Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold986
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: 3606
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.29
Warning! 516 characters in sequence are not A, C, G, or T
Found at i:1540 original size:116 final size:114
Alignment explanation
Indices: 1336--1897 Score: 845
Period size: 111 Copynumber: 4.9 Consensus size: 114
1326 AAAATTATTT
* *
1336 TTTTGTGGCGTTTTTTATAAAAAACGCCGCTAAATGTTTTGCTATATAAAATGACTATTTTTTAA
1 TTTTGCGGCG-TTTTTAT-AAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAA
*
1401 ATTAAAATTATTTTTTGTGGCGTTTTTTATAAAACGCCGCTATTGCTTACC
64 AGTAAAATTATTTTTTGTGGCGTTTTTTATAAAACGCCGCTATTGCTTACC
* * *
1452 TTTTGCGGTGTTTTTTTATAAAAACACCGCTAAATATTTTGCTATATAAAATGGCTATTTTTTAA
1 TTTTGCGGCG--TTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAA
1517 AGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTACC
64 AGTAAAATTATTTTTTGTGGCGTTTTTTAT-AAAACGCCGCTATTGCTTACC
*
1569 TTTTGCGGCG--TTT-T-AAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTATAG
1 TTTTGCGGCGTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAAAG
*
1630 TAAAATTATTTTTTGTGACGTTTTTTTTATAAAACGCCGCTATTGCTTACC
66 TAAAATTATTTTTTGTGGCG--TTTTTTATAAAACGCCGCTATTGCTTACC
* *
1681 TTTTGTGGC----ATA-AAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAAAG
1 TTTTGCGGCGTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAAAG
* *
1741 TAAAATTATTTTTTGTGGTGTTTTTTATAAAACACCGCTATTGCTTACC
66 TAAAATTATTTTTTGTGGCGTTTTTTATAAAACGCCGCTATTGCTTACC
* *
1790 TTTTGCAGCGTTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCTATTTTTTTTAA
1 TTTTGCGGCGTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTA--TTTTTTAA
1855 AGTAAAATTATTTTTTGTGGCGTTTTTTATAAAAACGCCGCTA
64 AGTAAAATTATTTTTTGTGGCGTTTTTTAT-AAAACGCCGCTA
1898 AATTTTTTGC
Statistics
Matches: 409, Mismatches: 23, Indels: 27
0.89 0.05 0.06
Matches are distributed among these distances:
109 35 0.09
110 1 0.00
111 127 0.31
112 30 0.07
113 13 0.03
114 37 0.09
116 117 0.29
117 49 0.12
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (114 bp):
TTTTGCGGCGTTTTTATAAAAACGCCGCTAAATGTTTTGCTATATAAAATGGCTATTTTTTAAAG
TAAAATTATTTTTTGTGGCGTTTTTTATAAAACGCCGCTATTGCTTACC
Found at i:1896 original size:78 final size:79
Alignment explanation
Indices: 1800--1974 Score: 284
Period size: 79 Copynumber: 2.2 Consensus size: 79
1790 TTTTGCAGCG
1800 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAAT-G-GCTATTTTTTTTAAAGTAAAAT
1 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTA-TTTTTTTAAAGTAAAAT
1863 TATTTTTTGTGGCGT
65 TATTTTTTGTGGCGT
* *
1878 TTTTTATAAAAACGCCGCTAAATTTTTTGCTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
1 TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
1943 ATTTTTTGTGGCGT
66 ATTTTTTGTGGCGT
*
1957 TTTTCT-TTAAAACGCCGC
1 TTTT-TATAAAAACGCCGC
1975 AAAAAATTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
78 38 0.42
79 48 0.53
80 5 0.05
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.45
Consensus pattern (79 bp):
TTTTTATAAAAACGCCGCTAAATGTTTTACTATATAAAATGGCGCTATTTTTTTAAAGTAAAATT
ATTTTTTGTGGCGT
Found at i:2855 original size:96 final size:93
Alignment explanation
Indices: 2737--2922 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 93
2727 CTAACTCTTA
*
2737 ACCCCAAACCCTAAACCACTAA-CCTCTAAACCTTATTTAATATAGAAATTAAAAAAACACTAAT
1 ACCCCAAACCCTAAACCACTAACCCT-TAAACATTATTTAATATAGAAATT-AAAAAACACTAAT
*
2801 TAATCTAAATCATAAACCCTAACCCTAACCCG
64 TAATCTAAACCATAAACCC-AA-CCTAACCCG
* * *
2833 ACCCCAAATCCCTAATCC-CTAACCCTTAAACATTATTTAATATATAAATTAAAATACACTAATT
1 ACCCCAAA-CCCTAAACCACTAACCCTTAAACATTATTTAATATAGAAATTAAAAAACACTAATT
*
2897 AATCTAAACCCTAAACCCAACCTAAC
65 AATCTAAACCATAAACCCAACCTAAC
2923 TTATTTAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
93 6 0.07
94 2 0.02
95 29 0.35
96 34 0.41
97 11 0.13
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (93 bp):
ACCCCAAACCCTAAACCACTAACCCTTAAACATTATTTAATATAGAAATTAAAAAACACTAATTA
ATCTAAACCATAAACCCAACCTAACCCG
Found at i:3127 original size:89 final size:89
Alignment explanation
Indices: 3015--3190 Score: 244
Period size: 89 Copynumber: 2.0 Consensus size: 89
3005 CTAACTCTTA
* * * *
3015 ACCCCAAACCCCAAACTACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACATTAATCA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
*
3080 ATCTAAATCATAAACCCTAACTCG
66 ATCTAAACCATAAACCCTAACTCG
* * * * * *
3104 ACCCCAAATCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTA
1 ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
*
3169 ATCTAAACCCTAAACCCTAACT
66 ATCTAAACCATAAACCCTAACT
3191 TGACACTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (89 bp):
ACCCCAAACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCA
ATCTAAACCATAAACCCTAACTCG
Found at i:3188 original size:278 final size:274
Alignment explanation
Indices: 2663--3185 Score: 863
Period size: 278 Copynumber: 1.9 Consensus size: 274
2653 NNNNNNNNNA
* * * *
2663 AAAAATACTAATTAATCTAAACCTTAAACCCTAACTCGACCCTAAATCTTTAAACCCTAGATAAC
1 AAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCCCAAATCTCTAAACCCTAAATAAC
*
2728 TAACTCTTAACCCCAAACCCTAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAA
66 TAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAA
* *
2793 ACACTAATTAATCTAAATCATAAACCCTAACCCTAACCCGACCCCAAATCCCTAATCCCTAACCC
131 ACACTAATCAATCTAAATCATAAACCCTAA-CCT-A--CGACCCCAAATCCCTAACCCCTAACCC
* *
2858 TTAAACATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACCCTAAACCCAACCTAAC
192 CTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCAACCTAAC
2923 TTATTTAAGATATAAATT
257 TTATTTAAGATATAAATT
* * *
2941 AAAAATACTAATTAATCTAAACCTTAAAACTTAACTCGACCCCGAATCTCTAAACCCTAAATCAC
1 AAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCCCAAATCTCTAAACCCTAAATAAC
*
3006 TAACTCTTAACCCCAAACCCCAAACTACTAACCTCTAAACCTTATTTAATATAGAAATT-AAAAA
66 TAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAA
*
3070 ACATTAATCAATCTAAATCATAAACCCTAA-CT-CGACCCCAAATCCCTAACCCCTAACCCCTAA
131 ACACTAATCAATCTAAATCATAAACCCTAACCTACGACCCCAAATCCCTAACCCCTAACCCCTAA
3133 ACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCC
196 ACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCC
3186 TAACTTGACA
Statistics
Matches: 231, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
271 81 0.35
275 2 0.01
277 33 0.14
278 115 0.50
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.26
Consensus pattern (274 bp):
AAAAATACTAATTAATCTAAACCTTAAAACCTAACTCGACCCCAAATCTCTAAACCCTAAATAAC
TAACTCTTAACCCCAAACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAA
ACACTAATCAATCTAAATCATAAACCCTAACCTACGACCCCAAATCCCTAACCCCTAACCCCTAA
ACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCAACCTAACTTAT
TTAAGATATAAATT
Found at i:3213 original size:89 final size:89
Alignment explanation
Indices: 3033--3214 Score: 238
Period size: 89 Copynumber: 2.0 Consensus size: 89
3023 CCCCAAACTA
* * * *
3033 CTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACATTAATCAATCTAAATCATAAACCCT
1 CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
* * *
3098 AACTCGACCCCAAATCCCTAACCC
66 AACTCGACACCAAATCCATAAACC
* * * *
3122 CTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCT
1 CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
* * *
3187 AACTTGACACTAAATCTATAAACC
66 AACTCGACACCAAATCCATAAACC
3211 CTAA
1 CTAA
3215 ATCCCTAACT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (89 bp):
CTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATCAATCTAAACCATAAACCCT
AACTCGACACCAAATCCATAAACC
Found at i:3242 original size:14 final size:14
Alignment explanation
Indices: 3207--3271 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
3197 TAAATCTATA
* *
3207 AACCCTAAATCCCT
1 AACCCTTAACCCCT
* *
3221 AACTCTTAACCTCT
1 AACCCTTAACCCCT
3235 AACCCTTAACCCCT
1 AACCCTTAACCCCT
* *
3249 AACCCCTAACCCAT
1 AACCCTTAACCCCT
*
3263 AAACCTTAA
1 AACCCTTAA
3272 ATCACAACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTTAACCCCT
Found at i:3310 original size:14 final size:15
Alignment explanation
Indices: 3291--3323 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3281 CTTAAATTAG
3291 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
3305 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
3320 AATC
1 AATC
3324 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Done.