Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2742
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: 31006
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Found at i:1617 original size:35 final size:37
Alignment explanation
Indices: 1536--1617 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 37
1526 ATAAATATTA
* * *
1536 AAAAATTTATTAAATTATTTATATTTTAAAATTTAAT
1 AAAAATATATTAAATTATTGATATATTAAAATTTAAT
*
1573 AAAAA-ATATTAAATTATTGA-ATATTAAAATTT-TT
1 AAAAATATATTAAATTATTGATATATTAAAATTTAAT
1607 AAAAATATATT
1 AAAAATATATT
1618 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 6 0.15
35 16 0.40
36 13 0.32
37 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAAATATATTAAATTATTGATATATTAAAATTTAAT
Found at i:9612 original size:25 final size:25
Alignment explanation
Indices: 9578--9627 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
9568 CTAGACATCT
9578 GACGAATGCAGGATATTTGGCAATG
1 GACGAATGCAGGATATTTGGCAATG
*
9603 GACGGATGCAGGATATTTGGCAATG
1 GACGAATGCAGGATATTTGGCAATG
9628 CAAAGCCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.24
Consensus pattern (25 bp):
GACGAATGCAGGATATTTGGCAATG
Found at i:13069 original size:12 final size:12
Alignment explanation
Indices: 13052--13097 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
13042 ATTAAAATAT
13052 AATATTTTTTAA
1 AATATTTTTTAA
13064 AATA-TTTTTAA
1 AATATTTTTTAA
* *
13075 AATATATTTAAA
1 AATATTTTTTAA
13087 AATATTATTTT
1 AATATT-TTTT
13098 TATATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 11 0.39
12 14 0.50
13 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AATATTTTTTAA
Found at i:13545 original size:20 final size:20
Alignment explanation
Indices: 13492--13606 Score: 73
Period size: 20 Copynumber: 5.9 Consensus size: 20
13482 TCGCATCGAT
*
13492 TTAATATAATTTAAATTTTAAA
1 TTAATTTAA-TTAAA-TTTAAA
**
13514 -TAATTTGTTTAAATTTAAA
1 TTAATTTAATTAAATTTAAA
*
13533 TTAATTTAATTAAATTAAAA
1 TTAATTTAATTAAATTTAAA
*
13553 AT-ATTT-ATT-AA-TTAAGA
1 TTAATTTAATTAAATTTAA-A
*
13570 TGTAATTTAA-AAAATTTAAA
1 T-TAATTTAATTAAATTTAAA
* *
13590 TT-TTTTATTTAAATTTA
1 TTAATTTAATTAAATTTA
13607 TTTTTAATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 19
0.69 0.12 0.18
Matches are distributed among these distances:
16 3 0.04
17 3 0.04
18 8 0.11
19 22 0.31
20 27 0.38
21 9 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTAATTTAATTAAATTTAAA
Found at i:14423 original size:21 final size:22
Alignment explanation
Indices: 14397--14445 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
14387 TCTTTCTTAG
*
14397 ATTTAAATT-GAAATTAATTTA
1 ATTTAAATTCGAAATTAATCTA
* *
14418 ATTT-AATTCGAATTTGATCTA
1 ATTTAAATTCGAAATTAATCTA
14439 ATTTAAA
1 ATTTAAA
14446 AGATTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
ATTTAAATTCGAAATTAATCTA
Found at i:16023 original size:16 final size:17
Alignment explanation
Indices: 15992--16024 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15982 AATAAATATC
15992 AAATATAAATATTTAAA
1 AAATATAAATATTTAAA
16009 AAATATAAA-ATTTAAA
1 AAATATAAATATTTAAA
16025 TAACAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAAATATTTAAA
Found at i:19278 original size:2 final size:2
Alignment explanation
Indices: 19271--19309 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
19261 GTTATAGCAT
* *
19271 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19310 TTGTCCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:19379 original size:18 final size:17
Alignment explanation
Indices: 19346--19379 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
19336 TTATTACTTA
*
19346 ATAATTTTTAATAAAAC
1 ATAATTTTTAAAAAAAC
19363 ATAATTTTTTAAAAAAA
1 ATAA-TTTTTAAAAAAA
19380 ATCAAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTTTTAAAAAAAC
Found at i:21857 original size:23 final size:22
Alignment explanation
Indices: 21816--21873 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
21806 GTTTAATAAA
21816 AAATTTAA-AAATTAAATATGATA-
1 AAATTTAATAAA--AAATAT-ATAT
21839 AATATTTAATAAAAAATATATATT
1 AA-ATTTAATAAAAAATATATA-T
21863 AAATTTAATAA
1 AAATTTAATAA
21874 TATAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 3 0.10
23 17 0.55
24 8 0.26
25 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATTTAATAAAAAATATATAT
Found at i:22186 original size:13 final size:15
Alignment explanation
Indices: 22155--22187 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
22145 AAAAATAATT
22155 TTAATCTTAATTGAA
1 TTAATCTTAATTGAA
22170 TTAAT-TTAATT-AA
1 TTAATCTTAATTGAA
22183 TTAAT
1 TTAAT
22188 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
TTAATCTTAATTGAA
Found at i:22347 original size:20 final size:20
Alignment explanation
Indices: 22322--22362 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22312 TATATGATAT
*
22322 AAATATTATAAAAATAATTA
1 AAATATAATAAAAATAATTA
* *
22342 AAATATAATATAAATTATTA
1 AAATATAATAAAAATAATTA
22362 A
1 A
22363 TTTATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAATAAAAATAATTA
Found at i:22417 original size:37 final size:38
Alignment explanation
Indices: 22330--22418 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 38
22320 ATAAATATTA
* *
22330 TAAAAATAATTAAAATATAATATAAATTATTAATTTAT
1 TAAATATAATAAAAATATAATATAAATTATTAATTTAT
*
22368 TAAATATTATAAAAATAT-ATA-ATAATT-TTAATTTAAT
1 TAAATATAATAAAAATATAATATA-AATTATTAATTT-AT
22405 TATAATA-AATAAAA
1 TA-AATATAATAAAA
22419 CTCATAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
36 8 0.18
37 17 0.39
38 19 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (38 bp):
TAAATATAATAAAAATATAATATAAATTATTAATTTAT
Found at i:22849 original size:17 final size:18
Alignment explanation
Indices: 22817--22851 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
22807 TTAAAGAAAA
22817 ATAAATATATATTTTTAT
1 ATAAATATATATTTTTAT
*
22835 ATAAGTATA-ATTTTTAT
1 ATAAATATATATTTTTAT
22852 GTAACTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATAAATATATATTTTTAT
Found at i:23100 original size:12 final size:13
Alignment explanation
Indices: 23075--23106 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23065 TTTATATCGA
23075 TAAA-TAAAATAT
1 TAAATTAAAATAT
23087 TAAATTAAAA-AT
1 TAAATTAAAATAT
23099 TAAATTAA
1 TAAATTAA
23107 TCTAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAATTAAAATAT
Found at i:24030 original size:21 final size:21
Alignment explanation
Indices: 24006--24067 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
23996 ATTAGATCTT
24006 AATTAATTAATTAATTATTTA
1 AATTAATTAATTAATTATTTA
*
24027 AATTTAACTTAA--AATAATTTA
1 AA-TTAA-TTAATTAATTATTTA
*
24048 AATTTA-T-ATT-ATTATTTA
1 AATTAATTAATTAATTATTTA
24066 AA
1 AA
24068 AAATAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
20 3 0.09
21 12 0.35
22 4 0.12
23 4 0.12
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAATTAATTAATTATTTA
Found at i:24112 original size:22 final size:22
Alignment explanation
Indices: 24086--24136 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
24076 AAATATAAAC
* *
24086 TAATTTTATAATTAATTAAAAA-
1 TAATTTAAT-ATTAATAAAAAAT
*
24108 TAATTAAATATTAATAAAAAAT
1 TAATTTAATATTAATAAAAAAT
24130 TAATTTA
1 TAATTTA
24137 CTTATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTAATATTAATAAAAAAT
Found at i:24131 original size:11 final size:11
Alignment explanation
Indices: 24095--24134 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
24085 CTAATTTTAT
24095 AATTAATTAAA
1 AATTAATTAAA
24106 AA-TAATTAAA
1 AATTAATTAAA
* *
24116 TATTAATAAAA
1 AATTAATTAAA
24127 AATTAATT
1 AATTAATT
24135 TACTTATAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATTAATTAAA
Found at i:24608 original size:17 final size:16
Alignment explanation
Indices: 24592--24633 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24582 AAGTTATATT
*
24592 TTTATTA-ATTATTTA
1 TTTATTATAATATTTA
24607 TTATATTATAATATTTA
1 TT-TATTATAATATTTA
*
24624 TTTAATATAA
1 TTTATTATAA
24634 AAATTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATTATAATATTTA
Found at i:25090 original size:29 final size:29
Alignment explanation
Indices: 25049--25116 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
25039 CTCCTTTTTT
* *
25049 ATTATCTTTATATTTTTTTATA-ATTA-A
1 ATTATATTTATATATTTTTATATATTATA
25076 ATTTTATATTTATATATTTTTATATATTATA
1 A--TTATATTTATATATTTTTATATATTATA
25107 ATTATATTTA
1 ATTATATTTA
25117 AAATATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 1 0.03
29 28 0.80
30 4 0.11
31 2 0.06
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTATATTTATATATTTTTATATATTATA
Found at i:25131 original size:43 final size:43
Alignment explanation
Indices: 25066--25149 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 43
25056 TTATATTTTT
* *
25066 TTATAATTAAATTTTATATTTATAT-ATTTTTATATATTATAA
1 TTATAATTAAATATTATATTTATATAATTTTAATATATTATAA
*
25108 TTATATTTAAAATATTATATTTATATAAATTTTAATATATTA
1 TTATAATT-AAATATTATATTTATAT-AATTTTAATATATTA
25150 AAAATTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 7 0.19
43 16 0.44
45 13 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (43 bp):
TTATAATTAAATATTATATTTATATAATTTTAATATATTATAA
Found at i:25151 original size:33 final size:33
Alignment explanation
Indices: 25088--25195 Score: 102
Period size: 32 Copynumber: 3.3 Consensus size: 33
25078 TTTATATTTA
* * *
25088 TATATTTTTATATATTATAATTATATTTAAAATAT
1 TATATTTATATAAATTTTAA-TATA-TTAAAATAT
25123 TATATTTATATAAATTTTAATATATTAAAA-AT
1 TATATTTATATAAATTTTAATATATTAAAATAT
*
25155 T-TATATTATATAAAATTTT-ATATATT--TATAT
1 TATAT-TTATAT-AAATTTTAATATATTAAAATAT
25186 TAT-TTTATAT
1 TATATTTATAT
25196 CATTATTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
30 7 0.11
31 7 0.11
32 17 0.26
33 13 0.20
34 4 0.06
35 17 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATTTATATAAATTTTAATATATTAAAATAT
Found at i:25154 original size:17 final size:16
Alignment explanation
Indices: 25134--25180 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
25124 ATATTTATAT
25134 AAATTTTAATATATTA
1 AAATTTTAATATATTA
*
25150 AAAATTT-ATATTATATA
1 AAATTTTAATA-TAT-TA
25167 AAATTTT-ATATATT
1 AAATTTTAATATATT
25181 TATATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 12 0.44
17 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTAATATATTA
Found at i:25178 original size:32 final size:34
Alignment explanation
Indices: 25088--25180 Score: 111
Period size: 35 Copynumber: 2.8 Consensus size: 34
25078 TTTATATTTA
* * * *
25088 TATATTTTTATATATTATAATTATATTTAAAATAT
1 TATATTTATATAAATTTTAA-TATATTAAAAATAT
25123 TATATTTATATAAATTTTAATATATTAAAAAT-T
1 TATATTTATATAAATTTTAATATATTAAAAATAT
25156 TATA-TTATATAAAATTTT-ATATATT
1 TATATTTATAT-AAATTTTAATATATT
25181 TATATTATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
32 13 0.25
33 12 0.23
34 11 0.21
35 17 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TATATTTATATAAATTTTAATATATTAAAAATAT
Found at i:29923 original size:27 final size:27
Alignment explanation
Indices: 29842--29945 Score: 79
Period size: 27 Copynumber: 3.8 Consensus size: 27
29832 AAATATAATT
* *
29842 ATATGAATATAAAATATAAAAAAATTAAA
1 ATAT-AATAT-AAATATAAATATATTAAA
* *
29871 ATATAATATAATTATTAATATATTAAA
1 ATATAATATAAATATAAATATATTAAA
* *
29898 AT-TTATATAAATATAAATTATTTTAAA
1 ATATAATATAAATATAAA-TATATTAAA
* *
29925 TACATGATA-AAATA-AAATATA
1 -ATATAATATAAATATAAATATA
29946 CAATATATAA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
26 15 0.25
27 27 0.44
28 11 0.18
29 8 0.13
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (27 bp):
ATATAATATAAATATAAATATATTAAA
Done.