAGATAGTTAATTAAATAA
AAAGGATTAAATTGAAAAAGGTGAAA
Found at i:30300 original size:23 final size:22
Alignment explanation
Indices: 30274--30350 Score: 109
Period size: 23 Copynumber: 3.4 Consensus size: 22
30264 TAGCGCAAAT
*
30274 CAGTAGGCACACAAGGTGTGAAA
1 CAGTAAGCACACAA-GTGTGAAA
*
30297 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACAC-AAGTGTGAAA
30320 CAGTAAGCACACAAAGTGTGAAA
1 CAGTAAGCACAC-AAGTGTGAAA
30343 CAGTAAGC
1 CAGTAAGC
30351 GCGCTAGCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 47 0.96
24 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (22 bp):
CAGTAAGCACACAAGTGTGAAA
Found at i:32465 original size:42 final size:42
Alignment explanation
Indices: 32391--32744 Score: 369
Period size: 42 Copynumber: 8.4 Consensus size: 42
32381 GAATCACTTG
*
32391 ATGTATAAATGGAAGACTCATGTCTC-GAGATGAGCATGAGATT
1 ATGTTTAAA-GGAAGACTCATGTCTCAG-GATGAGCATGAGATT
* *
32434 ATGTTTAAAGGAAGATTCACGTCTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
** * *
32476 ATGTTTAAAGGAAGACTCATGTCTTGGGATGGGAATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
* * * **
32518 ATGTTTAAAGGAAGAGTCATGTCGCGGGATGAGGGTGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
* * *
32560 ATGTTTAAAGGAAGACT-AGTGACTGAAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCA-TGTCTCAGGATGAGCATGAGATT
* * *
32602 ATGTTTGAAGGAAGACTCGTGACTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
* * * *
32644 ATGTTTAAAGGAAGAC-CTGTGTCTCGGGAAGAGCATTAGATT
1 ATGTTTAAAGGAAGACTC-ATGTCTCAGGATGAGCATGAGATT
* * * *
32686 ATGTTTGAAGGAAGAATTATGTCTCA--ATAGAGCATAAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGAT-GAGCATGAGATT
32727 -TGTTTAAAAAGGAAGACT
1 ATGTTT--AAAGGAAGACT
32745 TATGACTTGG
Statistics
Matches: 262, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
40 6 0.02
41 13 0.05
42 234 0.89
43 9 0.03
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
Found at i:34064 original size:17 final size:17
Alignment explanation
Indices: 34042--34118 Score: 100
Period size: 17 Copynumber: 4.5 Consensus size: 17
34032 CCCAATCAGC
*
34042 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAT
*
34059 TTAAATTTATTCTAAAT
1 TTAAATTTATTTTAAAT
** *
34076 TTAAATTTGGTTGAAAT
1 TTAAATTTATTTTAAAT
*
34093 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
34110 TTAAATTTA
1 TTAAATTTA
34119 AAATTTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:34080 original size:6 final size:6
Alignment explanation
Indices: 34042--34125 Score: 54
Period size: 6 Copynumber: 14.5 Consensus size: 6
34032 CCCAATCAGC
* * **
34042 TTAAAT TT-ATT TTAAAA TTAAAT TT--AT TCTAAAT TTAAAT TT-GGT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAAT
*
34087 TGAAAT TTAAAT TT--AT TATAAAT TTAAAT TTAAAAT TTA
1 TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TT-AAAT TTA
34126 TTTTAAAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
4 6 0.10
5 8 0.14
6 33 0.56
7 12 0.20
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (6 bp):
TTAAAT
Done.