Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold834
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: 5555
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.26
Warning! 648 characters in sequence are not A, C, G, or T
Found at i:158 original size:10 final size:10
Alignment explanation
Indices: 143--206 Score: 64
Period size: 10 Copynumber: 6.5 Consensus size: 10
133 TCAGTGGGGG
143 AAAAAAGCAA
1 AAAAAAGCAA
153 AAAAAAGCAA
1 AAAAAAGCAA
*
163 AAAAAACGAGAA
1 AAAAAA-G-CAA
175 AACAAAAGC-A
1 AA-AAAAGCAA
185 AAAAAA-C-A
1 AAAAAAGCAA
193 AAAAAA-CAA
1 AAAAAAGCAA
202 AAAAA
1 AAAAA
207 TAAAAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
8 9 0.19
9 10 0.21
10 19 0.40
11 1 0.02
12 5 0.10
13 4 0.08
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:191 original size:22 final size:23
Alignment explanation
Indices: 151--203 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
141 GGAAAAAAGC
* *
151 AAAA-AAAAGCAAAAAAAACGAG
1 AAAACAAAAGCAAAAAAAACAAA
173 AAAACAAAAGC-AAAAAAACAAA
1 AAAACAAAAGCAAAAAAAACAAA
195 AAAACAAAA
1 AAAACAAAA
204 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAACAAAAGCAAAAAAAACAAA
Found at i:211 original size:22 final size:22
Alignment explanation
Indices: 151--213 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
141 GGAAAAAAGC
* *
151 AAAA-AAAAGCAAAAAAAACGAG
1 AAAACAAAAG-AAAAAAAACAAA
*
173 AAAACAAAAGCAAAAAAACAAA
1 AAAACAAAAGAAAAAAAACAAA
*
195 AAAACAAAAAAATAAAAAA
1 AAAACAAAAGAA-AAAAAA
214 ATAAGAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.02
Consensus pattern (22 bp):
AAAACAAAAGAAAAAAAACAAA
Found at i:217 original size:8 final size:8
Alignment explanation
Indices: 152--214 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
142 GAAAAAAGCA
152 AAAAAAAGC
1 AAAAAAA-C
161 AAAAAAAAC
1 -AAAAAAAC
* *
170 GAGAAAAC
1 AAAAAAAC
*
178 --AAAAGC
1 AAAAAAAC
184 AAAAAAAC
1 AAAAAAAC
192 AAAAAAAC
1 AAAAAAAC
*
200 AAAAAAAT
1 AAAAAAAC
208 AAAAAAA
1 AAAAAAA
215 TAAGAGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 4 0.09
8 33 0.73
9 1 0.02
10 7 0.16
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:681 original size:18 final size:18
Alignment explanation
Indices: 641--688 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
631 ACTTTACTTT
*
641 AAAAAAAGAAACGAAAAG
1 AAAAAAAGAAAAGAAAAG
*
659 AAAAAAAGAAAAGAATA-
1 AAAAAAAGAAAAGAAAAG
*
676 ACAAAAAGAAAAG
1 AAAAAAAGAAAAG
689 GGAGAGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAGAAAAG
Found at i:1894 original size:88 final size:87
Alignment explanation
Indices: 1681--2001 Score: 401
Period size: 88 Copynumber: 3.7 Consensus size: 87
1671 GGTTGCAATG
* *
1681 GAGCTGGTCAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAAACAAAG
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAA-
* * **
1745 CCTTTCCTCTATCGGTTGCAGTG
65 CCTTGCCTCTATCGGTTGTAGCA
* * *
1768 GAGTTGGTTGAAGACAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAACACACAAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAA
* *
1833 CCTTGCATCTTTCGGTTGTAGCA
65 CCTTGCCTCTATCGGTTGTAGCA
* *
1856 GAGCTGGTTGAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAA
* *
1921 CCTTGCCTCTCTCGTTTGTAGCA
65 CCTTGCCTCTATCGGTTGTAGCA
* * * * ** *
1944 GAACTGGTTAAAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGACGCAGATCGAA
1 GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCA-TTAACAGCGAAGCAGATCGAA
2002 GATGGCAGAT
Statistics
Matches: 204, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
87 50 0.25
88 130 0.64
89 24 0.12
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (87 bp):
GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAC
CTTGCCTCTATCGGTTGTAGCA
Found at i:2024 original size:46 final size:46
Alignment explanation
Indices: 1974--2160 Score: 105
Period size: 46 Copynumber: 4.1 Consensus size: 46
1964 ATCATGCCTT
1974 CCTGTATTTGGCAG-CGACGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATTTGGCAGACGA-GCAGATCGAAGATGGCAGATTTTACCTC
* * * * * ** ** * * * *
2020 CCTGTGA-CT-ACAGACGAGTACATTGAAGCCGATA-ACTCTATCTT
1 CCTGT-ATTTGGCAGACGAGCAGATCGAAGATGGCAGATTTTACCTC
** ** * * * * * *
2064 CCTGTATTTGGCAGTGGAATAGATTGAAGATTGCATATCTTGCCTT
1 CCTGTATTTGGCAGACGAGCAGATCGAAGATGGCAGATTTTACCTC
2110 CCTGTATTTGGCAG-CGAAGCAGATCGAAGATGGCAGATTTTACCTC
1 CCTGTATTTGGCAGACG-AGCAGATCGAAGATGGCAGATTTTACCTC
2156 CCTGT
1 CCTGT
2161 GACTACAGAC
Statistics
Matches: 97, Mismatches: 38, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
43 1 0.01
44 12 0.12
45 29 0.30
46 54 0.56
47 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (46 bp):
CCTGTATTTGGCAGACGAGCAGATCGAAGATGGCAGATTTTACCTC
Found at i:2092 original size:45 final size:45
Alignment explanation
Indices: 2041--2228 Score: 105
Period size: 46 Copynumber: 4.2 Consensus size: 45
2031 AGACGAGTAC
* *
2041 ATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAATAG
1 ATTGAAGCCGATAACTCTACCTTCCTGTATTTGGCAGTCGAATAG
** * * *
2086 ATTGAAGATTGCATATCT-TGCCTTCCTGTATTTGGCAG-CGAAGCAG
1 ATTGAAG-CCG-ATAACTCTACCTTCCTGTATTTGGCAGTCGAA-TAG
* ** ** * * * * * * * *
2132 ATCGAAGATGGCAGATTTTACCTCCCTGTGA-CT-ACAGACGAGTAC
1 ATTGAAGCCGATA-ACTCTACCTTCCTGT-ATTTGGCAGTCGAATAG
* *
2177 ATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAATAG
1 ATTGAAGCCGATAACTCTACCTTCCTGTATTTGGCAGTCGAATAG
2222 ATTGAAG
1 ATTGAAG
2229 ATTGCANNNN
Statistics
Matches: 99, Mismatches: 35, Indels: 18
0.65 0.23 0.12
Matches are distributed among these distances:
43 1 0.01
44 13 0.13
45 39 0.39
46 40 0.40
47 6 0.06
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ATTGAAGCCGATAACTCTACCTTCCTGTATTTGGCAGTCGAATAG
Found at i:2198 original size:136 final size:136
Alignment explanation
Indices: 1954--2234 Score: 535
Period size: 136 Copynumber: 2.1 Consensus size: 136
1944 GAACTGGTTA
*
1954 AAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGACGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
2019 CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
66 CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
2084 AGATTG
131 AGATTG
* *
2090 AAGATTGCATATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
1 AAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
2155 CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
66 CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
2220 AGATTG
131 AGATTG
2226 AAGATTGCA
1 AAGATTGCA
2235 NNNNNNNNNN
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (136 bp):
AAGATTGCAGATCATGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTACCT
CCCTGTGACTACAGACGAGTACATTGAAGCCGATAACTCTATCTTCCTGTATTTGGCAGTGGAAT
AGATTG
Found at i:3250 original size:84 final size:84
Alignment explanation
Indices: 2884--3525 Score: 909
Period size: 84 Copynumber: 7.7 Consensus size: 84
2874 NNNNNNNNNT
* * *
2884 CCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGAGCGGACAAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
**
2949 A-CCA-CAGATCTTATCTC
66 AGAAACCAGATCTTATCTC
* *
2966 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGAGCGGACAAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
** * *
3031 A-CCA-TAGATCTGATCTC
66 AGAAACCAGATCTTATCTC
*
3048 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGCGGAGCAGACAAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
**
3113 A-CCA-CAGATCTTATCTC
66 AGAAACCAGATCTTATCTC
* * *
3130 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTTCCTAAGTAATAGTGGAGCAGACAAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
*
3195 AGAAACCAGATTTTATCTC
66 AGAAACCAGATCTTATCTC
* * * * * *
3214 CCTAAGCAGTAGTGGAGCAGATCACATCAACTCTTATCTACCTAAACAGTAGTGGAGCAGACGAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
3279 AGAAACCAGATCTTATCTC
66 AGAAACCAGATCTTATCTC
* * *
3298 CCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
3363 AGAAACCAGATCTTATCTC
66 AGAAACCAGATCTTATCTC
* * * * * *
3382 CCTAAGCAGTAGTGGAGCAAATCACATCAAGTCTTATCTCCCTAAGAAATAGTGGAGCAGACGAA
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
*
3447 AGAAACTAGATCTTATCTC
66 AGAAACCAGATCTTATCTC
* * *
3466 CCTAAGCAGTGGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAACAGTAGTGGAGCAG
1 CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAG
3526 GTTGAAGATA
Statistics
Matches: 523, Mismatches: 35, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
82 220 0.42
83 1 0.00
84 302 0.58
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (84 bp):
CCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAA
AGAAACCAGATCTTATCTC
Done.