Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2680
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: 42296
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:866 original size:56 final size:56
Alignment explanation
Indices: 801--971 Score: 283
Period size: 56 Copynumber: 3.1 Consensus size: 56
791 ACAAGGGATG
* *
801 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
*
857 ATGGGCAAAACATGTCATGAAACATGTT-TGTGTAATTGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGT-TAATGGAAGAATAAAATAAGAAGC
*
913 AT-GGAAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
968 ATGG
1 ATGG
972 ATAAACTAAT
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
55 52 0.49
56 55 0.51
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:953 original size:55 final size:55
Alignment explanation
Indices: 807--977 Score: 272
Period size: 55 Copynumber: 3.1 Consensus size: 55
797 GATGATGGGC
* * *
807 AAAACATGTCATGAAACATGTTGTGTTAATGGAAAAAAAAAATAAGAAGCATGGGC
1 AAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCAT-GGA
*
863 AAAACATGTCATGAAACATGTT-TGTGTAATTGAAGAATAAAATAAGAAGCATGGA
1 AAAACATGTCATGAAACATGTTGTGT-TAATGGAAGAATAAAATAAGAAGCATGGA
918 AAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGA
1 AAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGA
*
973 TAAAC
1 AAAAC
978 TAATAAGAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
55 59 0.55
56 48 0.45
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.23
Consensus pattern (55 bp):
AAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGA
Found at i:2228 original size:79 final size:81
Alignment explanation
Indices: 2092--2274 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
2082 TCGAATGATG
* *
2092 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
2156 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
2171 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
2233 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
2251 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
2275 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:2290 original size:40 final size:40
Alignment explanation
Indices: 2093--2276 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
2083 CGAATGATGT
* * * *
2093 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
2133 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
2173 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2211 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
2252 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
2277 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:2298 original size:79 final size:79
Alignment explanation
Indices: 2145--2309 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
2135 GGACTAAGAT
* **
2145 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
2210 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
2224 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
2287 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
2303 CCGAAGG
1 CCGAAGG
2310 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:8957 original size:40 final size:40
Alignment explanation
Indices: 8898--9079 Score: 260
Period size: 40 Copynumber: 4.6 Consensus size: 40
8888 TATTCGGATG
**
8898 ATAACCGGGCTAAACCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
8938 ATAACCGGGCTAAGTCCCGAAGGTATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
8978 ATAACCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
9018 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* **
9058 ATATCC-GGCTAAACCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
9080 TACTTGGTTG
Statistics
Matches: 129, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 16 0.12
40 113 0.88
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:19932 original size:40 final size:40
Alignment explanation
Indices: 19805--19948 Score: 191
Period size: 40 Copynumber: 3.5 Consensus size: 40
19795 ACCCAAGTAT
* * *
19805 CTTCGGGATTTAG-CCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
* *
19844 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACT--T-GCACAAATGC
* *
19887 CTTCGGGACTTCGCCCGGATATAGTAACTTGCACAAATGG
1 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
19927 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
19949 CATCCGAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
39 12 0.13
40 42 0.46
41 1 0.01
43 36 0.40
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
Found at i:33131 original size:40 final size:40
Alignment explanation
Indices: 33022--33169 Score: 210
Period size: 40 Copynumber: 3.7 Consensus size: 40
33012 TATTCAGATG
* *
33022 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
33062 A-ATTCTGGGCTAAG-CCTGAAGGCATTTGTGCGAGTTAGT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
33101 ATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
33141 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
33170 AGCAAGTAGC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 31 0.33
40 62 0.67
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:33183 original size:40 final size:41
Alignment explanation
Indices: 33022--33202 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 41
33012 TATTCAGATG
* *
33022 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAGCT
* * *
33062 A-ATTCTGGGCTAAG-CCTGAAGGCATTTGTGCGAGTTAG-T
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAGCT
*
33101 ATAATCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAGCT
* *
33141 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAGCT
* * *
33181 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
33203 TACTTGGTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
39 47 0.39
40 73 0.61
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (41 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAGCT
Found at i:33191 original size:79 final size:79
Alignment explanation
Indices: 33029--33202 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 79
33019 ATGATAACCG
* * * * * *
33029 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTGGGCTAAGCCTGAAGGCATTTGTGCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCA
*
33094 AGTTAGTATAATCG
66 AGTTAGTATAATCC
*
33108 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTTGAG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAG
33172 CAAG-TAGCTAT-ATCC
64 CAAGTTAG-TATAATCC
* *
33187 GGCTAAATTCCGAAGG
1 GGCTAAGTCCCGAAGG
33203 TACTTGGTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.02
79 60 0.73
80 20 0.24
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCA
AGTTAGTATAATCC
Found at i:41185 original size:82 final size:82
Alignment explanation
Indices: 41043--41194 Score: 213
Period size: 82 Copynumber: 1.9 Consensus size: 82
41033 TATTCGGATG
*
41043 ATAACCGGGCTAAGTCCGAAGGCATTTTGTGCTAAGTGAACTAATTCCGGGCTAAGCCCGAAGGC
1 ATAACCGGGCTAAGTCCGAAGGCATTTTGTGCTAAGTGAACTAATACCGGGCTAAGCCCGAAGGC
41108 ATTTGTGCGAGTTACTT
66 ATTTGTGCGAGTTACTT
* *
41125 ATAACCGGGCCTAAGTCCCGAAGGCA-TTTGTGC-GAGT-TACT-ATAACCGGGCTAAGTCCCGA
1 ATAACCGGG-CTAAGT-CCGAAGGCATTTTGTGCTAAGTGAACTAAT-ACCGGGCTAAG-CCCGA
41186 AGGCATTTG
62 AGGCATTTG
41195 AGCAAGTAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
80 2 0.03
81 13 0.21
82 26 0.41
83 13 0.21
84 9 0.14
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (82 bp):
ATAACCGGGCTAAGTCCGAAGGCATTTTGTGCTAAGTGAACTAATACCGGGCTAAGCCCGAAGGC
ATTTGTGCGAGTTACTT
Found at i:41190 original size:40 final size:40
Alignment explanation
Indices: 41043--41194 Score: 202
Period size: 42 Copynumber: 3.7 Consensus size: 40
41033 TATTCGGATG
* *
41043 ATAACCGGGCTAAGT-CCGAAGGCATTTTGTGCTAAGTGAACT
1 ATAACCGGGCTAAGTCCCGAAGGCA-TTTGTGC-GAGT-TACT
*
41085 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAC-T
41125 ATAACCGGGCCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGG-CTAAGTCCCGAAGGCATTTGTGCGAGTTACT
41166 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
41195 AGCAAGTAGC
Statistics
Matches: 100, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
39 2 0.02
40 30 0.30
41 24 0.24
42 44 0.44
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:41208 original size:40 final size:40
Alignment explanation
Indices: 41043--41217 Score: 198
Period size: 42 Copynumber: 4.3 Consensus size: 40
41033 TATTCGGATG
*
41043 ATAACCGGGCTAAGT-CCGAAGGCATTTTGTGCTAAGTGAACT
1 ATAACCGGGCTAAGTCCCGAAGGCA-TTTGTGC-AAGT-TACT
* *
41085 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTAC-T
*
41125 ATAACCGGGCCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGG-CTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
41166 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-CT
*
41206 ATATCC-GGCTAA
1 ATAACCGGGCTAA
41218 ATTCCGAGGT
Statistics
Matches: 119, Mismatches: 7, Indels: 17
0.83 0.05 0.12
Matches are distributed among these distances:
39 10 0.08
40 41 0.34
41 24 0.20
42 44 0.37
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Done.