Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 25
Found at i:5702574 original size:16 final size:16
Alignment explanation
Indices: 5702547--5702662 Score: 62
Period size: 16 Copynumber: 7.1 Consensus size: 16
5702537 ATGATAATAA
5702547 TTTATATTATATATATT
1 TTTAT-TTATATATATT
5702564 TTTATTTATAT-TATT
1 TTTATTTATATATATT
* * *
5702579 TTT-GTAATATGATATA
1 TTTATTTATAT-ATATT
*
5702595 TTT-TTTAT-TAAATT
1 TTTATTTATATATATT
* *
5702609 TTTATTTTTTTAATTATT
1 TTTATTTATAT-A-TATT
*
5702627 TTATATTATATATATTTAT
1 TT-TATT-TATATATAT-T
5702646 TTTATTTA-ATATTATT
1 TTTATTTATATA-TATT
5702662 T
1 T
5702663 ATCGTATTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
14 11 0.14
15 12 0.16
16 21 0.28
17 10 0.13
18 11 0.14
19 8 0.11
20 3 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTATTTATATATATT
Found at i:5702663 original size:19 final size:19
Alignment explanation
Indices: 5702622--5702679 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
5702612 ATTTTTTTAA
5702622 TTATTTTATATT-ATATATAT
1 TTATTTTAT-TTAATAT-TAT
5702642 TTATTTTATTTAATATTAT
1 TTATTTTATTTAATATTAT
**
5702661 TTATCGTATTTAATATTAT
1 TTATTTTATTTAATATTAT
5702680 CGATATTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 22 0.63
20 13 0.37
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTTTATTTAATATTAT
Found at i:5704221 original size:15 final size:14
Alignment explanation
Indices: 5704192--5704218 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5704182 TTAATATATA
5704192 TTAAAAAAATTAAT
1 TTAAAAAAATTAAT
5704206 TTAAAAAAATTAA
1 TTAAAAAAATTAA
5704219 ATTATATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAAAATTAAT
Found at i:5705683 original size:13 final size:13
Alignment explanation
Indices: 5705650--5705688 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5705640 TCTTTTATAA
* *
5705650 ATTAAATATAAAT
1 ATTAAATTTTAAT
5705663 ATTAAATTTTAAT
1 ATTAAATTTTAAT
5705676 ATTAAA-TTTAAT
1 ATTAAATTTTAAT
5705688 A
1 A
5705689 AATAATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTAAATTTTAAT
Found at i:5706467 original size:3 final size:3
Alignment explanation
Indices: 5706459--5706489 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5706449 TTCACTCCAT
5706459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5706490 ATTGTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5706957 original size:21 final size:21
Alignment explanation
Indices: 5706914--5706961 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
5706904 ATTCCAAATA
* * *
5706914 AAATGAATTTTAATTTTAATT
1 AAATTAATTTAAATATTAATT
5706935 AAATTAATTTAAATATT-ATT
1 AAATTAATTTAAATATTAATT
*
5706955 TAATTAA
1 AAATTAA
5706962 AAAATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATTAATTTAAATATTAATT
Found at i:5706968 original size:16 final size:17
Alignment explanation
Indices: 5706931--5706978 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
5706921 TTTTAATTTT
* *
5706931 AATTAAATTAATTTAAA
1 AATTAATTTAATTAAAA
*
5706948 TATT-ATTTAATTAAAA
1 AATTAATTTAATTAAAA
5706964 AATTAAATTTAATTA
1 AATT-AATTTAATTA
5706979 GGAAATATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 13 0.52
17 3 0.12
18 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATTTAATTAAAA
Found at i:5706984 original size:18 final size:19
Alignment explanation
Indices: 5706952--5706995 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5706942 TTTAAATATT
5706952 ATTTAATTAAAAAAT-TAA
1 ATTTAATTAAAAAATATAA
** *
5706970 ATTTAATTAGGAAATATGA
1 ATTTAATTAAAAAATATAA
5706989 ATTTAAT
1 ATTTAAT
5706996 ATAACATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
ATTTAATTAAAAAATATAA
Found at i:5707289 original size:19 final size:21
Alignment explanation
Indices: 5707251--5707290 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
5707241 TCATATTAAT
5707251 CAAATGTTAAATAAAATTTTA
1 CAAATGTTAAATAAAATTTTA
*
5707272 CAAAT-TTAAAT-TAATTTTA
1 CAAATGTTAAATAAAATTTTA
5707291 TTTTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (21 bp):
CAAATGTTAAATAAAATTTTA
Found at i:5708054 original size:16 final size:15
Alignment explanation
Indices: 5708020--5708061 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5708010 AAATAATATA
*
5708020 TTATTTATATATTTAT
1 TTATTTATAT-TTAAT
5708036 TTATTTATATTTAATT
1 TTATTTATATTTAA-T
5708052 TTATTT-TATT
1 TTATTTATATT
5708062 CATTTGATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTATATTTAAT
Found at i:5711454 original size:11 final size:11
Alignment explanation
Indices: 5711440--5711494 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
5711430 AAATATATTT
5711440 ATATAATATAA
1 ATATAATATAA
*
5711451 ATATGATATAA
1 ATATAATATAA
5711462 A-A-AAT-TAA
1 ATATAATATAA
*
5711470 AAATAATATAA
1 ATATAATATAA
5711481 ATATAATA-AA
1 ATATAATATAA
5711491 ATAT
1 ATAT
5711495 TAAAATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
8 4 0.11
9 3 0.08
10 10 0.26
11 21 0.55
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
ATATAATATAA
Found at i:5711476 original size:30 final size:30
Alignment explanation
Indices: 5711440--5711520 Score: 105
Period size: 28 Copynumber: 2.8 Consensus size: 30
5711430 AAATATATTT
5711440 ATATAATATAAATATGATATAAAAAATTAAA
1 ATATAATATAAATAT-ATATAAAAAATTAAA
*
5711471 A-ATAATATAAATATA-ATAAAATATTAAA
1 ATATAATATAAATATATATAAAAAATTAAA
* *
5711499 ATATATTA-AAATTTATATAAAA
1 ATATAATATAAATATATATAAAA
5711521 TAAATTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 19 0.42
29 12 0.27
30 13 0.29
31 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (30 bp):
ATATAATATAAATATATATAAAAAATTAAA
Found at i:5711494 original size:10 final size:10
Alignment explanation
Indices: 5711440--5711522 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 10
5711430 AAATATATTT
5711440 ATATAATATAA
1 ATATAATA-AA
5711451 ATATGATATAAA
1 ATAT-A-ATAAA
*
5711463 A-A-ATTAAA
1 ATATAATAAA
5711471 A-ATAATATAA
1 ATATAATA-AA
5711481 ATATAATAAA
1 ATATAATAAA
5711491 ATAT--TAAA
1 ATATAATAAA
*
5711499 ATATATTAAA
1 ATATAATAAA
*
5711509 ATTTATATAAA
1 ATATA-ATAAA
5711520 ATA
1 ATA
5711523 AATTATTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
8 14 0.24
9 4 0.07
10 17 0.29
11 17 0.29
12 4 0.07
13 3 0.05
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
ATATAATAAA
Found at i:5712016 original size:3 final size:3
Alignment explanation
Indices: 5712008--5712041 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5711998 ACTTAATAGC
5712008 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5712042 TATCTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5712232 original size:16 final size:17
Alignment explanation
Indices: 5712213--5712247 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5712203 TTTAAATATA
*
5712213 AATATATGA-TTTATTT
1 AATATATAATTTTATTT
5712229 AATATATAATTTTATTT
1 AATATATAATTTTATTT
5712246 AA
1 AA
5712248 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
AATATATAATTTTATTT
Found at i:5713469 original size:17 final size:17
Alignment explanation
Indices: 5713444--5713491 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
5713434 AAATATATTA
5713444 AAATTTTATATAATAT-
1 AAATTTTATATAATATC
5713460 AAATTATTAT-T-ATATC
1 AAATT-TTATATAATATC
*
5713476 AAAATTTATATAATAT
1 AAATTTTATATAATAT
5713492 TTTAAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AAATTTTATATAATATC
Found at i:5724570 original size:19 final size:20
Alignment explanation
Indices: 5724534--5724574 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5724524 CTCCTACCTT
*
5724534 TTTGCTTATGATTTTTTACC
1 TTTGCTTATGACTTTTTACC
5724554 TTTGCTTATG-CTTTTTACC
1 TTTGCTTATGACTTTTTACC
5724573 TT
1 TT
5724575 AAAAGATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTGCTTATGACTTTTTACC
Found at i:5725125 original size:23 final size:25
Alignment explanation
Indices: 5725074--5725122 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
5725064 TTAACTAGTT
5725074 ATTTGTTTATAATAAAAATATAAAA
1 ATTTGTTTATAATAAAAATATAAAA
5725099 ATTTGTTTA-AAT-AAAATGATAAAA
1 ATTTGTTTATAATAAAAAT-ATAAAA
5725123 TTTAGAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.22
24 9 0.39
25 9 0.39
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
ATTTGTTTATAATAAAAATATAAAA
Found at i:5726689 original size:11 final size:10
Alignment explanation
Indices: 5726673--5726697 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5726663 AATTCATCAT
5726673 AAAAAAAAAG
1 AAAAAAAAAG
5726683 AAAAAAAAAG
1 AAAAAAAAAG
5726693 AAAAA
1 AAAAA
5726698 TCCGAGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:5727185 original size:24 final size:24
Alignment explanation
Indices: 5727156--5727206 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5727146 AAAAATTGTA
5727156 TAATACATTATTTCTTTTATTAAT
1 TAATACATTATTTCTTTTATTAAT
5727180 TAATACATTATTTCTTTTATTAAT
1 TAATACATTATTTCTTTTATTAAT
5727204 TAA
1 TAA
5727207 AAGTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATACATTATTTCTTTTATTAAT
Done.