Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2337
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: 17116
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:195 original size:21 final size:20
Alignment explanation
Indices: 150--211 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
140 TTTCAACCAT
* *
150 TACCAATCGTTACCAAATACCA
1 TACCATTCG-TACC-AATTCCA
172 TACCATTTCGTACCAATTCCA
1 TACCA-TTCGTACCAATTCCA
* *
193 TACTATTCGAACCAATTCC
1 TACCATTCGTACCAATTCC
212 CAAATACCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.37
21 10 0.29
22 9 0.26
23 3 0.09
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (20 bp):
TACCATTCGTACCAATTCCA
Found at i:3462 original size:15 final size:15
Alignment explanation
Indices: 3442--3480 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3432 CTTCTTCTTC
3442 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
3457 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
3472 TTTTTTTCA
1 TTTTTTTCA
3481 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:7780 original size:11 final size:11
Alignment explanation
Indices: 7759--7793 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
7749 GGAGAGAATT
7759 TTTGTTCATCC
1 TTTGTTCATCC
7770 TTT-TCTCATCC
1 TTTGT-TCATCC
7781 TTTGTTCATCC
1 TTTGTTCATCC
7792 TT
1 TT
7794 GGCCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.05
11 20 0.91
12 1 0.05
ACGTcount: A:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (11 bp):
TTTGTTCATCC
Found at i:8259 original size:79 final size:78
Alignment explanation
Indices: 8123--8346 Score: 206
Period size: 79 Copynumber: 2.8 Consensus size: 78
8113 TTGAATGCTG
* * * * * * *
8123 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
8186 TTGTGCGAG-A-TACAA
63 TTGTGCGAGCATTA-AA
* * * *
8201 GTTCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCAT
1 --TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCAT
*
8265 TCGTGCGAGTCATTAAA
63 TTGTGCGAG-CATTAAA
* * *
8282 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
8347 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
78 1 0.01
79 87 0.71
80 28 0.23
81 4 0.03
82 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGCATTAAA
Found at i:8271 original size:40 final size:40
Alignment explanation
Indices: 8123--8346 Score: 210
Period size: 40 Copynumber: 5.7 Consensus size: 40
8113 TTGAATGCTG
* * * *
8123 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ATTAAA
** * *
8163 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATATTAA-A
*
8203 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
*
8242 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAT-ATTAAA
* * *
8282 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
* * *
8321 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
8347 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
39 65 0.42
40 80 0.51
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
Found at i:8364 original size:79 final size:80
Alignment explanation
Indices: 8203--8379 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
8193 AGATACAAGT
* * * *
8203 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
8267 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
8282 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
8346 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
8361 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
8380 AATGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 16 0.20
79 58 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:14736 original size:40 final size:40
Alignment explanation
Indices: 14612--14837 Score: 194
Period size: 40 Copynumber: 5.7 Consensus size: 40
14602 TTGAATGCTG
* * * *
14612 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ATTAAA
** * *
14652 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATATTAA-A
* *
14692 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
*
14732 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGAT-ATTAAA
* * * *
14772 TCCGGGTTAAGTCCCGAAGGCA-CTGTGTGAGGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GATATTAAA
* * *
14812 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
14838 AACGAGGAGC
Statistics
Matches: 154, Mismatches: 22, Indels: 19
0.79 0.11 0.10
Matches are distributed among these distances:
39 7 0.05
40 131 0.85
41 15 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATATTAAA
Found at i:14855 original size:80 final size:80
Alignment explanation
Indices: 14692--14870 Score: 184
Period size: 80 Copynumber: 2.2 Consensus size: 80
14682 AGATACAAGT
* * * * * *
14692 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCTGTGTGAGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
14757 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* *
14772 TCCGGGTTAAGTCCCGAAGGCACTGTGTGAG-GTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGC-CTGTGTGAGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATT
* * *
14836 TGAACGAG-GAGCTATA
65 CGAACGAGTCA-CTAAA
*
14852 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
14871 TATGTGATTT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
79 16 0.20
80 59 0.72
81 7 0.09
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTGTGTGAGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Done.