Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold544
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: 18176
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Found at i:2831 original size:15 final size:16
Alignment explanation
Indices: 2811--2843 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2801 TTATCAATTC
2811 AACTAAAAAT-AAATA
1 AACTAAAAATAAAATA
2826 AACTAAAAATAAAATA
1 AACTAAAAATAAAATA
2842 AA
1 AA
2844 AATGCAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AACTAAAAATAAAATA
Found at i:6190 original size:8 final size:8
Alignment explanation
Indices: 6172--6216 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
6162 AACTCTGTTT
6172 TATATTTAA
1 TATA-TTAA
6181 TATATTAA
1 TATATTAA
*
6189 TATATTTA
1 TATATTAA
6197 TATATTTAAA
1 TATA-TT-AA
6207 TATATTAA
1 TATATTAA
6215 TA
1 TA
6217 AAACAAACAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 19 0.59
9 8 0.25
10 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TATATTAA
Found at i:6208 original size:18 final size:17
Alignment explanation
Indices: 6172--6216 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
6162 AACTCTGTTT
6172 TATATTTAATATATTAA
1 TATATTTAATATATTAA
6189 TATATTT-ATATATTTAA
1 TATATTTAATATA-TTAA
6206 -ATATATTAATA
1 TATAT-TTAATA
6217 AAACAAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.36
17 13 0.52
18 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTTAATATATTAA
Found at i:6938 original size:2 final size:2
Alignment explanation
Indices: 6931--6968 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6921 TTAGTTATCC
*
6931 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6969 TGTCTGTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12906 original size:13 final size:13
Alignment explanation
Indices: 12888--12913 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12878 AATTATTTAT
12888 TAAATATAAATAA
1 TAAATATAAATAA
12901 TAAATATAAATAA
1 TAAATATAAATAA
12914 CTTAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATATAAATAA
Found at i:13300 original size:13 final size:13
Alignment explanation
Indices: 13284--13324 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
13274 GTTTTAAGCC
* *
13284 ATTTATTTATTTA
1 ATTTAATTAATTA
13297 ATTTAATTAATTA
1 ATTTAATTAATTA
13310 A-TTAATTAATTA
1 ATTTAATTAATTA
13322 ATT
1 ATT
13325 AATAGTCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTAATTAATTA
Found at i:13306 original size:4 final size:4
Alignment explanation
Indices: 13294--13327 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
13284 ATTTATTTAT
13294 TTAA TTTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA -TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
13328 AGTCCTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:13602 original size:26 final size:28
Alignment explanation
Indices: 13573--13635 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 28
13563 AAAATAAATA
13573 ATTTATAA-TTAAA-AATATAATTATTT
1 ATTTATAATTTAAATAATATAATTATTT
* * *
13599 ATTTTTAATTTTAAATTATGTAATTATTT
1 ATTTATAA-TTTAAATAATATAATTATTT
*
13628 ATTCATAA
1 ATTTATAA
13636 AATATGATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.24
28 5 0.17
29 17 0.59
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTATAATTTAAATAATATAATTATTT
Found at i:13806 original size:6 final size:6
Alignment explanation
Indices: 13797--13829 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
13787 GAAGAAAAAG
13797 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
13830 AATTACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:13849 original size:3 final size:3
Alignment explanation
Indices: 13801--13864 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
13791 AAAAAGATTT
* * * * *
13801 TTA TTT TTA TTT TTA TTT TTA TTT TTA TTAA TTA CTA TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT-A TTA TTA
13848 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
13865 TCTTTTTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:14216 original size:12 final size:12
Alignment explanation
Indices: 14194--14232 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
14184 TTAAAATTTT
*
14194 TTATATTTTTATG
1 TTAT-TTTTTATA
14207 TTATTTTTTATA
1 TTATTTTTTATA
*
14219 TTATTTATTATA
1 TTATTTTTTATA
14231 TT
1 TT
14233 TTAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTATTTTTTATA
Found at i:14234 original size:20 final size:21
Alignment explanation
Indices: 14189--14234 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
14179 TTTATTTAAA
14189 ATTTTTTATATT-TTTATGTT
1 ATTTTTTATATTATTTATGTT
14209 ATTTTTTATATTATTTAT-TAT
1 ATTTTTTATATTATTTATGT-T
14230 ATTTT
1 ATTTT
14235 AATAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTTTATATTATTTATGTT
Found at i:14243 original size:20 final size:19
Alignment explanation
Indices: 14207--14245 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
14197 TATTTTTATG
* *
14207 TTATTTTTTATATTATTTA
1 TTATTTTTAATAATATTTA
14226 TTATATTTTAATAATATTTA
1 TTAT-TTTTAATAATATTTA
14246 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTAATAATATTTA
Found at i:14270 original size:20 final size:20
Alignment explanation
Indices: 14245--14283 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
14235 AATAATATTT
*
14245 AAATATTATATATTTATATA
1 AAATATTATACATTTATATA
14265 AAATATTATACATTTATAT
1 AAATATTATACATTTATAT
14284 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATATTATACATTTATATA
Found at i:14798 original size:49 final size:48
Alignment explanation
Indices: 14713--14809 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 48
14703 TAATTTATAT
*
14713 TATTTATATTTATTATTTATAATTAATAAAAATAAAAA-ATTATTTTA
1 TATTAATATTTATTATTTATAATTAATAAAAATAAAAATATTATTTTA
* * *
14760 TATTAATATTTATATATTTTATAATTAA-ATTAATTAAAAATATTTTTTTA
1 TATTAATATTTAT-TA-TTTATAATTAATA-AAAATAAAAATATTATTTTA
14810 ATTCTTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 12 0.29
48 3 0.07
49 19 0.45
50 8 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (48 bp):
TATTAATATTTATTATTTATAATTAATAAAAATAAAAATATTATTTTA
Found at i:15609 original size:11 final size:9
Alignment explanation
Indices: 15578--15604 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
15568 TATTTAAAAG
15578 AAAAAAATT
1 AAAAAAATT
15587 AAAAAAATT
1 AAAAAAATT
15596 AAAAAAATT
1 AAAAAAATT
15605 TTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAAAATT
Found at i:15709 original size:15 final size:15
Alignment explanation
Indices: 15689--15734 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
15679 ATCAATTAAA
15689 AAATAAATATAATTT
1 AAATAAATATAATTT
15704 AAATAAATA-AATTT
1 AAATAAATATAATTT
*
15718 AAA-AATATATATTTT
1 AAATAA-ATATAATTT
15733 AA
1 AA
15735 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAAATATAATTT
Found at i:16217 original size:18 final size:18
Alignment explanation
Indices: 16191--16234 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
16181 TTTTAAAATT
* *
16191 TTAATTTATTTAATATTAA
1 TTAAATTATTT-AGATTAA
16210 -TAAATTATTTAGATTAA
1 TTAAATTATTTAGATTAA
16227 TTAAATTA
1 TTAAATTA
16235 AATTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTAAATTATTTAGATTAA
Found at i:16355 original size:14 final size:14
Alignment explanation
Indices: 16300--16366 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
16290 TAAATTATTC
*
16300 ATTAAA-ATAAAAT
1 ATTAAATATATAAT
*
16313 TTTAAATATA-AAT
1 ATTAAATATATAAT
*
16326 A-T-AATATAT-GT
1 ATTAAATATATAAT
*
16337 ATTAAATATATCAT
1 ATTAAATATATAAT
*
16351 ATTAATTATATAAT
1 ATTAAATATATAAT
16365 AT
1 AT
16367 AATATTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.19
12 2 0.05
13 15 0.35
14 18 0.42
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (14 bp):
ATTAAATATATAAT
Found at i:16522 original size:21 final size:21
Alignment explanation
Indices: 16481--16523 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16471 ATAAAGAGGT
* **
16481 TTAAAAATAATTATTTTTGAG
1 TTAAAAATAATAATTGGTGAG
16502 TTAAAAATAATAATTGGTGAG
1 TTAAAAATAATAATTGGTGAG
16523 T
1 T
16524 AGAATACATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (21 bp):
TTAAAAATAATAATTGGTGAG
Found at i:16802 original size:22 final size:22
Alignment explanation
Indices: 16777--16823 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
16767 AAAATAATTT
**
16777 ATATTTATATTAATAATAAAAA
1 ATATTTATAAAAATAATAAAAA
* *
16799 ATATTTTTAAAAATATTAAAAA
1 ATATTTATAAAAATAATAAAAA
16821 ATA
1 ATA
16824 AAAATTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTTATAAAAATAATAAAAA
Done.