Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2491
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: 25558
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:1123 original size:23 final size:23
Alignment explanation
Indices: 1102--1166 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 23
1092 TTTGAATTTT
1102 ATTTAATAATTAAAAATTATTTAA
1 ATTTAATAA-TAAAAATTATTTAA
*
1126 ATTTAATTATAAAAA-TA--TAA
1 ATTTAATAATAAAAATTATTTAA
*
1146 ATATTAAT-ATAAAAATAATTT
1 AT-TTAATAATAAAAATTATTT
1167 TTTAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 12 0.34
21 6 0.17
22 2 0.06
23 7 0.20
24 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATAATAAAAATTATTTAA
Found at i:1134 original size:21 final size:21
Alignment explanation
Indices: 1108--1162 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
1098 TTTTATTTAA
1108 TAATTAAAAATTATTTAAAT-T
1 TAATTAAAAA-TATTTAAATAT
*
1129 TAATTATAAAA-ATATAAATAT
1 TAATTA-AAAATATTTAAATAT
1150 TAATATAAAAATA
1 TAAT-TAAAAATA
1163 ATTTTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.24
21 15 0.52
22 7 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATTAAAAATATTTAAATAT
Found at i:1326 original size:21 final size:19
Alignment explanation
Indices: 1289--1327 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1279 TTTTATTTAA
*
1289 TAATTAAAATTTTTAAATT
1 TAATTAAAATTTATAAATT
1308 TAATTATAAATTATATAAAT
1 TAATTA-AAATT-TATAAAT
1328 AAGATAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTAAAATTTATAAATT
Found at i:1768 original size:2 final size:2
Alignment explanation
Indices: 1741--1791 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
1731 TATTTTTTCT
*
1741 TA TA TGA TA TA AA T- TA TA TCA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA T-A TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
*
1783 TA TC TA TA T
1 TA TA TA TA T
1792 TCTGAAAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 35 0.85
3 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1777 original size:19 final size:20
Alignment explanation
Indices: 1741--1791 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1731 TATTTTTTCT
* *
1741 TATATGATATAAATTATATCA
1 TATAT-ATATATATTATATAA
1762 TATATATATATA-TATATAA
1 TATATATATATATTATATAA
*
1781 TATATCTATAT
1 TATATATATAT
1792 TCTGAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 6 0.22
21 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TATATATATATATTATATAA
Found at i:3345 original size:12 final size:12
Alignment explanation
Indices: 3328--3357 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3318 AAATTTATAT
3328 TTATTTAGTTTA
1 TTATTTAGTTTA
3340 TTATTTAGTTTA
1 TTATTTAGTTTA
*
3352 TAATTT
1 TTATTT
3358 TTTAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
TTATTTAGTTTA
Found at i:4600 original size:2 final size:2
Alignment explanation
Indices: 4593--4620 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4583 TATTAAACTA
4593 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
4621 CATACTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5640 original size:14 final size:14
Alignment explanation
Indices: 5621--5647 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5611 ATTCACTACT
5621 ATAATTAAATGAAC
1 ATAATTAAATGAAC
5635 ATAATTAAATGAA
1 ATAATTAAATGAA
5648 TATACACTAT
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:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
ATAATTAAATGAAC
Found at i:6699 original size:21 final size:21
Alignment explanation
Indices: 6663--6708 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6653 CAACTTTTCA
*
6663 AAAATTATACCTACTTATTCTT
1 AAAATTATACCCACTTATT-TT
6685 AAAATT-TACCCACTTATTTT
1 AAAATTATACCCACTTATTTT
6705 AAAA
1 AAAA
6709 AATAACCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 11 0.48
22 6 0.26
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATTATACCCACTTATTTT
Found at i:6711 original size:22 final size:22
Alignment explanation
Indices: 6657--6709 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
6647 AATTAGCAAC
*
6657 TTTTCAAAAATTATACCTACTTA
1 TTTT-AAAAATTATACCCACTTA
6680 TTCTT-AAAATT-TACCCACTTA
1 TT-TTAAAAATTATACCCACTTA
6701 TTTTAAAAA
1 TTTTAAAAA
6710 ATAACCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 6 0.22
23 2 0.07
24 2 0.07
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAATTATACCCACTTA
Found at i:6717 original size:20 final size:21
Alignment explanation
Indices: 6675--6717 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
6665 AATTATACCT
** *
6675 ACTTATTCTTAAAATTTACCC
1 ACTTATTCTTAAAAAATAACC
6696 ACTTATT-TTAAAAAATAACC
1 ACTTATTCTTAAAAAATAACC
6716 AC
1 AC
6718 ATATAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (21 bp):
ACTTATTCTTAAAAAATAACC
Found at i:7046 original size:7 final size:7
Alignment explanation
Indices: 7034--7064 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
7024 AATTAGATTG
7034 AAGGTAA
1 AAGGTAA
7041 AAGGTAA
1 AAGGTAA
7048 AAGGTAA
1 AAGGTAA
7055 AAGGTAA
1 AAGGTAA
7062 AAG
1 AAG
7065 AAAAAAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (7 bp):
AAGGTAA
Found at i:8041 original size:13 final size:12
Alignment explanation
Indices: 7997--8056 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 12
7987 TTAAAATATT
7997 TTATATTTTATA
1 TTATATTTTATA
*
8009 -TAAATTTTA-A
1 TTATATTTTATA
*
8019 -AATATTTATATA
1 TTATATTT-TATA
8031 TT-TATTTTATA
1 TTATATTTTATA
8042 TTATATTTTA-A
1 TTATATTTTATA
8053 TTAT
1 TTAT
8057 TTTAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.15
11 21 0.52
12 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:8065 original size:18 final size:21
Alignment explanation
Indices: 7999--8065 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
7989 AAAATATTTT
**
7999 ATATTT-TATATAAATTTTAAA
1 ATATTTATATATTTATTTT-AA
8020 ATATTTATATATTTATTTTATA
1 ATATTTATATATTTATTTTA-A
8042 TTATATTT-TA-A-TTATTTTAA
1 --ATATTTATATATTTATTTTAA
8062 ATAT
1 ATAT
8066 ATAATCATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 4 0.10
20 1 0.03
21 15 0.38
22 12 0.30
23 2 0.05
24 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTATATATTTATTTTAA
Found at i:8607 original size:13 final size:13
Alignment explanation
Indices: 8573--8612 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
8563 TATGTTTAAA
* *
8573 AATAAAATAAAAT
1 AATAAAATTAATT
8586 AATAAAATTAATT
1 AATAAAATTAATT
8599 AATAAAATT-ATT
1 AATAAAATTAATT
8611 AA
1 AA
8613 AATATTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 5 0.20
13 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAAATTAATT
Found at i:8669 original size:20 final size:21
Alignment explanation
Indices: 8634--8672 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
8624 TATATTTAAT
*
8634 TTTAACTAAAATTAAATGTGA
1 TTTAACTAAAAATAAATGTGA
8655 TTTAA-TAAAAATAAATGT
1 TTTAACTAAAAATAAATGT
8673 AAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTAACTAAAAATAAATGTGA
Found at i:9850 original size:21 final size:20
Alignment explanation
Indices: 9809--9850 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
9799 ATCTATATTT
*
9809 TAAATTAAATCAAATTTAAA
1 TAAATTAAATCAAATTAAAA
9829 TAAATATAAAT-AATATTAAAA
1 TAAAT-TAAATCAA-ATTAAAA
9850 T
1 T
9851 TTTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATTAAATCAAATTAAAA
Found at i:10087 original size:2 final size:2
Alignment explanation
Indices: 10074--10137 Score: 58
Period size: 2 Copynumber: 32.0 Consensus size: 2
10064 TTGTACCCCA
* * * * **
10074 AT AT AT AC AT AT AT AT AT AT AT AT AT AA AT GT ACC CC A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
10116 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
10138 CCACCAGCCG
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:10116 original size:38 final size:38
Alignment explanation
Indices: 10065--10137 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
10055 ATTTACATTT
10065 TGTACCCCAATATATACATATATATATATATATATAAA
1 TGTACCCCAATATATACATATATATATATATATATAAA
*
10103 TGTACCCCAATATATATATATATATATATATATAT
1 TGTACCCCAATATATACATATATATATATATATAT
10138 CCACCAGCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (38 bp):
TGTACCCCAATATATACATATATATATATATATATAAA
Found at i:19817 original size:23 final size:23
Alignment explanation
Indices: 19773--19820 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19763 AACGTAATAA
*
19773 AAAATTATTAAATTATTAAAAAT
1 AAAATTATCAAATTATTAAAAAT
* * *
19796 AAAATTATCAATTTTTTTAAAAT
1 AAAATTATCAAATTATTAAAAAT
19819 AA
1 AA
19821 TATAAACCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATTATCAAATTATTAAAAAT
Found at i:20255 original size:3 final size:3
Alignment explanation
Indices: 20247--20287 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20237 AGCTCACTTC
20247 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20288 ACTTAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:21009 original size:16 final size:17
Alignment explanation
Indices: 20979--21011 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20969 GTTTTTTTTT
20979 AATTAAATTTAAATTGA
1 AATTAAATTTAAATTGA
*
20996 AATT-AATTTGAATTGA
1 AATTAAATTTAAATTGA
21012 TTCAATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
AATTAAATTTAAATTGA
Found at i:21059 original size:33 final size:33
Alignment explanation
Indices: 21022--21085 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
21012 TTCAATACTT
21022 ATTTTATTATTTA-AATAATATTAAAATATTTAA
1 ATTTTATT-TTTATAATAATATTAAAATATTTAA
* * *
21055 ATTTTATTTTTATATTAATATTTATATATTT
1 ATTTTATTTTTATAATAATATTAAAATATTT
21086 TTATAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
ATTTTATTTTTATAATAATATTAAAATATTTAA
Done.