Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1157
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: 36800
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Found at i:2180 original size:27 final size:27
Alignment explanation
Indices: 2149--2326 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
2139 TAAATTGTAC
2149 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
2176 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2202 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
2230 GGCACTAAGTGTGCGAGTTTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
2258 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
2285 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
2312 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2327 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 105 0.83
28 22 0.17
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:2266 original size:82 final size:81
Alignment explanation
Indices: 2150--2305 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
2140 AAATTGTACA
* * *
2150 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
2214 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
2231 GCACTAAGTGTGCGAGTTTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
2296 TGCGAGTTGA
65 TGCGAATTGA
2306 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:2317 original size:82 final size:81
Alignment explanation
Indices: 2146--2326 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
2136 GATTAAATTG
* * *
2146 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
2211 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
2227 TGCGGCACTAAGTGTGCGAGTTTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
2291 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
2309 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
2327 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:3925 original size:43 final size:43
Alignment explanation
Indices: 3809--3927 Score: 116
Period size: 43 Copynumber: 2.8 Consensus size: 43
3799 AGGAAAAAAA
* * * * * *
3809 CTCGTTGAGTGGTCCAGGTTCGTGATATATGTG-GCATCCGAG
1 CTCGTTGAGTGGTTCAAGTTCATAATAGATGCGAGCATCCGAG
* * * * *
3851 CTCGTTGAGTGG-TCTGAGCTCATTATGGATGCGAGCATCTGAG
1 CTCGTTGAGTGGTTC-AAGTTCATAATAGATGCGAGCATCCGAG
3894 CTCGTTGAGTGGTTCAAGTTCATAATAGATGCGA
1 CTCGTTGAGTGGTTCAAGTTCATAATAGATGCGA
3928 TACATGTGAT
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.02
42 22 0.37
43 35 0.58
44 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (43 bp):
CTCGTTGAGTGGTTCAAGTTCATAATAGATGCGAGCATCCGAG
Found at i:9765 original size:19 final size:19
Alignment explanation
Indices: 9730--9767 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
9720 TTGCAATTTA
*
9730 AATTTTTATGTTCTTTTCT
1 AATTTTTATGTTATTTTCT
9749 AATTCTTTAT-TTATTTTCT
1 AATT-TTTATGTTATTTTCT
9768 TCTGACAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.68
Consensus pattern (19 bp):
AATTTTTATGTTATTTTCT
Found at i:17380 original size:39 final size:39
Alignment explanation
Indices: 17201--17364 Score: 276
Period size: 39 Copynumber: 4.2 Consensus size: 39
17191 TATACATATA
* *
17201 TGCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
* *
17240 TGCTTCAGTTAGCCTTCGGGCTTTCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
17279 TGCTTCAGTTAGCC-TCTGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTC-GGGCTTCCATTTAGCACTTATG
17318 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
17357 TGCTTCAG
1 TGCTTCAG
17365 CAAGATTTCA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
38 2 0.02
39 115 0.97
40 2 0.02
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
Found at i:29554 original size:31 final size:31
Alignment explanation
Indices: 29513--29619 Score: 110
Period size: 31 Copynumber: 3.4 Consensus size: 31
29503 GTGAAAGCAG
*
29513 TAGCTTCGGCTACCTGATCAGTGAAAAGTGT
1 TAGCTCCGGCTACCTGATCAGTGAAAAGTGT
* * *
29544 TAGCTCCGGCTACCTGAT-AGATAAAAAAATGG
1 TAGCTCCGGCTACCTGATCAG-T-GAAAAGTGT
* *
29576 TAGCTCCAGCTACCTGATCAGTGAATAGTGGT
1 TAGCTCCGGCTACCTGATCAGTGAAAAGT-GT
*
29608 T-GCTTCGGCTAC
1 TAGCTCCGGCTAC
29620 AAGTGACAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
30 2 0.03
31 31 0.51
32 26 0.43
33 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (31 bp):
TAGCTCCGGCTACCTGATCAGTGAAAAGTGT
Found at i:31654 original size:77 final size:77
Alignment explanation
Indices: 31523--31687 Score: 269
Period size: 77 Copynumber: 2.1 Consensus size: 77
31513 TTCTAACATA
* *
31523 TATG-CTTCAGTTAGCCTCCGAGCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTT
1 TATGTCTTCAGTTAGCCTCCGAGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGAGCTT
31587 CCATTTAGCACT
66 CCATTTAGCACT
* *
31599 TATGTCTTCAGTTAGCCTCTGGGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGAGCTT
1 TATGTCTTCAGTTAGCCTCCGAGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGAGCTT
*
31664 CCTTTTAGCACT
66 CCATTTAGCACT
31676 TATGTGCTTCAG
1 TATGT-CTTCAG
31688 CTAGATTTGG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 4 0.05
77 72 0.88
78 6 0.07
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (77 bp):
TATGTCTTCAGTTAGCCTCCGAGCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGAGCTT
CCATTTAGCACT
Found at i:31703 original size:39 final size:39
Alignment explanation
Indices: 31525--31687 Score: 258
Period size: 39 Copynumber: 4.2 Consensus size: 39
31515 CTAACATATA
* * *
31525 TGCTTCAGTTAGCCTCCGAGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
31564 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
31603 T-CTTCAGTTAGCC-TCTGGGCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTC-GGGCTTCCATTTAGCACTTATG
* *
31641 TGCTTCAGTTAGCCTTCGAGCTTCCTTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
31680 TGCTTCAG
1 TGCTTCAG
31688 CTAGATTTGG
Statistics
Matches: 116, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
37 2 0.02
38 35 0.30
39 77 0.66
40 2 0.02
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATG
Found at i:33077 original size:31 final size:31
Alignment explanation
Indices: 33039--33157 Score: 132
Period size: 31 Copynumber: 3.8 Consensus size: 31
33029 ACAAATGACA
* * *
33039 AGTGAAAAGTAGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
33070 AGTGAAAAGTGGTAGCTCCGGCTACCTGAT-
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
** *
33100 AGAAAAAAAAATGGTAGCTCCGGCTACCTGATC
1 AG--TGAAAAGTGGTAGCTCCGGCTACCTGATC
* * *
33133 AGTGAATAGTGGTTGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
33158 AAGTGACAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
30 2 0.03
31 44 0.60
32 25 0.34
33 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:33240 original size:46 final size:47
Alignment explanation
Indices: 33173--33266 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 47
33163 ACAAGTGATT
*
33173 TCCGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGA
* * * * *
33219 TCCGTGTAAGACCATGGCTGGGCTATGGCTTCGGTGTGTGATATGTGA
1 TCCGTATAAGACCATAGCTGGGATATGGCATC-GAGTGTGATATGTGA
33267 CTATGCGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 27 0.68
48 13 0.32
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (47 bp):
TCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGA
Found at i:35109 original size:38 final size:39
Alignment explanation
Indices: 35040--35213 Score: 252
Period size: 38 Copynumber: 4.6 Consensus size: 39
35030 TATACATATA
*
35040 TGCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
35079 TGCTTCAGTTAGCCTTC-GGCTTCCGTTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
* *
35117 TGCTTCAGGTAGCC-T---GCTTCCATTTAGCACTTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
35152 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCA-TTATG
1 TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
* **
35190 TGCTTCAGCTAGATTTCGGGCTTC
1 TGCTTCAGTTAGCCTTCGGGCTTC
35214 AGATCACGAT
Statistics
Matches: 123, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
35 32 0.26
36 1 0.01
37 1 0.01
38 60 0.49
39 29 0.24
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (39 bp):
TGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATG
Found at i:35163 original size:73 final size:73
Alignment explanation
Indices: 35059--35197 Score: 253
Period size: 73 Copynumber: 1.9 Consensus size: 73
35049 TAGCCTCCGG
*
35059 GCTTCCGTTTAGCACTTATGTGCTTCAGTTAGCCTTC-GGCTTCCGTTTAGCACTTATGTGCTTC
1 GCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCA-TTATGTGCTTC
35123 AGGTAGCCT
65 AGGTAGCCT
35132 GCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCATTATGTGCTTCA
1 GCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCATTATGTGCTTCA
35197 G
66 G
35198 CTAGATTTCG
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 49 0.77
74 15 0.23
ACGTcount: A:0.14, C:0.25, G:0.22, T:0.39
Consensus pattern (73 bp):
GCTTCCATTTAGCACTTATGTGCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCATTATGTGCTTCA
GGTAGCCT
Found at i:36556 original size:31 final size:30
Alignment explanation
Indices: 36518--36634 Score: 148
Period size: 31 Copynumber: 3.8 Consensus size: 30
36508 ACAAATGACA
*
36518 AGTGAAAAGTAGTAGCTTCGGCTACCTGAT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGAT
*
36548 CAGTGAAAAGTGGTAGCTCCGGCTACCTGAT
1 -AGTGAAAAGTGGTAGCTTCGGCTACCTGAT
*
36579 AGAT-AAAAATGGTAGC-TCTGGCTACCTGATT
1 AG-TGAAAAGTGGTAGCTTC-GGCTACCTGA-T
*
36610 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
36635 AAGTGGCAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.01
30 24 0.32
31 48 0.64
32 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (30 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGAT
Done.