Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009930.1 Kokia drynarioides strain JFW-HI SEQ_124671, 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: 17114
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:1923 original size:97 final size:96
Alignment explanation
Indices: 1745--1930 Score: 252
Period size: 97 Copynumber: 1.9 Consensus size: 96
1735 GAAAAGGATG
**
1745 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
**
1810 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAAAAACATTGCCTCGATTAAGGGTA
*
1841 TTCGATTAT-TCCGATTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAAC
1 TTCGATTATCT-CGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-
* *
1904 TTGAA-ATAAAAAAATATTGCCTCGATT
62 TCGAAGATAAAAAAACATTGCCTCGATT
1931 TTAAAGTTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
95 1 0.01
96 20 0.25
97 54 0.68
98 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGA
AGATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:2416 original size:57 final size:59
Alignment explanation
Indices: 2305--2559 Score: 229
Period size: 59 Copynumber: 4.3 Consensus size: 59
2295 CATCCACGGG
* * **
2305 AAAATTGGTAATTTTTGAAAGTTTCAAGG-TCAAAAATGGAAA-TTTTGGGGGTTCGAGGGT
1 AAAAATGG-AATTTTTGGAAGTTTC-AGGATCAAAAAT-GAAATTTTTGGAAGTTCGAGGGT
* *
2365 -AAAATGGAATTTTTGGAAGTTTCGGGATC-GAAATGAAATTTTTGGAAGTTCG-GGGT
1 AAAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGAAATTTTTGGAAGTTCGAGGGT
* * * **
2421 AAAAATAGAATTTTTGGAAGTTTTAGGATCAAAAATGGAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGAAATTTTTGGAAGTTCGAGGGT
* * ** * *
2480 CAAAAATGGGATTTTTTGAAGTTAGAGGGT-AAAAAT-AGAATTTTTGAAAGTTTC-AGGGTT
1 -AAAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGA-AATTTTTGGAAG-TTCGAGGG-T
*
2540 AAAAATGGGATTTTTGGAAG
1 AAAAATGGAATTTTTGGAAG
2560 CTCGAGGGTA
Statistics
Matches: 163, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
56 8 0.05
57 43 0.26
58 36 0.22
59 50 0.31
60 26 0.16
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTCAGGATCAAAAATGAAATTTTTGGAAGTTCGAGGGT
Found at i:2462 original size:30 final size:30
Alignment explanation
Indices: 2305--2582 Score: 243
Period size: 30 Copynumber: 9.5 Consensus size: 30
2295 CATCCACGGG
* * *
2305 AAAATTGGTAATTTTTGAAAGTTTCAAGGTC
1 AAAAATGG-AATTTTTGGAAGTTTCAGGGTC
* * *
2336 AAAAATGGAAATTTTGG-GGGTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-AGGGTC
2365 -AAAATGGAATTTTTGGAAGTTTC-GGGATC
1 AAAAATGGAATTTTTGGAAGTTTCAGGG-TC
* * *
2394 -GAAATGAAATTTTTGGAAG-TTCGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCAGGGTC
* * *
2421 AAAAATAGAATTTTTGGAAGTTTTAGGATC
1 AAAAATGGAATTTTTGGAAGTTTCAGGGTC
*
2451 AAAAATGGAATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCAGGGTC
* * **
2481 AAAAATGGGATTTTTTGAAGTTAGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCAGGGTC
* * *
2510 AAAAATAGAATTTTTGAAAGTTTCAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTCAGGGTC
* *
2540 AAAAATGGGATTTTTGGAAG-CTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-AGGGTC
*
2569 AAAAATGTAATTTT
1 AAAAATGGAATTTT
2583 CAGACAGTTT
Statistics
Matches: 202, Mismatches: 35, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.01
28 36 0.18
29 70 0.35
30 86 0.43
31 7 0.03
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCAGGGTC
Found at i:2531 original size:59 final size:58
Alignment explanation
Indices: 2395--2582 Score: 191
Period size: 59 Copynumber: 3.2 Consensus size: 58
2385 TTCGGGATCG
* * * * * ** *
2395 AAATGAAATTTTTGGAAG-TTCGGGGT-AAAAATAGAATTTTTGGAAGTTTTAGGATCAA
1 AAATG-AATTTTTGAAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTAGAGGGT-AA
* * * *
2453 AAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTTGAAGTTAGAGGGTAA
1 AAAT-GAATTTTTGAAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTAGAGGGTAA
* *
2512 AAATAGAATTTTTGAAAGTTTCAGGGTTAAAAATGGGATTTTTGGAAGCTCGAGGGTAA
1 AAAT-GAATTTTTGAAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTAGAGGGTAA
2571 AAATGTAATTTT
1 AAATG-AATTTT
2583 CAGACAGTTT
Statistics
Matches: 111, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
58 17 0.15
59 71 0.64
60 23 0.21
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (58 bp):
AAATGAATTTTTGAAAGTTTCAGGGTCAAAAATGGGATTTTTGGAAGCTAGAGGGTAA
Found at i:2568 original size:89 final size:87
Alignment explanation
Indices: 2365--2575 Score: 244
Period size: 89 Copynumber: 2.4 Consensus size: 87
2355 GTTCGAGGGT
* * ** ** *
2365 AAAATGGAATTTTTGGAAGTTTCG-GGATCGAAATGAAATTTTTGGAAGTTCGGGGTAAAAATAG
1 AAAATGGAATTTTTGGAAG-CTCGAGGGTAAAAATGGGATTTTTGGAAGTTAGGGGTAAAAATAG
* *
2429 AATTTTTGGAAGTTTTAGGATCA
65 AATTTTTGAAAGTTTCAGGATCA
* ** *
2452 AAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTTTGAAGTTAGAGGGTAAAAATA
1 AAAATGGAATTTTTGGAAGCTCGAGGGT-AAAAATGGGATTTTTGGAAGTTAG-GGGTAAAAATA
* *
2517 GAATTTTTGAAAGTTTCAGGGTTA
64 GAATTTTTGAAAGTTTCAGGATCA
*
2541 AAAATGGGATTTTTGGAAGCTCGAGGGTAAAAATG
1 AAAATGGAATTTTTGGAAGCTCGAGGGTAAAAATG
2576 TAATTTTCAG
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
86 2 0.02
87 22 0.21
88 25 0.24
89 55 0.53
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (87 bp):
AAAATGGAATTTTTGGAAGCTCGAGGGTAAAAATGGGATTTTTGGAAGTTAGGGGTAAAAATAGA
ATTTTTGAAAGTTTCAGGATCA
Found at i:3537 original size:3 final size:3
Alignment explanation
Indices: 3531--3618 Score: 149
Period size: 3 Copynumber: 29.0 Consensus size: 3
3521 TTAATTAATG
* *
3531 TTA TTA TTA ATA TCA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3619 ATGTCATTAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 78 0.98
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4332 original size:13 final size:13
Alignment explanation
Indices: 4314--4338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4304 TTGGGCTTGA
4314 TTTGTAATTGGAC
1 TTTGTAATTGGAC
4327 TTTGTAATTGGA
1 TTTGTAATTGGA
4339 AATTATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:4382 original size:17 final size:17
Alignment explanation
Indices: 4350--4437 Score: 101
Period size: 17 Copynumber: 5.4 Consensus size: 17
4340 ATTATTTAAA
4350 TAAATTTAAAAT---TT
1 TAAATTTAAAATAAATT
**
4364 TAAATTTATTATAAATT
1 TAAATTTAAAATAAATT
4381 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
* *
4398 TAAATTTCAAATAAACT
1 TAAATTTAAAATAAATT
**
4415 TATTTTTAAAATAAATT
1 TAAATTTAAAATAAATT
4432 TAAATT
1 TAAATT
4438 CTATTAGGCC
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
14 10 0.17
17 49 0.83
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:4409 original size:7 final size:6
Alignment explanation
Indices: 4350--4409 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
4340 ATTATTTAAA
*
4350 TAAATT TAAAATTT TAAATT T--ATT ATAAATT TAAATT TAAA-A TAAATT
1 TAAATT T-AAA-TT TAAATT TAAATT -TAAATT TAAATT TAAATT TAAATT
4398 TAAATT TCAAAT
1 TAAATT T-AAAT
4410 AAACTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
4 3 0.07
5 5 0.11
6 21 0.47
7 13 0.29
8 3 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:5167 original size:205 final size:205
Alignment explanation
Indices: 4796--5547 Score: 1040
Period size: 205 Copynumber: 3.7 Consensus size: 205
4786 TTTTGATCCA
* * * * ** * * *
4796 CTTCTCTGTGTATCATCAGGAAGATGGTTTTGGTTCACTT-TCCCGTATTTCATCAAGG-AGCTA
1 CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCT-CAGTATCTCATC-AGGAAGCTA
* * * * *
4859 ACCTTTTATTGCTTCGACTTGTTTCTCAGTGTCTCATCAAGAAACTGGGGTTTGAAGATTTGCTC
64 ACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTC
* * * *
4924 ACATCGAGCGTGGGTTTGATTTGGTCTCCTTTTCAGTATCTTATCAGGAAGATGACCGCGTCGTT
129 ACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATT
* *
4989 TGTCTCAATTTG
194 TGTTTCAATTCG
* * * * *
5001 CTTCTTTGTATCTCATCAGGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTATC
1 CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
*
5066 CTTTTATTGCTTCAACCTGCTTCTCGGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
66 CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
* *
5131 ATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCACGTCATTTG
131 ATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTG
*
5196 TTTCAATACG
196 TTTCAATTCG
*
5206 CTTCTCTGTATCTTATCAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
** * * *
5271 CTTTTATTGCTTCAATTTGCTTCTCAGTGTCTCATCAGGAAGCTGGAGTTCAAAGATTTGCTCAC
66 CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
* *
5336 ATCGAGCGTGGGTTAGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCGTCATTTG
131 ATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTG
5401 TTTCAATTCG
196 TTTCAATTCG
* * *
5411 CTTCTCTATACCTTATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAAC
1 CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
* *** * * * *
5476 CTTTTATTGTTTTGCCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGACTTGATCAC
66 CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
5541 ATCGAGC
131 ATCGAGC
5548 CCTGAGTTGG
Statistics
Matches: 486, Mismatches: 59, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
204 3 0.01
205 482 0.99
206 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (205 bp):
CTTCTCTGTATCTTATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
CTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCAC
ATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTG
TTTCAATTCG
Done.