Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2751
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: 32252
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:654 original size:2 final size:2
Alignment explanation
Indices: 647--677 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
637 TTCATAATTC
*
647 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
678 ACTAGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1117 original size:2 final size:2
Alignment explanation
Indices: 1067--1098 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1057 ACATACATAC
1067 AT AT 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
1099 GAGAGATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2658 original size:40 final size:40
Alignment explanation
Indices: 2609--2689 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
2599 AATTGTATAG
*
2609 TAAAAATTTATTTAAATATAATAA-AAATAAAATAA-AATTT
1 TAAAAATTTATCT-AATATAATAATAAA-AAAATAAGAATTT
* **
2649 TAAACATTTATCTAATATTTTAATAAAAAAATAAGAATTT
1 TAAAAATTTATCTAATATAATAATAAAAAAATAAGAATTT
2689 T
1 T
2690 CGTTTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 15 0.43
40 20 0.57
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (40 bp):
TAAAAATTTATCTAATATAATAATAAAAAAATAAGAATTT
Found at i:3177 original size:22 final size:21
Alignment explanation
Indices: 3135--3178 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3125 CCGCCATCCA
3135 CTTAAAACAATTTTTCGAAAAT
1 CTTAAAAC-ATTTTTCGAAAAT
3157 CTTAAAAC-TTTTATCGTAAAAT
1 CTTAAAACATTTT-TCG-AAAAT
3179 ATTATCATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (21 bp):
CTTAAAACATTTTTCGAAAAT
Found at i:4834 original size:20 final size:20
Alignment explanation
Indices: 4806--4849 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4796 ATAGAGACTT
*
4806 CCTCCTCCCTCTCAAGTATC
1 CCTCATCCCTCTCAAGTATC
**
4826 CCTCATCCCTCTCTTGTATC
1 CCTCATCCCTCTCAAGTATC
4846 CCTC
1 CCTC
4850 TTCAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.05, T:0.34
Consensus pattern (20 bp):
CCTCATCCCTCTCAAGTATC
Found at i:9290 original size:28 final size:27
Alignment explanation
Indices: 9231--9299 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
9221 CACCCATTTG
* * *
9231 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTAGTTATTTTATA
9258 TTTGTCAAAAATGGTAGTT-TCCTTTATA
1 TTTGTCAAAAATGGTAGTTAT--TTTATA
*
9286 TTTGTCAAATATGG
1 TTTGTCAAAAATGG
9300 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.50
28 17 0.47
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTAGTTATTTTATA
Found at i:9406 original size:20 final size:20
Alignment explanation
Indices: 9378--9421 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
9368 ATAGAGACTT
*
9378 CCTCCTCCCTCTCAAGTATC
1 CCTCATCCCTCTCAAGTATC
**
9398 CCTCATCCCTCTCTTGTATC
1 CCTCATCCCTCTCAAGTATC
9418 CCTC
1 CCTC
9422 TTCAATTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.50, G:0.05, T:0.34
Consensus pattern (20 bp):
CCTCATCCCTCTCAAGTATC
Found at i:10367 original size:19 final size:20
Alignment explanation
Indices: 10339--10388 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
10329 GATACGAAAG
*
10339 AATAACTAAAAT-ACGATATAA
1 AATAA-TAAAATGAC-ATAAAA
10360 AAT-ATAAAATGACATAAAA
1 AATAATAAAATGACATAAAA
10379 AATAATAAAA
1 AATAATAAAA
10389 ATATTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 14 0.54
20 9 0.35
21 3 0.12
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (20 bp):
AATAATAAAATGACATAAAA
Found at i:14329 original size:2 final size:2
Alignment explanation
Indices: 14324--14354 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14314 AGGAAAAAAA
14324 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
14355 ATATTCCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15760 original size:13 final size:13
Alignment explanation
Indices: 15738--15771 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15728 TTCAGTTTTC
* *
15738 TTTATCATTGATT
1 TTTATTATTGATA
15751 TTTATTATTGATA
1 TTTATTATTGATA
15764 TTTATTAT
1 TTTATTAT
15772 AATAGATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (13 bp):
TTTATTATTGATA
Found at i:20787 original size:19 final size:21
Alignment explanation
Indices: 20759--20814 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
20749 TATGTAAATA
20759 ATATAAATATGATATAA-TTT
1 ATATAAATATGATATAATTTT
* *
20779 ATA-AAATATGTTAAAATTTT
1 ATATAAATATGATATAATTTT
*
20799 ATATAAATATCATATA
1 ATATAAATATGATATA
20815 TATATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.38
20 9 0.31
21 9 0.31
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATAAATATGATATAATTTT
Found at i:20806 original size:49 final size:47
Alignment explanation
Indices: 20746--20838 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 47
20736 ATTTTGTATT
* *
20746 TTTTATGTAAATAAT-ATAAATATGATATAATTTATAAAATATGTTAAAA
1 TTTTATATAAAT-ATCATAAATAT-ATAT-ATATATAAAATATGTTAAAA
* *
20795 TTTTATATAAATATCATATATATATATATATATTAAATATGTTA
1 TTTTATATAAATATCATAAATATATATATATATAAAATATGTTA
20839 TGTTCATCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 15 0.38
48 6 0.15
49 18 0.46
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (47 bp):
TTTTATATAAATATCATAAATATATATATATATAAAATATGTTAAAA
Found at i:25686 original size:12 final size:12
Alignment explanation
Indices: 25670--25710 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
25660 TGATGAAAAA
*
25670 GATGAATATGAT
1 GATGAAGATGAT
*
25682 TATGAAGATGAT
1 GATGAAGATGAT
*
25694 GATGATGATGAT
1 GATGAAGATGAT
25706 GATGA
1 GATGA
25711 TGACGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:25726 original size:3 final size:3
Alignment explanation
Indices: 25677--25713 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
25667 AAAGATGAAT
* *
25677 ATG ATT ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
25714 CGAAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:27850 original size:2 final size:2
Alignment explanation
Indices: 27843--27877 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27833 TATAGCCATT
27843 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27878 TCCTTTCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27979 original size:23 final size:24
Alignment explanation
Indices: 27948--27999 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
27938 TTTACTTTGA
*
27948 AAAAAAAATCTAT-TTAAAACTTG
1 AAAAAAAATATATATTAAAACTTG
* * *
27971 AAAATAAATATATATTCAAATTTG
1 AAAAAAAATATATATTAAAACTTG
27995 AAAAA
1 AAAAA
28000 CATGATTACA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAAAAATATATATTAAAACTTG
Found at i:27999 original size:25 final size:24
Alignment explanation
Indices: 27943--27999 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
27933 TCATATTTAC
*
27943 TTTGAAAAAAAAATCTATTTAAAA
1 TTTGAAAAAAAAATATATTTAAAA
* * *
27967 CTTG-AAAATAAATATATATTCAAA
1 TTTGAAAAAAAAATATAT-TTAAAA
27991 TTTGAAAAA
1 TTTGAAAAA
28000 CATGATTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.42
24 11 0.42
25 4 0.15
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (24 bp):
TTTGAAAAAAAAATATATTTAAAA
Done.