Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold448
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: 34800
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Found at i:4067 original size:40 final size:40
Alignment explanation
Indices: 4012--4307 Score: 447
Period size: 40 Copynumber: 7.5 Consensus size: 40
4002 TGATGATAAT
* * *
4012 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATC
4052 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
4092 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
4132 C-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
4171 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
4211 CGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* * * *
4251 CGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATC
* *
4291 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
4308 TACTTGGCTT
Statistics
Matches: 240, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
39 55 0.23
40 185 0.77
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:4225 original size:119 final size:120
Alignment explanation
Indices: 4012--4307 Score: 447
Period size: 119 Copynumber: 2.5 Consensus size: 120
4002 TGATGATAAT
* * *
4012 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTTG
*
4076 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
65 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
* *
4132 C-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
*
4196 GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATATC
66 GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
* * * *
4251 CGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
4308 TACTTGGCTT
Statistics
Matches: 162, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
118 1 0.01
119 128 0.79
120 33 0.20
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (120 bp):
CGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC
Found at i:4303 original size:159 final size:159
Alignment explanation
Indices: 4012--4307 Score: 461
Period size: 159 Copynumber: 1.9 Consensus size: 159
4002 TGATGATAAT
* *
4012 CGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGT
* * * *
4077 GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTC
66 GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGTTACTATATCCGGCTAAATC
4142 CCGAAGGCATTTGTGCGAGTTACTATATC
131 CCGAAGGCATTTGTGCGAGTTACTATATC
* *
4171 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTGG
1 CGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTGG
* * *
4235 TGTGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATATCCGGTTAAA
65 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGTTA-CTATATCCGGCTAAA
4299 TCCCGAAGG
129 TCCCGAAGG
4308 TACTTGGCTT
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
158 3 0.02
159 121 0.98
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (159 bp):
CGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGGT
GCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGTTACTATATCCGGCTAAATC
CCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:12227 original size:40 final size:40
Alignment explanation
Indices: 12170--12392 Score: 322
Period size: 40 Copynumber: 5.6 Consensus size: 40
12160 TGGATGATAA
* * * *
12170 CCGGGCTAAGTCTCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
12210 CCGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
12250 CTGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
12290 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
12330 CTGGGCTAAGTCCCGAAGGCATTGGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
12370 TCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
12393 CGGGCAAGTA
Statistics
Matches: 166, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
39 1 0.01
40 165 0.99
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18588 original size:20 final size:20
Alignment explanation
Indices: 18563--18614 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
18553 AATCAAGTGT
18563 AAATGATTTTAACCATA-TCA
1 AAATGATTTTAACCA-AGTCA
* *
18583 AAATGATTTCAATCAAGTCA
1 AAATGATTTTAACCAAGTCA
*
18603 AAATCATTTTAA
1 AAATGATTTTAA
18615 AATAATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:22241 original size:80 final size:79
Alignment explanation
Indices: 22104--22328 Score: 256
Period size: 80 Copynumber: 2.8 Consensus size: 79
22094 TTGAATGCTG
* * * * * *
22104 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
22168 TGTGCGAGATA-CAAA
64 TGTGCGAGATATCAAA
* *
22183 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATT
* * *
22248 CGTGCGAGTTATTAAA
64 TGTGCGAGATATCAAA
* * * * *
22264 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
22329 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
79 39 0.32
80 70 0.57
81 14 0.11
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:22308 original size:39 final size:39
Alignment explanation
Indices: 22104--22326 Score: 225
Period size: 40 Copynumber: 5.6 Consensus size: 39
22094 TTGAATGCTG
* * * * * *
22104 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** *
22144 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAAA
* * *
22183 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
22224 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
22264 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
22303 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
22327 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
39 39 0.25
40 105 0.68
41 11 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:22346 original size:79 final size:80
Alignment explanation
Indices: 22184--22361 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
22174 AGATACAAAT
* * * *
22184 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
22249 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
22264 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
22328 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
22343 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
22362 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:30076 original size:39 final size:40
Alignment explanation
Indices: 29980--30203 Score: 240
Period size: 40 Copynumber: 5.7 Consensus size: 40
29970 TTGAATGCTG
* * * * *
29980 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
** * *
30020 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
30059 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
30099 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
30139 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
30178 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
30204 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
39 64 0.41
40 83 0.54
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:30116 original size:79 final size:79
Alignment explanation
Indices: 29980--30203 Score: 254
Period size: 79 Copynumber: 2.8 Consensus size: 79
29970 TTGAATGCTG
* * * * * *
29980 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
30044 TGTGCGAGATA-CAAT
64 TGTGCGAGATATCAAA
* * *
30059 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
* *
30124 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * * * *
30139 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
30204 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 89 0.73
80 32 0.26
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:30221 original size:79 final size:80
Alignment explanation
Indices: 30059--30235 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
30049 GAGATACAAT
* * * *
30059 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGGTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
30124 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
30139 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
30203 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
30218 TCC-GGTTAAAT-CCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
30236 TACGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
77 7 0.09
78 8 0.10
79 48 0.59
80 19 0.23
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGGTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Done.