Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1901
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: 22260
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:56 original size:15 final size:16
Alignment explanation
Indices: 23--63 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
13 TATGCACCAC
*
23 TAAAAATGTGAATAGA
1 TAAAAATATGAATAGA
*
39 TAAAAATATTAATA-A
1 TAAAAATATGAATAGA
54 TAAAAA-ATGA
1 TAAAAATATGA
64 CATATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 3 0.14
15 7 0.32
16 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (16 bp):
TAAAAATATGAATAGA
Found at i:6100 original size:35 final size:36
Alignment explanation
Indices: 6022--6100 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 36
6012 ATAAATACAT
*
6022 TTATTTATTTAGTTTTATATTATTCATATTTAAATA
1 TTATTTATTTAGATTTATATTATTCATATTTAAATA
*
6058 TGT-TTTATTT-GATTTA-ATTAATT-TTATTTAAAATA
1 T-TATTTATTTAGATTTATATT-ATTCATATTT-AAATA
6093 TTATTTAT
1 TTATTTAT
6101 ATCATTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
34 9 0.24
35 19 0.51
36 8 0.22
37 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (36 bp):
TTATTTATTTAGATTTATATTATTCATATTTAAATA
Found at i:6377 original size:12 final size:12
Alignment explanation
Indices: 6354--6384 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
6344 TGAACCAAAC
6354 TCTTTCTTCTTCT
1 TCTTT-TTCTTCT
6367 TCTTTTTCTTCT
1 TCTTTTTCTTCT
6379 TCTTTT
1 TCTTTT
6385 CGTTCTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:6971 original size:2 final size:2
Alignment explanation
Indices: 6959--6994 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6949 TGAAATTGTA
*
6959 AT AT AT CT 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
6995 GGTGGTGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8346 original size:30 final size:30
Alignment explanation
Indices: 8301--8369 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
8291 AGGGTTTATT
8301 TAAATATAAAAATTAATAATTTATTTAAATA
1 TAAAT-TAAAAATTAATAATTTATTTAAATA
* * *
8332 TAAATTAAAGATTAATAATTTATTTAAGTT
1 TAAATTAAAAATTAATAATTTATTTAAATA
8362 TAAATTAA
1 TAAATTAA
8370 TTTTTATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TAAATTAAAAATTAATAATTTATTTAAATA
Found at i:8565 original size:16 final size:16
Alignment explanation
Indices: 8544--8584 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
8534 AAATTAGATT
8544 AATTCAATCGAATTTA
1 AATTCAATCGAATTTA
8560 AATTCAATCGAATTTA
1 AATTCAATCGAATTTA
8576 AATTCAATC
1 AATTCAATC
8585 TAACTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (16 bp):
AATTCAATCGAATTTA
Found at i:8670 original size:22 final size:22
Alignment explanation
Indices: 8639--8693 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
8629 TTTAAACATA
8639 AAATAATTAAATTTGATAAATTC
1 AAAT-ATTAAATTTGATAAATTC
* * *
8662 AAGTATTAAATTTGATTAATTT
1 AAATATTAAATTTGATAAATTC
8684 AAATATTAAA
1 AAATATTAAA
8694 GTAGAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATATTAAATTTGATAAATTC
Found at i:8801 original size:23 final size:23
Alignment explanation
Indices: 8752--8819 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 23
8742 AACTTAAATC
*
8752 AAATAAATTTAAAATTAAAATAATTAA
1 AAAT-AATATAAAATT-AAAT--TTAA
8779 AAATTAATAT-AAATTAAATTTAA
1 AAA-TAATATAAAATTAAATTTAA
8802 AAATAATATAAAATTAAA
1 AAATAATATAAAATTAAA
8820 AAAATTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 6 0.16
23 15 0.39
25 4 0.11
26 5 0.13
27 7 0.18
28 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATAATATAAAATTAAATTTAA
Found at i:8805 original size:33 final size:31
Alignment explanation
Indices: 8747--8831 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 31
8737 TAATTAACTT
*
8747 AAATCAAATAAATTTAAAATTAAAATAAT-TAA
1 AAATTAAATAAA-TTAAAATTAAAATAATAT-A
*
8779 AAATTAATATAAATTAAATTTAAAAATAATATA
1 AAATTAA-ATAAATTAAAATT-AAAATAATATA
*
8812 AAATTAAAAAAATTAAAATT
1 AAATTAAATAAATTAAAATT
8832 GACCTAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 24 0.52
33 21 0.46
34 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (31 bp):
AAATTAAATAAATTAAAATTAAAATAATATA
Found at i:8831 original size:38 final size:37
Alignment explanation
Indices: 8755--8828 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
8745 TTAAATCAAA
* *
8755 TAAATTTAAAATTAAAATAATTAAAAATTAATATAAAT
1 TAAATTTAAAAATAAAAAAATTAAAAA-TAATATAAAT
8793 TAAATTTAAAAATAATATAAAATTAAAAA-AAT-TAAA
1 TAAATTTAAAAATAA-A-AAAATTAAAAATAATATAAA
8829 ATTGACCTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 4 0.12
38 17 0.53
39 1 0.03
40 10 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (37 bp):
TAAATTTAAAAATAAAAAAATTAAAAATAATATAAAT
Found at i:14301 original size:2 final size:2
Alignment explanation
Indices: 14296--14325 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14286 ATTCACACAC
14296 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
14326 TTGCTCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14701 original size:23 final size:23
Alignment explanation
Indices: 14675--14735 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
14665 TATATAAAAT
*
14675 AAATATAATATAAAAAATAATTA
1 AAATATAATATAAAAAATAATAA
*
14698 AAATAT-ATAATAAAATATAATAA
1 AAATATAAT-ATAAAAAATAATAA
*
14721 AAAAATACATATAAA
1 AAATATA-ATATAAA
14736 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.06
23 23 0.72
24 5 0.16
25 2 0.06
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
AAATATAATATAAAAAATAATAA
Found at i:14720 original size:44 final size:43
Alignment explanation
Indices: 14658--14805 Score: 117
Period size: 44 Copynumber: 3.4 Consensus size: 43
14648 AGATTACTCG
* * *
14658 ATATAATTATATAAAATAAATATAATATAAAAAATAATTAAAAT
1 ATATAATAAAATATAATAAATATAATATAAAAAAT-ATTAAAAT
* * * *
14702 ATATAATAAAATATAATAAA-AAAATACATATAAATA-TAAAAA
1 ATATAATAAAATATAATAAATATAATATA-AAAAATATTAAAAT
* *
14744 ATATATTAAAAT-TTATATAATATAA-ATTAATAAAATATTAAAAT
1 ATATAATAAAATATAATA-AATATAATA-TAA-AAAATATTAAAAT
*
14788 TTAT-ATAAATATATAATA
1 ATATAATAAA-ATATAATA
14806 TTTTAAATTT
Statistics
Matches: 80, Mismatches: 16, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
41 4 0.05
42 20 0.25
43 20 0.25
44 32 0.40
45 4 0.05
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (43 bp):
ATATAATAAAATATAATAAATATAATATAAAAAATATTAAAAT
Found at i:14766 original size:17 final size:17
Alignment explanation
Indices: 14746--14795 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
14736 TATAAAAAAT
14746 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
* *
14763 ATA-T-AAATTAATAAA
1 ATATTAAAATTTATATA
14778 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
14795 A
1 A
14796 ATATATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:14782 original size:32 final size:35
Alignment explanation
Indices: 14729--14806 Score: 117
Period size: 32 Copynumber: 2.3 Consensus size: 35
14719 AAAAAAATAC
14729 ATATAAATATAAAAAATATATTAAAATTTATAT-A
1 ATATAAATATAAAAAATATATTAAAATTTATATAA
*
14763 ATATAAAT-TAATAAA-ATATTAAAATTTATATAA
1 ATATAAATATAAAAAATATATTAAAATTTATATAA
14796 ATATATAATAT
1 ATATA-AATAT
14807 TTTAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 16 0.40
33 12 0.30
34 11 0.28
35 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
ATATAAATATAAAAAATATATTAAAATTTATATAA
Found at i:14805 original size:25 final size:28
Alignment explanation
Indices: 14763--14816 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
14753 AATTTATATA
14763 ATATAAATTAATAAAATA-TTAAAATTT
1 ATATAAATTAATAAAATATTTAAAATTT
* *
14790 ATATAAA-T-ATATAATATTTTAAATTT
1 ATATAAATTAATAAAATATTTAAAATTT
14816 A
1 A
14817 ATTATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 10 0.42
27 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATAAATTAATAAAATATTTAAAATTT
Found at i:14837 original size:61 final size:63
Alignment explanation
Indices: 14666--14838 Score: 144
Period size: 61 Copynumber: 2.8 Consensus size: 63
14656 CGATATAATT
* ** * * *
14666 ATATAAA-ATAAATATA-ATATAAAAAATAATTAAAATATATAATAAAATATAATAAAAAAATAC
1 ATATAAATATAAAAATATAT-TAAAATTTAATTATAATA-AAAATAAAATAAAATAAAAAAATAC
* * ** **
14729 ATATAAATATAAAAAATATATTAAAATTT-A-TATAATATAAAT-TAATAAAATATTAAAATTT
1 ATATAAATAT-AAAAATATATTAAAATTTAATTATAATAAAAATAAAATAAAATAAAAAAATAC
* *
14790 ATATAAATAT-ATAATAT-TTTAAATTTAATTATAATAAAAATAAAATAAA
1 ATATAAATATAAAAATATATTAAAATTTAATTATAATAAAAATAAAATAAA
14839 TGTAATATGA
Statistics
Matches: 88, Mismatches: 16, Indels: 14
0.75 0.14 0.12
Matches are distributed among these distances:
58 8 0.09
59 7 0.08
60 11 0.12
61 29 0.33
62 3 0.03
63 13 0.15
64 3 0.03
65 12 0.14
66 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (63 bp):
ATATAAATATAAAAATATATTAAAATTTAATTATAATAAAAATAAAATAAAATAAAAAAATAC
Found at i:15141 original size:2 final size:2
Alignment explanation
Indices: 15136--15178 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
15126 TGTGTGTGTG
*
15136 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15178 T
1 T
15179 CAATCTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18888 original size:193 final size:193
Alignment explanation
Indices: 18503--19026 Score: 881
Period size: 193 Copynumber: 2.7 Consensus size: 193
18493 ACAAGTAAAT
* *
18503 CTCCTAAAATTTCTTTTGTATGCTACTTAATCACCGTCTATTTGAGTGTAAGATGCAAGTTTGTA
1 CTCCTAAAATTTCTTTTGTATACTACTTAATCACCATCTATTTGAGTGTAAGATGCAAGTTTGTA
* * *
18568 TCTAAAATGAATATAGTTAAATTTTTTAAAAATTTTTTTTATATATTTAAAATATCATACCTTTT
66 TCTGAAATGAGTATAGTTAAATTTTTTAAAAA-TTTTTTTATATATTTAAAAAATCATACCTTTT
18633 GTAGTCATGTTCGAATATGTATTTGACATAGATTACTTTGCTTTTCGATATTCGTTTAAGTCTC
130 GTAGTCATGTTCGAATATGTATTTGACATAGATTACTTTGCTTTTCGATATTCGTTTAAGTCTC
18697 CTCCTAAAATTTCTTTTGTATACTACTTAATCACCATCTATTTGAGTGTAAGATGCAAGTTTGTA
1 CTCCTAAAATTTCTTTTGTATACTACTTAATCACCATCTATTTGAGTGTAAGATGCAAGTTTGTA
18762 TCTGAAATGAGTATAGTTAAATTTTTTAAAAATTTTTTTATATATTTAAAAAATCATACCTTTTG
66 TCTGAAATGAGTATAGTTAAATTTTTTAAAAATTTTTTTATATATTTAAAAAATCATACCTTTTG
18827 TAGTCATGTTCGAATATGTATTTGACATAGATTACTTTGCTTTTCGATATTCGTTTAAGTCTC
131 TAGTCATGTTCGAATATGTATTTGACATAGATTACTTTGCTTTTCGATATTCGTTTAAGTCTC
*
18890 CTCCTAAAATTTCTTTTGTATACTACTTAATCATCATCTATTTGAGTGTAAGATGCAAGTTTGTA
1 CTCCTAAAATTTCTTTTGTATACTACTTAATCACCATCTATTTGAGTGTAAGATGCAAGTTTGTA
* * * * * *
18955 TATGAAATGAGTGTAGTTAAATTTGTGT--AAGTTTTTTTCATATATTTAAAGAATCATATCTTT
66 TCTGAAATGAGTATAGTTAAATTT-TTTAAAAATTTTTTT-ATATATTTAAAAAATCATACCTTT
* *
19018 CGTATTCAT
129 TGTAGTCAT
19027 ATCTGAATAT
Statistics
Matches: 314, Mismatches: 14, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
192 9 0.03
193 210 0.67
194 95 0.30
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (193 bp):
CTCCTAAAATTTCTTTTGTATACTACTTAATCACCATCTATTTGAGTGTAAGATGCAAGTTTGTA
TCTGAAATGAGTATAGTTAAATTTTTTAAAAATTTTTTTATATATTTAAAAAATCATACCTTTTG
TAGTCATGTTCGAATATGTATTTGACATAGATTACTTTGCTTTTCGATATTCGTTTAAGTCTC
Found at i:22001 original size:2 final size:2
Alignment explanation
Indices: 21988--22040 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
21978 ATTTTTATTT
* * *
21988 TA TA TC TA TA TA TA TA TA TA TA CTA TA TA TA -A TT TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
22030 TT TA TA TA TA T
1 TA TA TA TA TA T
22041 TTATGAGATT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.