Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012033.1 Kokia drynarioides strain JFW-HI SEQ_127031, 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: 5986
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1423 original size:20 final size:19
Alignment explanation
Indices: 1399--1449 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1389 AATCATATAT
*
1399 TTTTTATATATTCGAAATA
1 TTTTTAAATATTCGAAATA
* * *
1418 TATTTTACATTTTTGAAATA
1 T-TTTTAAATATTCGAAATA
1438 TTTTTAAATATT
1 TTTTTAAATATT
1450 TTTAATATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTTTAAATATTCGAAATA
Found at i:1456 original size:9 final size:10
Alignment explanation
Indices: 1413--1458 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1403 TATATATTCG
1413 AAATATATTTT
1 AAATAT-TTTT
* *
1424 ACAT-TTTTG
1 AAATATTTTT
1433 AAATATTTTT
1 AAATATTTTT
1443 AAATATTTTT
1 AAATATTTTT
1453 -AATATT
1 AAATATT
1459 AACTAAACTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 12 0.40
10 15 0.50
11 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
AAATATTTTT
Found at i:2332 original size:94 final size:93
Alignment explanation
Indices: 2166--2353 Score: 349
Period size: 94 Copynumber: 2.0 Consensus size: 93
2156 GGCAAGAACG
*
2166 TACATCGACCATGGAGGATATTTTTGCCTCGACACCTCCGATCACTTAACACTCCGGAACTCCCG
1 TACACCGACCATGGAGGATATTTTTGCCTCGACACCTCCGATCACTTAACACTCCGGAACTCCCG
2231 ATGACGATACGTACGATTTTACCACCCT
66 ATGACGATACGTACGATTTTACCACCCT
*
2259 TNACACCGACCATGGAGGATATTTTTGCCTCGGCACCTCCGATCACTTAACACTCCGGAACTCCC
1 T-ACACCGACCATGGAGGATATTTTTGCCTCGACACCTCCGATCACTTAACACTCCGGAACTCCC
2324 GATGACGATACGTACGATTTTACCACCCT
65 GATGACGATACGTACGATTTTACCACCCT
2353 T
1 T
2354 CTACGTATGC
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
93 1 0.01
94 91 0.99
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.26
Consensus pattern (93 bp):
TACACCGACCATGGAGGATATTTTTGCCTCGACACCTCCGATCACTTAACACTCCGGAACTCCCG
ATGACGATACGTACGATTTTACCACCCT
Found at i:2562 original size:30 final size:30
Alignment explanation
Indices: 2528--2589 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2518 TTGATTTTCT
2528 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATTTTTTAAATTTAATTTGTAA
2558 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATTTTTTAAATTTAATTTGTAA
2588 TT
1 TT
2590 ATTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (30 bp):
TTTCGTTTATTTTTTAAATTTAATTTGTAA
Found at i:2629 original size:19 final size:19
Alignment explanation
Indices: 2585--2629 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2575 ATTTAATTTG
*
2585 TAATTA-TTATTTTTTCAA
1 TAATTATTTAATTTTTCAA
2603 T-ATATATTTAATTTTTCAA
1 TAAT-TATTTAATTTTTCAA
2622 TAATTATT
1 TAATTATT
2630 ATTTCTCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 3 0.13
19 16 0.70
20 2 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTATTTAATTTTTCAA
Found at i:4071 original size:102 final size:102
Alignment explanation
Indices: 3950--4157 Score: 371
Period size: 102 Copynumber: 2.0 Consensus size: 102
3940 GGATATGTTA
*
3950 TGTTATTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAAATTGCCTCCTCGG
1 TGTTATTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAAATTGCCTCCTAGG
*
4015 GTCCTCATGCTATTTGGAAGCACAGTTTGTGAATTGT
66 GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
* * *
4052 TGTTATTATTCATTCCCGCACCATTGTCGACCATATTTGGACCTGCTAAAAGATTGCCTCCTAGG
1 TGTTATTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAAATTGCCTCCTAGG
4117 GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
66 GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
4154 TGTT
1 TGTT
4158 CAGGAGAATG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (102 bp):
TGTTATTATTCATCCCCGCACCATTGTCAACCATATTTGGACCTGCTAAAAAATTGCCTCCTAGG
GTCCTCATGCTATTTGGAAGCACAGTTCGTGAATTGT
Found at i:5437 original size:202 final size:200
Alignment explanation
Indices: 5108--5696 Score: 754
Period size: 210 Copynumber: 2.9 Consensus size: 200
5098 AATCTCCTTG
* * * * *
5108 CATTAGCAAAAATGTGCATACCAATCGATCTAAGTTAATATTACAACTTAATCTAAATCACTAAT
1 CATTAGCAAGAATGTTCATACCAATC-AACTTA-TTAATATTACACCTTAATCTAAATCACTAAT
*
5173 ACCGTTAAAAATTCAATTAGCCAGTTTATATAAAAAGAAACTTGAAATAGGATTACTAATTAAAG
64 ACCGTTAAAAATTCAATTAGCCAGTTTATATAAAAAGAAACTTGAAATCGGATTACTAATTAAAG
*
5238 AATATGTCAAAATCGAAATAGAAATTTTAAAAAAATTTATGTATATTTTCATAAATAAGACCCAC
129 AATATGTC-AAATCGAAATAGAAA-TTTAAAAAAATTTATGTATATTTTCATAAATAAGA-CCAA
*
5303 A-T-CTTATTG
191 AGTAC-TATTA
* * *
5312 TATTAGCAAGAATGTTCATACCAATCAACTTATTAATATCACACCTTAATCTAAATCATTAATAC
1 CATTAGCAAGAATGTTCATACCAATCAACTTATTAATATTACACCTTAATCTAAATCACTAATAC
** * * *
5377 CACTAAAAATTCAATTATCTAGTTTATATAAAAAGAAACTTGAAATCGGATTAGTAATTAAAG-A
66 CGTTAAAAATTCAATTAGCCAGTTTATATAAAAAGAAACTTGAAATCGGATTACTAATTAAAGAA
* *
5441 TGATGTCAAATCGAAATAAAAATTTAAGAAAATTTATGTATATTTTCATAAATAAGACCAAAGTA
131 T-ATGTCAAATCGAAATAGAAATTTAAAAAAATTTATGTATATTTTCATAAATAAGACCAAAGTA
*
5506 CTCTTA
195 CTATTA
* *
5512 CATTAGCAAGAATGATCATACCAATCGATCTCAATCGATTTATTAATATTACACCTTAATCTAAT
1 CATTAGCAAGAATGTTCATACC-A---A--TCAA-C---TTATTAATATTACACCTTAATCTAAA
* * *
5577 TCACTAACACCGTTAAAAATTCAATTAGCCGGTTGATATAAAAAGAAACTTGAAATCGGATTACT
56 TCACTAATACCGTTAAAAATTCAATTAGCCAGTTTATATAAAAAGAAACTTGAAATCGGATTACT
* *
5642 AATTAAAGATTATGTCAAATCAAAATAGAAATTTAATAAAAA-TTATGTATATTTT
121 AATTAAAGAATATGTCAAATCGAAATAGAAATTTAA-AAAAATTTATGTATATTTT
5697 AATGAATATC
Statistics
Matches: 334, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
199 4 0.01
200 58 0.17
201 18 0.05
202 92 0.28
203 4 0.01
204 24 0.07
206 4 0.01
207 1 0.00
210 124 0.37
211 5 0.01
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (200 bp):
CATTAGCAAGAATGTTCATACCAATCAACTTATTAATATTACACCTTAATCTAAATCACTAATAC
CGTTAAAAATTCAATTAGCCAGTTTATATAAAAAGAAACTTGAAATCGGATTACTAATTAAAGAA
TATGTCAAATCGAAATAGAAATTTAAAAAAATTTATGTATATTTTCATAAATAAGACCAAAGTAC
TATTA
Done.