Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009340.1 Kokia drynarioides strain JFW-HI SEQ_124047, 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: 25368
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:177 original size:59 final size:57
Alignment explanation
Indices: 107--402 Score: 325
Period size: 59 Copynumber: 5.0 Consensus size: 57
97 AGAGTTTCGA
* * *
107 GGTCGAAAATGGAGTTTTTGGACA--TCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCAG
1 GGTCAAAAATGGAGTTTTTGGA-AGTTC-G-GGGTAAAATGG-AATTTTTGGAAGTTTTAG
* * * *
166 TGTCAAAAATGGAATTTTAGGAAGTTCGGGGCTAAAAATGGAATTTTTGGAAGTTTTGG
1 GGTCAAAAATGGAGTTTTTGGAAGTTCGGGG-T-AAAATGGAATTTTTGGAAGTTTTAG
* * *
225 GGTCAAAAATGG-GATTTTAGAAAGTTCGGGAGTAAAAATGGAATTTTTGGAAGTTTTGG
1 GGTCAAAAATGGAG-TTTTTGGAAGTTCGGG-GT-AAAATGGAATTTTTGGAAGTTTTAG
284 GGTCAAAAATGG-GATTTTTGGAAGTTCGGGGGTAAAATGGAATTTTTGGAAGTTTTAG
1 GGTCAAAAATGGAG-TTTTTGGAAGTTC-GGGGTAAAATGGAATTTTTGGAAGTTTTAG
342 GGTCAAAAATAGGA-TTTTTGGAAGTTCAGGGGTAAAAATGGAATTTTTGGACAG-TTTAG
1 GGTCAAAAAT-GGAGTTTTTGGAAGTTC-GGGGT-AAAATGGAATTTTTGGA-AGTTTTAG
401 GG
1 GG
403 ACCCTCGAGG
Statistics
Matches: 212, Mismatches: 14, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
58 56 0.26
59 141 0.67
60 15 0.07
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (57 bp):
GGTCAAAAATGGAGTTTTTGGAAGTTCGGGGTAAAATGGAATTTTTGGAAGTTTTAG
Found at i:191 original size:30 final size:30
Alignment explanation
Indices: 99--398 Score: 277
Period size: 30 Copynumber: 10.2 Consensus size: 30
89 TAATTTTGAG
* * *
99 AGTTTCGAGGTCGAAAATGGAGTTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
* *
129 CA-TCT-GAGGGT--AAAATGGTAATTTTTGAA
1 -AGTTTCG-GGGTCAAAAATGG-AATTTTTGGA
* * *
158 AGTTTCAGTGTCAAAAATGGAATTTTAGGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
188 AG-TTCGGGG-CTAAAAATGGAATTTTTGGA
1 AGTTTCGGGGTC-AAAAATGGAATTTTTGGA
* * * *
217 AGTTTTGGGGTCAAAAATGGGATTTTAGAA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
247 AG-TTCGGGAGT-AAAAATGGAATTTTTGGA
1 AGTTTCGGG-GTCAAAAATGGAATTTTTGGA
* *
276 AGTTTTGGGGTCAAAAATGGGATTTTTGGA
1 AGTTTCGGGGTCAAAAATGGAATTTTTGGA
306 AG-TTCGGGGGT--AAAATGGAATTTTTGGA
1 AGTTTC-GGGGTCAAAAATGGAATTTTTGGA
**
334 AGTTTTAGGGTCAAAAATAGG-ATTTTTGGA
1 AGTTTCGGGGTCAAAAAT-GGAATTTTTGGA
364 AG-TTCAGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTC-GGGGTCAAAAATGGAATTTTTGGA
393 CAGTTT
1 -AGTTT
399 AGGGACCCTC
Statistics
Matches: 220, Mismatches: 28, Indels: 42
0.76 0.10 0.14
Matches are distributed among these distances:
28 33 0.15
29 83 0.38
30 91 0.41
31 13 0.06
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (30 bp):
AGTTTCGGGGTCAAAAATGGAATTTTTGGA
Found at i:1401 original size:19 final size:20
Alignment explanation
Indices: 1362--1411 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1352 TTTCCTTTTT
*
1362 TTATTATTAAAACGTTATTTA
1 TTATTATTAAAAC-ATATTTA
1383 TTATTATTAAAA-ATATTTA
1 TTATTATTAAAACATATTTA
1402 TTATTATTAA
1 TTATTATTAA
1412 TAGTCATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTATTAAAACATATTTA
Found at i:1468 original size:3 final size:3
Alignment explanation
Indices: 1460--1516 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1450 TTAACGTTAC
1460 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1508 TAT TAT TAT
1 TAT TAT TAT
1517 ACTTATGAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2088 original size:15 final size:15
Alignment explanation
Indices: 2068--2137 Score: 95
Period size: 15 Copynumber: 4.7 Consensus size: 15
2058 CATTGAGCCG
*
2068 TTTGTACTTGGGCCA
1 TTTGTAATTGGGCCA
*
2083 TTTGTACTTGGGCCA
1 TTTGTAATTGGGCCA
**
2098 TTTGTAATTGGGCTG
1 TTTGTAATTGGGCCA
*
2113 TTTGTAATTGGGCAA
1 TTTGTAATTGGGCCA
2128 TTTGTAATTG
1 TTTGTAATTG
2138 TACTTTGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.44
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:10223 original size:22 final size:22
Alignment explanation
Indices: 10168--10223 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
10158 TATTAGTGTG
* *
10168 ATTAGTGCTCTCCGTTTAGCAC
1 ATTAGTGCTCTCCGTATAACAC
* *
10190 ATTCGTGGTCTCCGTATAACAC
1 ATTAGTGCTCTCCGTATAACAC
*
10212 CTTAGTGCTCTC
1 ATTAGTGCTCTC
10224 TGTTCATTAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTAGTGCTCTCCGTATAACAC
Found at i:16109 original size:43 final size:43
Alignment explanation
Indices: 16048--16132 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
16038 GCAGCATCGT
*
16048 TAGGGGACAATTATATAAAAAGACACCGTACCGATGGCTGGGA
1 TAGGGGACAATTATATAAAAAGACACCATACCGATGGCTGGGA
* * *
16091 TAGGGGACAATTATATAAACAGACACCATATCGATGGTTGGG
1 TAGGGGACAATTATATAAAAAGACACCATACCGATGGCTGGG
16133 GTACCACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (43 bp):
TAGGGGACAATTATATAAAAAGACACCATACCGATGGCTGGGA
Found at i:19630 original size:37 final size:37
Alignment explanation
Indices: 19580--19651 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
19570 GGGCGCGACT
* *
19580 ATTACTTCGGTTTATCCGATGAGGCAATGGGTGTCAA
1 ATTACTTCGGTTTAACCGATGAGACAATGGGTGTCAA
* *
19617 ATTACTTTGGTTTAACCGATGAGACACTGGGTGTC
1 ATTACTTCGGTTTAACCGATGAGACAATGGGTGTC
19652 GCTTGCATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (37 bp):
ATTACTTCGGTTTAACCGATGAGACAATGGGTGTCAA
Found at i:19668 original size:99 final size:99
Alignment explanation
Indices: 19497--19716 Score: 307
Period size: 99 Copynumber: 2.2 Consensus size: 99
19487 GACCACAAGT
* *
19497 CGATGAGGCACTAGGTGTCAAATTACTTAGATTTAACCGATACGACACTAGGTGTCGCTTACATT
1 CGATGAGGCAATGGGTGTCAAATTACTTAGATTTAACCGATACGACACTAGGTGTCGCTTACATT
*
19562 TTAGCGCTGGGCGCGACTATTACTTCGGTTTATC
66 ATAGCGCTGGGCGCGACTATTACTTCGGTTTATC
* * * *
19596 CGATGAGGCAATGGGTGTCAAATTACTTTGGTTTAACCGATGA-GACACTGGGTGTCGCTTGCAT
1 CGATGAGGCAATGGGTGTCAAATTACTTAGATTTAACCGAT-ACGACACTAGGTGTCGCTTACAT
* * *
19660 TATAGCGCTGGGGGCGACTATTACTTCTGTTTATT
65 TATAGCGCTGGGCGCGACTATTACTTCGGTTTATC
* * *
19695 TGATGAGGCATTGGGTGCCAAA
1 CGATGAGGCAATGGGTGTCAAA
19717 CTGGGGTGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
99 106 0.99
100 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (99 bp):
CGATGAGGCAATGGGTGTCAAATTACTTAGATTTAACCGATACGACACTAGGTGTCGCTTACATT
ATAGCGCTGGGCGCGACTATTACTTCGGTTTATC
Found at i:23170 original size:2 final size:2
Alignment explanation
Indices: 23163--23188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23153 TGATAGTAAG
23163 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23189 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24648 original size:99 final size:99
Alignment explanation
Indices: 24471--24671 Score: 350
Period size: 99 Copynumber: 2.0 Consensus size: 99
24461 AATGTTCGCT
*
24471 AAATTACTTCGGTTTAACCGATAAGACATTGGGTGTCAGTTACATTATAGCGCTGGGCGCGACTA
1 AAATTACTTCGGTTTAACCGATAAGACATTGGGTGTCACTTACATTATAGCGCTGGGCGCGACTA
24536 TTACTTCGATTTATCTGATGAGGCACTGGGTGCC
66 TTACTTCGATTTATCTGATGAGGCACTGGGTGCC
* * *
24570 AAATTACTTCGGTTTAACCGATGAGACATTGGGTGTCACTTGCATTATAGCGCTGGGGGCGACTA
1 AAATTACTTCGGTTTAACCGATAAGACATTGGGTGTCACTTACATTATAGCGCTGGGCGCGACTA
24635 TTACTTCTG-TTTATCTGATGAGGCACTGGGTGCC
66 TTACTTC-GATTTATCTGATGAGGCACTGGGTGCC
24669 AAA
1 AAA
24672 CTGGGGTGTT
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
99 96 0.99
100 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (99 bp):
AAATTACTTCGGTTTAACCGATAAGACATTGGGTGTCACTTACATTATAGCGCTGGGCGCGACTA
TTACTTCGATTTATCTGATGAGGCACTGGGTGCC
Done.