Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1753
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: 35230
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:365 original size:17 final size:16
Alignment explanation
Indices: 334--376 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
324 CGGGCTTACA
334 AAAATTAAA-AAAAAT
1 AAAATTAAACAAAAAT
*
349 GAAATTAAACGAAAAAT
1 AAAATTAAAC-AAAAAT
366 AAAATTAAACA
1 AAAATTAAACA
377 GTCCATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 1 0.04
17 15 0.62
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAATTAAACAAAAAT
Found at i:1643 original size:25 final size:24
Alignment explanation
Indices: 1609--1669 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1599 TTAATCCTTT
* *
1609 TTTATATATTTCTAAAT-TTTATTTA
1 TTTATTTATTT-TAAATATTT-TATA
1634 TTTATTTATTTTAAATATTTTATA
1 TTTATTTATTTTAAATATTTTATA
1658 TATTATTTATTT
1 T-TTATTTATTT
1670 ACTATAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.28
25 23 0.72
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTATTTATTTTAAATATTTTATA
Found at i:1677 original size:29 final size:31
Alignment explanation
Indices: 1631--1691 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
1621 TAAATTTTAT
* * *
1631 TTATTTATTTATTTTAAATATT-TT-ATATA
1 TTATTTATTTACTATAAACATTATTCATATA
1660 TTATTTATTTACTATAAACATTATTCATATA
1 TTATTTATTTACTATAAACATTATTCATATA
1691 T
1 T
1692 AAAAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 19 0.70
30 2 0.07
31 6 0.22
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTTATTTACTATAAACATTATTCATATA
Found at i:1786 original size:22 final size:21
Alignment explanation
Indices: 1750--1799 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1740 TTATGTTGTC
1750 TATTATATATATTATC-TATTATT
1 TATT-TATATATTATCATA-TA-T
*
1773 TATTTATATTTTATCATATAT
1 TATTTATATATTATCATATAT
1794 TATTTA
1 TATTTA
1800 CTATGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTATATATTATCATATAT
Found at i:15929 original size:44 final size:44
Alignment explanation
Indices: 15878--16262 Score: 488
Period size: 44 Copynumber: 8.7 Consensus size: 44
15868 CATTTACAAG
*
15878 GAGCAGATCGAAGATAGCAGATTTGGCATCTTTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* * * *
15922 GAACAGATCGAAGATAGCAAATTTGGCGTCTCTGTATTGTTAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* **
15966 GAGCAGATTGAAGATAGCAGATTTGGTGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* * *
16010 GAGC-GAATCAAAGATAGCAAATTTGGCATCTCTGTATTGTTAGA
1 GAGCAG-ATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* *
16054 GAGCAGATCGAAGATAGCAGATTTGACATCTCAGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
** * *
16098 GAATAGATCGAAGATAGCAGATTTGGCATCTATGTATTATCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* *
16142 GAGCAGATCAAAGATAGCAGATTTGGCATCTCTATATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* * *
16186 GAGCAGATCGAAGATAGTAGATTTGGCATCT-TCGTATTTTGACGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCT-GTATTGTCA-GA
* * *
16231 GGAGCAAATCCAAGA-AGCAAATTTGGCATCTC
1 -GAGCAGATCGAAGATAGCAGATTTGGCATCTC
16263 CAGATCCAAG
Statistics
Matches: 293, Mismatches: 42, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.01
44 262 0.89
45 17 0.06
46 12 0.04
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.28
Consensus pattern (44 bp):
GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
Found at i:16569 original size:17 final size:17
Alignment explanation
Indices: 16547--16579 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16537 AAAAAAATTA
*
16547 AAAAATGAAATTAAACG
1 AAAAATAAAATTAAACG
16564 AAAAATAAAATTAAAC
1 AAAAATAAAATTAAAC
16580 AGTCCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATTAAACG
Found at i:17904 original size:25 final size:22
Alignment explanation
Indices: 17858--17906 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 22
17848 TATATATTCC
17858 TAAATTTTTTATTTATTTATTT
1 TAAATTTTTTATTTATTTATTT
17880 TAAATATTTTATATATTATTTATTT
1 TAAAT-TTTT-TAT-TTATTTATTT
17905 TA
1 TA
17907 CTATAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.21
23 4 0.17
24 3 0.12
25 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TAAATTTTTTATTTATTTATTT
Found at i:18019 original size:29 final size:30
Alignment explanation
Indices: 17933--18049 Score: 96
Period size: 33 Copynumber: 3.7 Consensus size: 30
17923 TATATAAAAA
*
17933 ATTATTTATCGTATATTATTT-TATTATATAT
1 ATTATTTAT--TATGTTATTTATATTATATAT
*
17964 -TTATATTATTATGTTATGTTGCCTATTATATAT
1 ATTAT-TTATTATGTTAT-TT--ATATTATATAT
*
17997 ATTATCTATTAT-TTATTTATATTTTATCATAT
1 ATTATTTATTATGTTATTTATA--TTAT-ATAT
*
18029 ATTATTTATTATGTTGTTTAT
1 ATTATTTATTATGTTATTTAT
18050 CTTTATCTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
29 9 0.13
30 6 0.08
31 10 0.14
32 19 0.27
33 23 0.32
34 4 0.06
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (30 bp):
ATTATTTATTATGTTATTTATATTATATAT
Found at i:18039 original size:32 final size:32
Alignment explanation
Indices: 17948--18065 Score: 100
Period size: 32 Copynumber: 3.7 Consensus size: 32
17938 TTATCGTATA
*
17948 TTAT-TTTATTATATATTTATATTATTATGTTAT
1 TTATCTTTATCATATA-TTAT-TTATTATGTTAT
** *
17981 GTTGCCTATTAT-ATATATTATCTATTAT-TTAT
1 -TTATCT-TTATCATATATTATTTATTATGTTAT
* *
18013 TTATATTTTATCATATATTATTTATTATGTTGT
1 TTAT-CTTTATCATATATTATTTATTATGTTAT
*
18046 TTATCTTTATC-TTTATTATT
1 TTATCTTTATCATATATTATT
18066 ATAATTTTAA
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
31 14 0.20
32 26 0.38
33 13 0.19
34 6 0.09
35 6 0.09
36 4 0.06
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (32 bp):
TTATCTTTATCATATATTATTTATTATGTTAT
Found at i:18417 original size:18 final size:18
Alignment explanation
Indices: 18394--18435 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
18384 AGTATGTTAA
18394 TTTTATCTTAAATTATT-T
1 TTTTATCTT-AATTATTGT
* *
18412 TTTTATGTTATTTATTGT
1 TTTTATCTTAATTATTGT
18430 TTTTAT
1 TTTTAT
18436 ATATTTGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTATCTTAATTATTGT
Found at i:32114 original size:44 final size:44
Alignment explanation
Indices: 32063--32446 Score: 497
Period size: 44 Copynumber: 8.7 Consensus size: 44
32053 CATTTACAAG
* *
32063 GAGCAGATCGAAGATAGTAGATTTGGCATCTTTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* * *
32107 GAACAGAT-TAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* *
32150 GAGCAGATTGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
*
32194 GAGC-GAATCGAAGATAGCATATTTGGCATCTCTGTATTGTCAGA
1 GAGCAG-ATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* *
32238 GAGCAGATCGAAGATAGCAGATTTGACATCTCAGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
** *
32282 GAATAGATCGAAGATAGCAGATTTGGCATCTCTGTATTATCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* *
32326 GAGTAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
* * * * *
32370 GAGCAGATTGAAGATAGTAGATTTGGAATCT-TCGTATTTTGACGA
1 GAGCAGATCGAAGATAGCAGATTTGGCATCTCT-GTATTGTCA-GA
* * *
32415 GGAGCAAATCCAAGA-AGCAAATTTGGCATCTC
1 -GAGCAGATCGAAGATAGCAGATTTGGCATCTC
32447 CAGATCCAAG
Statistics
Matches: 299, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
43 40 0.13
44 232 0.78
45 16 0.05
46 11 0.04
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (44 bp):
GAGCAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGA
Found at i:33385 original size:17 final size:17
Alignment explanation
Indices: 33356--33393 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33346 AAAGGTGATA
33356 TTTT-GTTTATTGTTATT
1 TTTTCGTTTATTGTT-TT
33373 TTTTCGTTT-TTGTTTT
1 TTTTCGTTTATTGTTTT
33389 TTTTC
1 TTTTC
33394 AATACATACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.79
Consensus pattern (17 bp):
TTTTCGTTTATTGTTTT
Found at i:34223 original size:32 final size:32
Alignment explanation
Indices: 34132--34249 Score: 100
Period size: 32 Copynumber: 3.7 Consensus size: 32
34122 TTATCGTATA
* *
34132 TTAT-TTTATTATATATTTATATTATTGTGTTAT
1 TTATCTTTATCATATA-TTAT-TTATTATGTTAT
* *
34165 GTTGTCTATTAT-ATATATTATCTATTAT-TTAT
1 -TTATCT-TTATCATATATTATTTATTATGTTAT
* *
34197 TTATATTTTATCATATATTATTTATTATGTTGT
1 TTAT-CTTTATCATATATTATTTATTATGTTAT
*
34230 TTATCTTTATC-TTTATTATT
1 TTATCTTTATCATATATTATT
34250 ATAATTTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
31 15 0.21
32 26 0.37
33 12 0.17
34 7 0.10
35 6 0.09
36 4 0.06
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.64
Consensus pattern (32 bp):
TTATCTTTATCATATATTATTTATTATGTTAT
Done.