Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2493
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: 23149
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:856 original size:16 final size:17
Alignment explanation
Indices: 830--861 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
820 CTTTTCACTT
830 TTTTTTGTTCTTTTTTC
1 TTTTTTGTTCTTTTTTC
847 TTTTTT-TTCTTTTTT
1 TTTTTTGTTCTTTTTT
862 TTTGCTCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTGTTCTTTTTTC
Found at i:863 original size:9 final size:9
Alignment explanation
Indices: 827--863 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
817 AGACTTTTCA
827 CTTTTTTTT
1 CTTTTTTTT
*
836 GTTCTTTTTT
1 CTT-TTTTTT
846 CTTTTTTTT
1 CTTTTTTTT
855 CTTTTTTTT
1 CTTTTTTTT
864 TGCTCACTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:864 original size:19 final size:19
Alignment explanation
Indices: 827--863 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
817 AGACTTTTCA
*
827 CTTTTTTTTGTTCTTTTTT
1 CTTTTTTTTCTTCTTTTTT
846 CTTTTTTTTCTT-TTTTTT
1 CTTTTTTTTCTTCTTTTTT
864 TGCTCACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (19 bp):
CTTTTTTTTCTTCTTTTTT
Found at i:1486 original size:13 final size:13
Alignment explanation
Indices: 1468--1495 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1458 AATCCCCTTT
1468 TCTTGTTGTCCAA
1 TCTTGTTGTCCAA
1481 TCTTGTTGTCCAA
1 TCTTGTTGTCCAA
1494 TC
1 TC
1496 CCTAGAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.46
Consensus pattern (13 bp):
TCTTGTTGTCCAA
Found at i:3965 original size:30 final size:30
Alignment explanation
Indices: 3931--4027 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
3921 TAAACTAAAA
3931 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
3961 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
3991 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
4020 ATGAGCTA
1 -TGAGCTA
4028 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:6180 original size:12 final size:12
Alignment explanation
Indices: 6165--6195 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6155 TTCTTTTTGC
6165 TTTTCAAAGGCT
1 TTTTCAAAGGCT
6177 TTTTCAAAGGCT
1 TTTTCAAAGGCT
6189 TTTTCAA
1 TTTTCAA
6196 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:6271 original size:6 final size:6
Alignment explanation
Indices: 6255--6304 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
6245 TTTCTTTTTA
*
6255 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
6304 T
1 T
6305 ATTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:6301 original size:37 final size:37
Alignment explanation
Indices: 6244--6314 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
6234 CTTGCCTCTC
6244 TTTTCTTTTTATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTATTTCATTTTCTTTATT-TTCTCTTGCT
*
6281 TTTTCTTTTTCTTTTC-TTTTCTTTATTTTCTCTT
1 TTTTCTTTTT-ATTTCATTTTCTTTATTTTCTCTT
6315 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTATTTCATTTTCTTTATTTTCTCTTGCT
Found at i:7177 original size:20 final size:20
Alignment explanation
Indices: 7152--7200 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
7142 TTTTCACTCC
7152 TTTTTTT-ATATACTTCGAT
1 TTTTTTTAATATACTTCGAT
* **
7171 TTTTTTTAATTTTTTTCGAT
1 TTTTTTTAATATACTTCGAT
7191 TTTTTTTAAT
1 TTTTTTTAAT
7201 TTTTTTTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTTTTAATATACTTCGAT
Found at i:7184 original size:10 final size:10
Alignment explanation
Indices: 7169--7207 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
7159 ATATACTTCG
7169 ATTTTTTTTA
1 ATTTTTTTTA
**
7179 ATTTTTTTCG
1 ATTTTTTTTA
7189 ATTTTTTTTA
1 ATTTTTTTTA
7199 ATTTTTTTT
1 ATTTTTTTT
7208 TCGAATTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:7201 original size:20 final size:20
Alignment explanation
Indices: 7165--7206 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
7155 TTTTATATAC
7165 TTCGATTTTTTTTAATTTTT
1 TTCGATTTTTTTTAATTTTT
7185 TTCGATTTTTTTTAATTTTT
1 TTCGATTTTTTTTAATTTTT
7205 TT
1 TT
7207 TTCGAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (20 bp):
TTCGATTTTTTTTAATTTTT
Found at i:8945 original size:30 final size:30
Alignment explanation
Indices: 8911--9067 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
8901 AAAACTAAAA
8911 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
8941 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
8971 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
9001 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
9031 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
9060 ATGAGCTA
1 -TGAGCTA
9068 GGAGTGAGCT
Statistics
Matches: 97, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
29 6 0.06
30 85 0.88
31 6 0.06
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:9004 original size:60 final size:60
Alignment explanation
Indices: 8911--9066 Score: 287
Period size: 60 Copynumber: 2.6 Consensus size: 60
8901 AAAACTAAAA
8911 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
8971 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
*
9031 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-TATGAGCT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT-TGAGCT
9067 AGGAGTGAGC
Statistics
Matches: 94, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
59 1 0.01
60 93 0.99
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (60 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGTTGAGCTGAGGCTAAACTCCTAAGCTGAAGT
Found at i:14754 original size:33 final size:32
Alignment explanation
Indices: 14717--14806 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
14707 ACATTTCTTG
14717 TTTTCTTTCTTCTATTTCTTTTTCTTTTTCAAT
1 TTTTCTTTCTTC-ATTTCTTTTTCTTTTTCAAT
* * **
14750 TTTTCTCAATC-TCA-ATCTCAATTCTTTTTCAAT
1 TTTTCT--TTCTTCATTTCT-TTTTCTTTTTCAAT
14783 TTTTCTTTCTTCATTTCTTTTTCT
1 TTTTCTTTCTTCATTTCTTTTTCT
14807 CTCACTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
31 2 0.05
32 10 0.23
33 28 0.64
34 2 0.05
35 2 0.05
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTTCTTTCTTCATTTCTTTTTCTTTTTCAAT
Done.